NCBO Wiki - User contributions [en]

Resource Index REST Web Service User Guide

2010-10-08T13:40:24Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

* Test HTML Page : http://rest.bioontology.org/resource_index/test

* Test HTML Page ('''element per concept(s)''') : http://rest.bioontology.org/resource_index/test/search

* Resources Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoints===
* To retrieve "annotations" either per element or per concept(s) : http://rest.bioontology.org/resource_index/

* To retrieve "element" per concept(s) : http://rest.bioontology.org/resource_index/search

=== POST calls ===

POST your requests at the service endpoints.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology ids. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotation results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, rdf, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response. RDF and OWL outputs are defined according to a RDFS schema and OWL ontology respectively available here: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs and http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|-valign="top"
|width="10%"|'''rdf'''
|width="90%"| Returns RDF representation of the annotations in ObrResultBean(Detailled). The elements of the result are described as instances in the following ontology: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailed and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailed'''

Response ObrResultBeanDetailed contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailed :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| One '''annotation''' is represented by ''ObrAnnotationBean''.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| One '''annotation''' is represented by ''ObrAnnotationBean''.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| One '''annotation''' is represented by ''ObrAnnotationBean''.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultId'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''resultStatistics'''
|width="90%"| Each '''statistics''' contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and annotationCount is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ''ObrAnnotationBean/ObrAnnotationBeanDetailed'' is a representation of one '''annotation/annotationDetailed'''. If ''elementDetails'' parameter is true the service return response of type '''annotation''', otherwise '''annotationDetailed'''. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailed contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailed :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementId'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIds'''
|width="90%"|map contain ontologyIds for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementId'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression. Attention, those values are in number of bytes, not characters e.g., ½ is a two-byte character, thus will count for 2 characters.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementId localConceptIds mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptId.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''. If request parameter withContext is true, then returns representation of the '''resultDetailed''' and if request parameter withContext is false, then returns representation of the '''result'''.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptId using BioPortal virtual ontology id.

*GET Request Format : '''/byconcept/virtual/{virtual_ontology_id}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptId for given resourceId.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptId using BioPortal virtual ontology id and using particular resourceId.

*GET Request Format : '''/byconcept/virtual/{virtual_ontology_id}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

'''For Multiple resources using service at basis URL'''
*GET Request Format : '''/?conceptids={conceptids}&isVirtualOntologyId=true&resourceids={resourceids}&withContext={withContext}&counts={counts}&offset={offset}&limit={limit}&levelMax=2147483647&filterNumber=false'''
*Example : http://rest.bioontology.org/resource_index/?conceptids=1032/Melanoma&isVirtualOntologyId=true&resourceids=CT,DBK,OMIM,RXRD&withContext=true&counts=true&offset=0&limit=10&levelMax=2147483647&filterNumber=false&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''result/resultDetailed''' for each resource. ''ObrResultBean/ObrResultBeanDetailed'' is a representation of one '''result/resultDetailed'''

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementId for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementId for given conceptId

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}/{offset}/{limit}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ''ObrAnnotationBean/ObrAnnotationBeanDetailed'' is a representation of one '''annotation/annotationDetailed'''. annotationDetailed if elementDetails is true otherwise annotation.

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementId for given conceptId of BioPortal virtual ontologyId

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtual_ontology_id}/resource/{resourceid}/{offset}/{limit}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ''ObrAnnotationBean/ObrAnnotationBeanDetailed'' is a representation of one '''annotation/annotationDetailed'''. annotationDetailed if elementDetails is true otherwise annotation.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIds'''
|width="90%"|map contain ontology ids for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resource id and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : ''Resource'' is a representation of one '''resource'''.

====Resource Element Service ====
Service returns elementURL for given localElementId and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ''Element'' is a representation of one '''element'''.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyId'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyId'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : '''resource''' is represented by ''ObrResourceBean''.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each '''ontology''' is represented by ''ObrOntologyBean''.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each '''resource''' is of type ''Resource''.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''ontology''' is represented by ''ObrOntologyBean''.

====Virtual Ontology Service with resources indexed ====
Returns the ontology versions in resource index with list of resources for given virtual_ontology_id.

*GET Request Format : ''/virtual/ontology/{virtual_ontology_id}?withresources={true|false}''
*Example: http://rest.bioontology.org/resource_index/virtual/ontology/1032?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : List of '''ontology''' represented by ''ObrOntologyBean''.

====Concept Frequency Service====
Returns the get most used concepts for given resource id.

*GET Request Format : ''/most-used-concepts/{resourceid}?method={counts|score}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/most-used-concepts/AE?method=counts&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''conceptFrequency''' with format ''ObrConceptFrequencyBean''.

'''Response Content: ObrConceptFrequencyBean'''

Following are contents for ObrConceptFrequencyBean:
{| border="2" 
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|ConceptBean is a representation of concept

|-valign="top"
|width="10%"|'''counts'''
|width="90%"|Frequency counts for a concept .

|-valign="top"
|width="10%"|'''score'''
|width="90%"|score for a concept .

|}

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All '''statistics' represented by ''ObrStatisticsBean''.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''ontologyStatistics''' with format ''ObrOntologyStatisticsBean''.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''ontologyStatistics''' with format ''ObrOntologyStatisticsBean''.

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''resourceStatistics''' with format ''ObrResourceStatisticsBean''.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyId'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|''ObrStatisticsBean'' is a representation of '''statistics'''.

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''resourceStatistics''' with format ''ObrResourceStatisticsBean''.

====All Executions Service====
Returns the information about all workflow executions done in resource index.

*GET Request Format : ''/executions''
*Web Page Request Format : ''/executions/list/''
*Examples:
**http://rest.bioontology.org/resource_index/executions?email=example@bioontology.org&applicationid=NCBOtest
**http://rest.bioontology.org/resource_index/executions/list/?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : List of all '''execution'' represented by ''ObrExecutionBean''.

'''Response Content: ObrExecutionBean'''
Following are remaining contents for ObrExecutionBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|Identifier of the resource.

|-valign="top"
|width="10%"|'''dictionaryId'''
|width="90%"|Identifier of the dictionary used for execution.

|-valign="top"
|width="10%"|'''withCompleteDictionary'''
|width="90%"|Specifies if complete dictionary is used for execution or not (true/false).

|-valign="top"
|width="10%"|'''elementCount'''
|width="90%"|Number of elements updated/annotated in execution.

|-valign="top"
|width="10%"|'''firstExecution'''
|width="90%"|Boolean value specifies if execution is first execution.

|-valign="top"
|width="10%"|'''executionBeginning'''
|width="90%"|Specifies Date/Time at which execution started.

|-valign="top"
|width="10%"|'''executionEnd'''
|width="90%"|Specifies Date/Time at which execution ended..

|-valign="top"
|width="10%"|'''executionTime'''
|width="90%"|Time required (in HH:mm:ss format) to complete current execution.

|}

====Resource Executions Service====
Returns the information about workflow executions done for given resource in resource index.

*GET Request Format : ''/executions/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/executions/WP?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''execution'' represented by ''ObrExecutionBean''.
----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-10-04T10:29:40Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

* Test HTML Page : http://rest.bioontology.org/resource_index/test

* Test HTML Page ('''element per concept(s)''') : http://rest.bioontology.org/resource_index/test/search

* Resources Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoints===
* To retrieve "annotations" either per element or per concept(s) : http://rest.bioontology.org/resource_index/

* To retrieve "element" per concept(s) : http://rest.bioontology.org/resource_index/search

=== POST calls ===

POST your requests at the service endpoints.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology ids. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotation results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, rdf, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response. RDF and OWL outputs are defined according to a RDFS schema and OWL ontology respectively available here: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs and http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|-valign="top"
|width="10%"|'''rdf'''
|width="90%"| Returns RDF representation of the annotations in ObrResultBean(Detailled). The elements of the result are described as instances in the following ontology: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailed and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailed'''

Response ObrResultBeanDetailed contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailed :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| One '''annotation''' is represented by ''ObrAnnotationBean''.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| One '''annotation''' is represented by ''ObrAnnotationBean''.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| One '''annotation''' is represented by ''ObrAnnotationBean''.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultId'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''resultStatistics'''
|width="90%"| Each '''statistics''' contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and annotationCount is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ''ObrAnnotationBean/ObrAnnotationBeanDetailed'' is a representation of one '''annotation/annotationDetailed'''. If ''elementDetails'' parameter is true the service return response of type '''annotation''', otherwise '''annotationDetailed'''. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailed contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailed :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementId'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIds'''
|width="90%"|map contain ontologyIds for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementId'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression. Attention, those values are in number of bytes, not characters e.g., ½ is a two-byte character, thus will count for 2 characters.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementId localConceptIds mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptId.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''. If request parameter withContext is true, then returns representation of the '''resultDetailed''' and if request parameter withContext is false, then returns representation of the '''result'''.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptId using BioPortal virtual ontology id.

*GET Request Format : '''/byconcept/virtual/{virtual_ontology_id}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptId for given resourceId.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptId using BioPortal virtual ontology id and using particular resourceId.

*GET Request Format : '''/byconcept/virtual/{virtual_ontology_id}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

'''For Multiple resources using service at basis URL'''
*GET Request Format : '''/?conceptids={conceptids}&isVirtualOntologyId=true&resourceids={resourceids}&withContext={withContext}&counts={counts}&offset={offset}&limit={limit}&levelMax=2147483647&filterNumber=false'''
*Example : http://rest.bioontology.org/resource_index/?conceptids=1032/Melanoma&isVirtualOntologyId=true&resourceids=CT,DBK,OMIM,RXRD&withContext=true&counts=true&offset=0&limit=10&levelMax=2147483647&filterNumber=false&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''result/resultDetailed''' for each resource. ''ObrResultBean/ObrResultBeanDetailed'' is a representation of one '''result/resultDetailed'''

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementId for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementId for given conceptId

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ''ObrAnnotationBean/ObrAnnotationBeanDetailed'' is a representation of one '''annotation/annotationDetailed'''. annotationDetailed if elementDetails is true otherwise annotation.

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementId for given conceptId of BioPortal virtual ontologyId

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtual_ontology_id}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ''ObrAnnotationBean/ObrAnnotationBeanDetailed'' is a representation of one '''annotation/annotationDetailed'''. annotationDetailed if elementDetails is true otherwise annotation.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIds'''
|width="90%"|map contain ontology ids for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resource id and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : ''Resource'' is a representation of one '''resource'''.

====Resource Element Service ====
Service returns elementURL for given localElementId and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ''Element'' is a representation of one '''element'''.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyId'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyId'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : '''resource''' is represented by ''ObrResourceBean''.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each '''ontology''' is represented by ''ObrOntologyBean''.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each '''resource''' is of type ''Resource''.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''ontology''' is represented by ''ObrOntologyBean''.

====Virtual Ontology Service with resources indexed ====
Returns the ontology versions in resource index with list of resources for given virtual_ontology_id.

*GET Request Format : ''/virtual/ontology/{virtual_ontology_id}?withresources={true|false}''
*Example: http://rest.bioontology.org/resource_index/virtual/ontology/1032?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : List of '''ontology''' represented by ''ObrOntologyBean''.

====Concept Frequency Service====
Returns the get most used concepts for given resource id.

*GET Request Format : ''/most-used-concepts/{resourceid}?method={counts|score}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/most-used-concepts/AE?method=counts&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''conceptFrequency''' with format ''ObrConceptFrequencyBean''.

'''Response Content: ObrConceptFrequencyBean'''

Following are contents for ObrConceptFrequencyBean:
{| border="2" 
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|ConceptBean is a representation of concept

|-valign="top"
|width="10%"|'''counts'''
|width="90%"|Frequency counts for a concept .

|-valign="top"
|width="10%"|'''score'''
|width="90%"|score for a concept .

|}

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All '''statistics' represented by ''ObrStatisticsBean''.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''ontologyStatistics''' with format ''ObrOntologyStatisticsBean''.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''ontologyStatistics''' with format ''ObrOntologyStatisticsBean''.

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''resourceStatistics''' with format ''ObrResourceStatisticsBean''.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyId'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|''ObrStatisticsBean'' is a representation of '''statistics'''.

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''resourceStatistics''' with format ''ObrResourceStatisticsBean''.

====All Executions Service====
Returns the information about all workflow executions done in resource index.

*GET Request Format : ''/executions''
*Web Page Request Format : ''/executions/list/''
*Examples:
**http://rest.bioontology.org/resource_index/executions?email=example@bioontology.org&applicationid=NCBOtest
**http://rest.bioontology.org/resource_index/executions/list/?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : List of all '''execution'' represented by ''ObrExecutionBean''.

'''Response Content: ObrExecutionBean'''
Following are remaining contents for ObrExecutionBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|Identifier of the resource.

|-valign="top"
|width="10%"|'''dictionaryId'''
|width="90%"|Identifier of the dictionary used for execution.

|-valign="top"
|width="10%"|'''withCompleteDictionary'''
|width="90%"|Specifies if complete dictionary is used for execution or not (true/false).

|-valign="top"
|width="10%"|'''elementCount'''
|width="90%"|Number of elements updated/annotated in execution.

|-valign="top"
|width="10%"|'''firstExecution'''
|width="90%"|Boolean value specifies if execution is first execution.

|-valign="top"
|width="10%"|'''executionBeginning'''
|width="90%"|Specifies Date/Time at which execution started.

|-valign="top"
|width="10%"|'''executionEnd'''
|width="90%"|Specifies Date/Time at which execution ended..

|-valign="top"
|width="10%"|'''executionTime'''
|width="90%"|Time required (in HH:mm:ss format) to complete current execution.

|}

====Resource Executions Service====
Returns the information about workflow executions done for given resource in resource index.

*GET Request Format : ''/executions/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/executions/WP?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''execution'' represented by ''ObrExecutionBean''.
----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-10-04T07:45:21Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

* Test HTML Page : http://rest.bioontology.org/resource_index/test

* Test HTML Page ('''element per concept(s)''') : http://rest.bioontology.org/resource_index/test/search

* Resources Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoints===
* To retrieve "annotations" either per element or per concept(s) : http://rest.bioontology.org/resource_index/

* To retrieve "element" per concept(s) : http://rest.bioontology.org/resource_index/search

=== POST calls ===

POST your requests at the service endpoints.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotation results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, rdf, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response. RDF and OWL outputs are defined according to a RDFS schema and OWL ontology respectively available here: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs and http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|-valign="top"
|width="10%"|'''rdf'''
|width="90%"| Returns RDF representation of the annotations in ObrResultBean(Detailled). The elements of the result are described as instances in the following ontology: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailed and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailed'''

Response ObrResultBeanDetailed contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailed :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| One '''annotation''' is represented by ''ObrAnnotationBean''.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| One '''annotation''' is represented by ''ObrAnnotationBean''.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| One '''annotation''' is represented by ''ObrAnnotationBean''.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultId'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''resultStatistics'''
|width="90%"| Each '''statistics''' contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and annotationCount is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ''ObrAnnotationBean/ObrAnnotationBeanDetailed'' is a representation of one '''annotation/annotationDetailed'''. If ''elementDetails'' parameter is true the service return response of type '''annotation''', otherwise '''annotationDetailed'''. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailed contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailed :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementId'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIds'''
|width="90%"|map contain ontologyIds for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementId'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression. Attention, those values are in number of bytes, not characters e.g., ½ is a two-byte character, thus will count for 2 characters.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementId localConceptIds mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptId.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''. If request parameter withContext is true, then returns representation of the '''resultDetailed''' and if request parameter withContext is false, then returns representation of the '''result'''.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptId using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptId for given resourceId.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptId using BioPortal virtual ontology ID and using particular resourceId.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

'''For Multiple resources using service at basis URL'''
*GET Request Format : '''/?conceptids={conceptids}&isVirtualOntologyId=true&resourceids={resourceids}&withContext={withContext}&counts={counts}&offset={offset}&limit={limit}&levelMax=2147483647&filterNumber=false'''
*Example : http://rest.bioontology.org/resource_index/?conceptids=1032/Melanoma&isVirtualOntologyId=true&resourceids=CT,DBK,OMIM,RXRD&withContext=true&counts=true&offset=0&limit=10&levelMax=2147483647&filterNumber=false&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''result/resultDetailed''' for each resource. ''ObrResultBean/ObrResultBeanDetailed'' is a representation of one '''result/resultDetailed'''

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementId for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementId for given conceptId

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ''ObrAnnotationBean/ObrAnnotationBeanDetailed'' is a representation of one '''annotation/annotationDetailed'''. annotationDetailed if elementDetails is true otherwise annotation.

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementId for given conceptId of BioPortal virtual ontologyId

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ''ObrAnnotationBean/ObrAnnotationBeanDetailed'' is a representation of one '''annotation/annotationDetailed'''. annotationDetailed if elementDetails is true otherwise annotation.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIds'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : ''Resource'' is a representation of one '''resource'''.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ''Element'' is a representation of one '''element'''.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyId'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyId'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : '''resource''' is represented by ''ObrResourceBean''.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each '''ontology''' is represented by ''ObrOntologyBean''.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each '''resource''' is of type ''Resource''.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''ontology''' is represented by ''ObrOntologyBean''.

====Virtual Ontology Service with resources indexed ====
Returns the ontology versions in resource index with list of resources for given virtual_ontology_id.

*GET Request Format : ''/virtual/ontology/{virtual_ontology_id}?withresources={true|false}''
*Example: http://rest.bioontology.org/resource_index/virtual/ontology/1032?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : List of '''ontology''' represented by ''ObrOntologyBean''.

====Concept Frequency Service====
Returns the get most used concepts for given resource id.

*GET Request Format : ''/most-used-concepts/{resourceid}?method={counts|score}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/most-used-concepts/AE?method=counts&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''conceptFrequency''' with format ''ObrConceptFrequencyBean''.

'''Response Content: ObrConceptFrequencyBean'''

Following are contents for ObrConceptFrequencyBean:
{| border="2" 
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|ConceptBean is a representation of concept

|-valign="top"
|width="10%"|'''counts'''
|width="90%"|Frequency counts for a concept .

|-valign="top"
|width="10%"|'''score'''
|width="90%"|score for a concept .

|}

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All '''statistics' represented by ''ObrStatisticsBean''.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''ontologyStatistics''' with format ''ObrOntologyStatisticsBean''.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''ontologyStatistics''' with format ''ObrOntologyStatisticsBean''.

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''resourceStatistics''' with format ''ObrResourceStatisticsBean''.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyId'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|''ObrStatisticsBean'' is a representation of '''statistics'''.

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''resourceStatistics''' with format ''ObrResourceStatisticsBean''.

====All Executions Service====
Returns the information about all workflow executions done in resource index.

*GET Request Format : ''/executions''
*Web Page Request Format : ''/executions/list/''
*Examples:
**http://rest.bioontology.org/resource_index/executions?email=example@bioontology.org&applicationid=NCBOtest
**http://rest.bioontology.org/resource_index/executions/list/?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : List of all '''execution'' represented by ''ObrExecutionBean''.

'''Response Content: ObrExecutionBean'''
Following are remaining contents for ObrExecutionBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|Identifier of the resource.

|-valign="top"
|width="10%"|'''dictionaryId'''
|width="90%"|Identifier of the dictionary used for execution.

|-valign="top"
|width="10%"|'''withCompleteDictionary'''
|width="90%"|Specifies if complete dictionary is used for execution or not (true/false).

|-valign="top"
|width="10%"|'''elementCount'''
|width="90%"|Number of elements updated/annotated in execution.

|-valign="top"
|width="10%"|'''firstExecution'''
|width="90%"|Boolean value specifies if execution is first execution.

|-valign="top"
|width="10%"|'''executionBeginning'''
|width="90%"|Specifies Date/Time at which execution started.

|-valign="top"
|width="10%"|'''executionEnd'''
|width="90%"|Specifies Date/Time at which execution ended..

|-valign="top"
|width="10%"|'''executionTime'''
|width="90%"|Time required (in HH:mm:ss format) to complete current execution.

|}

====Resource Executions Service====
Returns the information about workflow executions done for given resource in resource index.

*GET Request Format : ''/executions/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/executions/WP?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : '''execution'' represented by ''ObrExecutionBean''.
----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-10-01T12:27:45Z

Optra: Undo revision 10211 by Optra (Talk)

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

* Test HTML Page : http://rest.bioontology.org/resource_index/test

* Test HTML Page ('''element per concept(s)''') : http://rest.bioontology.org/resource_index/test/search

* Resources Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoints===
* To retrieve "annotations" either per element or per concept(s) : http://rest.bioontology.org/resource_index/

* To retrieve "element" per concept(s) : http://rest.bioontology.org/resource_index/search

=== POST calls ===

POST your requests at the service endpoints.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotation results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, rdf, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response. RDF and OWL outputs are defined according to a RDFS schema and OWL ontology respectively available here: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs and http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|-valign="top"
|width="10%"|'''rdf'''
|width="90%"| Returns RDF representation of the annotations in ObrResultBean(Detailled). The elements of the result are described as instances in the following ontology: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailed and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailed'''

Response ObrResultBeanDetailed contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailed :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailed is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailed contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailed :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression. Attention, those values are in number of bytes, not characters e.g., ½ is a two-byte character, thus will count for 2 characters.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailed and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed.

'''For Multiple resources using service at basis URL'''
*GET Request Format : '''/?conceptids={conceptids}&isVirtualOntologyId=true&resourceids={resourceids}&withContext={withContext}&counts={counts}&offset={offset}&limit={limit}&levelMax=2147483647&filterNumber=false'''
*Example : http://rest.bioontology.org/resource_index/?conceptids=1032/Melanoma&isVirtualOntologyId=true&resourceids=CT,DBK,OMIM,RXRD&withContext=true&counts=true&offset=0&limit=10&levelMax=2147483647&filterNumber=false&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrResultBean/ObrResultBeanDetailed for each resource.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailed if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailed if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Element is a representation of one element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====Virtual Ontology Service with resources indexed ====
Returns the ontology versions in resource index with list of resources for given virtual_ontology_id.

*GET Request Format : ''/virtual/ontology/{virtual_ontology_id}?withresources={true|false}''
*Example: http://rest.bioontology.org/resource_index/virtual/ontology/1032?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : List of ontologies represented by ObrOntologyBean.

====Concept Frequency Service====
Returns the get most used concepts for given resource id.

*GET Request Format : ''/most-used-concepts/{resourceid}?method={counts|score}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/most-used-concepts/AE?method=counts&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource Index Concepts with format ObrConceptFrequencyBean.

'''Response Content: ObrConceptFrequencyBean'''

Following are contents for ObrConceptFrequencyBean:
{| border="2" 
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|ConceptBean is a representation of concept

|-valign="top"
|width="10%"|'''counts'''
|width="90%"|Frequency counts for a concept .

|-valign="top"
|width="10%"|'''score'''
|width="90%"|score for a concept .

|}

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

====All Executions Service====
Returns the information about all workflow executions done in resource index.

*GET Request Format : ''/executions''
*Web Page Request Format : ''/executions/list/''
*Examples:
**http://rest.bioontology.org/resource_index/executions?email=example@bioontology.org&applicationid=NCBOtest
**http://rest.bioontology.org/resource_index/executions/list/?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All executions represented by ObrExecutionBean.

'''Response Content: ObrExecutionBean'''
Following are remaining contents for ObrExecutionBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|Identifier of the resource.

|-valign="top"
|width="10%"|'''dictionaryId'''
|width="90%"|Identifier of the dictionary used for execution.

|-valign="top"
|width="10%"|'''withCompleteDictionary'''
|width="90%"|Specifies if complete dictionary is used for execution or not (true/false).

|-valign="top"
|width="10%"|'''nbElement'''
|width="90%"|Number of elements updated/annotated in execution.

|-valign="top"
|width="10%"|'''firstExecution'''
|width="90%"|Boolean value specifies if execution is first execution.

|-valign="top"
|width="10%"|'''executionBeginning'''
|width="90%"|Specifies Date/Time at which execution started.

|-valign="top"
|width="10%"|'''executionEnd'''
|width="90%"|Specifies Date/Time at which execution ended..

|-valign="top"
|width="10%"|'''executionTime'''
|width="90%"|Time required (in HH:mm:ss format) to complete current execution.

|}

====Resource Executions Service====
Returns the information about workflow executions done for given resource in resource index.

*GET Request Format : ''/executions/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/executions/WP?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All executions represented by ObrExecutionBean.
----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-10-01T12:04:33Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

* Test HTML Page : http://rest.bioontology.org/resource_index/test

* Test HTML Page ('''element per concept(s)''') : http://rest.bioontology.org/resource_index/test/search

* Resources Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoints===
* To retrieve "annotations" either per element or per concept(s) : http://rest.bioontology.org/resource_index/

* To retrieve "element" per concept(s) : http://rest.bioontology.org/resource_index/search

=== POST calls ===

POST your requests at the service endpoints.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotation results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, rdf, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response. RDF and OWL outputs are defined according to a RDFS schema and OWL ontology respectively available here: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs and http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the result/resultDetailed.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the result/resultDetailed.

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the result/resultDetailed. The elements of the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|-valign="top"
|width="10%"|'''rdf'''
|width="90%"| Returns RDF representation of the annotations in result/resultDetailed. The elements of the result are described as instances in the following ontology: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the resultDetailed and if request parameter withContext is false, then returns representation of the result.''

'''Response Content: resultDetailed'''

Response resultDetailed contains all the contents of result. Those contents are described in section Response Content: result.

Following are remaining contents for resultDetailed:

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| annotation is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| annotation is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| annotation is a representation of one annotation.

|}

'''Note :''' ''Response contents of the annotation are described in section result''

'''Response Content: result'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultId'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''resultStatistics'''
|width="90%"| resultStatisticscontains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and annotationCount is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: annotationCount, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| annotation/annotationDetailed is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type annotation, otherwise annotationDetailed. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: annotationDetailled'''

Response annotationDetailed contains all the contents of annotation. Those contents are described in section Response Content: annotation.

Following are remaining contents for annotationDetailed :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementId'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIds'''
|width="90%"|map contain ontology ids for each context (as String).
|}

|}

'''Response Content: annotation'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementId'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression. Attention, those values are in number of bytes, not characters e.g., ½ is a two-byte character, thus will count for 2 characters.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementId localConceptIds mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailed and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed.

'''For Multiple resources using service at basis URL'''
*GET Request Format : '''/?conceptids={conceptids}&isVirtualOntologyId=true&resourceids={resourceids}&withContext={withContext}&counts={counts}&offset={offset}&limit={limit}&levelMax=2147483647&filterNumber=false'''
*Example : http://rest.bioontology.org/resource_index/?conceptids=1032/Melanoma&isVirtualOntologyId=true&resourceids=CT,DBK,OMIM,RXRD&withContext=true&counts=true&offset=0&limit=10&levelMax=2147483647&filterNumber=false&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrResultBean/ObrResultBeanDetailed for each resource.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailed if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailed if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Element is a representation of one element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====Virtual Ontology Service with resources indexed ====
Returns the ontology versions in resource index with list of resources for given virtual_ontology_id.

*GET Request Format : ''/virtual/ontology/{virtual_ontology_id}?withresources={true|false}''
*Example: http://rest.bioontology.org/resource_index/virtual/ontology/1032?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : List of ontologies represented by ObrOntologyBean.

====Concept Frequency Service====
Returns the get most used concepts for given resource id.

*GET Request Format : ''/most-used-concepts/{resourceid}?method={counts|score}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/most-used-concepts/AE?method=counts&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource Index Concepts with format ObrConceptFrequencyBean.

'''Response Content: ObrConceptFrequencyBean'''

Following are contents for ObrConceptFrequencyBean:
{| border="2" 
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|ConceptBean is a representation of concept

|-valign="top"
|width="10%"|'''counts'''
|width="90%"|Frequency counts for a concept .

|-valign="top"
|width="10%"|'''score'''
|width="90%"|score for a concept .

|}

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

====All Executions Service====
Returns the information about all workflow executions done in resource index.

*GET Request Format : ''/executions''
*Web Page Request Format : ''/executions/list/''
*Examples:
**http://rest.bioontology.org/resource_index/executions?email=example@bioontology.org&applicationid=NCBOtest
**http://rest.bioontology.org/resource_index/executions/list/?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All executions represented by ObrExecutionBean.

'''Response Content: ObrExecutionBean'''
Following are remaining contents for ObrExecutionBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|Identifier of the resource.

|-valign="top"
|width="10%"|'''dictionaryId'''
|width="90%"|Identifier of the dictionary used for execution.

|-valign="top"
|width="10%"|'''withCompleteDictionary'''
|width="90%"|Specifies if complete dictionary is used for execution or not (true/false).

|-valign="top"
|width="10%"|'''nbElement'''
|width="90%"|Number of elements updated/annotated in execution.

|-valign="top"
|width="10%"|'''firstExecution'''
|width="90%"|Boolean value specifies if execution is first execution.

|-valign="top"
|width="10%"|'''executionBeginning'''
|width="90%"|Specifies Date/Time at which execution started.

|-valign="top"
|width="10%"|'''executionEnd'''
|width="90%"|Specifies Date/Time at which execution ended..

|-valign="top"
|width="10%"|'''executionTime'''
|width="90%"|Time required (in HH:mm:ss format) to complete current execution.

|}

====Resource Executions Service====
Returns the information about workflow executions done for given resource in resource index.

*GET Request Format : ''/executions/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/executions/WP?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All executions represented by ObrExecutionBean.
----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-08-27T08:57:57Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

* Test HTML Page : http://rest.bioontology.org/resource_index/test

* Test HTML Page ('''element per concept(s)''') : http://rest.bioontology.org/resource_index/test/search

* Resources Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoints===
* To retrieve "annotations" either per element or per concept(s) : http://rest.bioontology.org/resource_index/

* To retrieve "element" per concept(s) : http://rest.bioontology.org/resource_index/search

=== POST calls ===

POST your requests at the service endpoints.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotation results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, rdf, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response. RDF and OWL outputs are defined according to a RDFS schema and OWL ontology respectively available here: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs and http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|-valign="top"
|width="10%"|'''rdf'''
|width="90%"| Returns RDF representation of the annotations in ObrResultBean(Detailled). The elements of the result are described as instances in the following ontology: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailed and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailed'''

Response ObrResultBeanDetailed contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailed :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailed is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailed contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailed :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression. Attention, those values are in number of bytes, not characters e.g., ½ is a two-byte character, thus will count for 2 characters.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailed and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed.

'''For Multiple resources using service at basis URL'''
*GET Request Format : '''/?conceptids={conceptids}&isVirtualOntologyId=true&resourceids={resourceids}&withContext={withContext}&counts={counts}&offset={offset}&limit={limit}&levelMax=2147483647&filterNumber=false'''
*Example : http://rest.bioontology.org/resource_index/?conceptids=1032/Melanoma&isVirtualOntologyId=true&resourceids=CT,DBK,OMIM,RXRD&withContext=true&counts=true&offset=0&limit=10&levelMax=2147483647&filterNumber=false&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrResultBean/ObrResultBeanDetailed for each resource.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailed.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailed if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailed if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Element is a representation of one element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====Virtual Ontology Service with resources indexed ====
Returns the ontology versions in resource index with list of resources for given virtual_ontology_id.

*GET Request Format : ''/virtual/ontology/{virtual_ontology_id}?withresources={true|false}''
*Example: http://rest.bioontology.org/resource_index/virtual/ontology/1032?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : List of ontologies represented by ObrOntologyBean.

====Concept Frequency Service====
Returns the get most used concepts for given resource id.

*GET Request Format : ''/most-used-concepts/{resourceid}?method={counts|score}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/most-used-concepts/AE?method=counts&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource Index Concepts with format ObrConceptFrequencyBean.

'''Response Content: ObrConceptFrequencyBean'''

Following are contents for ObrConceptFrequencyBean:
{| border="2" 
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|ConceptBean is a representation of concept

|-valign="top"
|width="10%"|'''counts'''
|width="90%"|Frequency counts for a concept .

|-valign="top"
|width="10%"|'''score'''
|width="90%"|score for a concept .

|}

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

====All Executions Service====
Returns the information about all workflow executions done in resource index.

*GET Request Format : ''/executions''
*Web Page Request Format : ''/executions/list/''
*Examples:
**http://rest.bioontology.org/resource_index/executions?email=example@bioontology.org&applicationid=NCBOtest
**http://rest.bioontology.org/resource_index/executions/list/?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All executions represented by ObrExecutionBean.

'''Response Content: ObrExecutionBean'''
Following are remaining contents for ObrExecutionBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|Identifier of the resource.

|-valign="top"
|width="10%"|'''dictionaryId'''
|width="90%"|Identifier of the dictionary used for execution.

|-valign="top"
|width="10%"|'''withCompleteDictionary'''
|width="90%"|Specifies if complete dictionary is used for execution or not (true/false).

|-valign="top"
|width="10%"|'''nbElement'''
|width="90%"|Number of elements updated/annotated in execution.

|-valign="top"
|width="10%"|'''firstExecution'''
|width="90%"|Boolean value specifies if execution is first execution.

|-valign="top"
|width="10%"|'''executionBeginning'''
|width="90%"|Specifies Date/Time at which execution started.

|-valign="top"
|width="10%"|'''executionEnd'''
|width="90%"|Specifies Date/Time at which execution ended..

|-valign="top"
|width="10%"|'''executionTime'''
|width="90%"|Time required (in HH:mm:ss format) to complete current execution.

|}

====Resource Executions Service====
Returns the information about workflow executions done for given resource in resource index.

*GET Request Format : ''/executions/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/executions/WP?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All executions represented by ObrExecutionBean.
----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-08-17T07:38:26Z

Optra: /* Annotation for BioPortal virtual ontology Concept And Resource Service */

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

* Test HTML Page : http://rest.bioontology.org/resource_index/test

* Test HTML Page ('''element per concept(s)''') : http://rest.bioontology.org/resource_index/test/search

* Resources Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoints===
* To retrieve "annotations" either per element or per concept(s) : http://rest.bioontology.org/resource_index/

* To retrieve "element" per concept(s) : http://rest.bioontology.org/resource_index/search

=== POST calls ===

POST your requests at the service endpoints.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotation results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, rdf, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response. RDF and OWL outputs are defined according to a RDFS schema and OWL ontology respectively available here: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs and http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|-valign="top"
|width="10%"|'''rdf'''
|width="90%"| Returns RDF representation of the annotations in ObrResultBean(Detailled). The elements of the result are described as instances in the following ontology: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression. Attention, those values are in number of bytes, not characters e.g., ½ is a two-byte character, thus will count for 2 characters.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

'''For Multiple resources using service at basis URL'''
*GET Request Format : '''/?conceptids={conceptids}&isVirtualOntologyId=true&resourceids={resourceids}&withContext={withContext}&counts={counts}&offset={offset}&limit={limit}&levelMax=2147483647&filterNumber=false'''
*Example : http://rest.bioontology.org/resource_index/?conceptids=1032/Melanoma&isVirtualOntologyId=true&resourceids=CT,DBK,OMIM,RXRD&withContext=true&counts=true&offset=0&limit=10&levelMax=2147483647&filterNumber=false&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrResultBean/ObrResultBeanDetailled for each resource.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Element is a representation of one element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====Virtual Ontology Service with resources indexed ====
Returns the ontology versions in resource index with list of resources for given virtual_ontology_id.

*GET Request Format : ''/virtual/ontology/{virtual_ontology_id}?withresources={true|false}''
*Example: http://rest.bioontology.org/resource_index/virtual/ontology/1032?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : List of ontologies represented by ObrOntologyBean.

====Concept Frequency Service====
Returns the get most used concepts for given resource id.

*GET Request Format : ''/most-used-concepts/{resourceid}?method={counts|score}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/most-used-concepts/AE?method=counts&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource Index Concepts with format ObrConceptFrequencyBean.

'''Response Content: ObrConceptFrequencyBean'''

Following are contents for ObrConceptFrequencyBean:
{| border="2" 
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|ConceptBean is a representation of concept

|-valign="top"
|width="10%"|'''counts'''
|width="90%"|Frequency counts for a concept .

|-valign="top"
|width="10%"|'''score'''
|width="90%"|score for a concept .

|}

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

====All Executions Service====
Returns the information about all workflow executions done in resource index.

*GET Request Format : ''/executions''
*Web Page Request Format : ''/executions/list/''
*Examples:
**http://rest.bioontology.org/resource_index/executions?email=example@bioontology.org&applicationid=NCBOtest
**http://rest.bioontology.org/resource_index/executions/list/?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All executions represented by ObrExecutionBean.

'''Response Content: ObrExecutionBean'''
Following are remaining contents for ObrExecutionBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|Identifier of the resource.

|-valign="top"
|width="10%"|'''dictionaryId'''
|width="90%"|Identifier of the dictionary used for execution.

|-valign="top"
|width="10%"|'''withCompleteDictionary'''
|width="90%"|Specifies if complete dictionary is used for execution or not (true/false).

|-valign="top"
|width="10%"|'''nbElement'''
|width="90%"|Number of elements updated/annotated in execution.

|-valign="top"
|width="10%"|'''firstExecution'''
|width="90%"|Boolean value specifies if execution is first execution.

|-valign="top"
|width="10%"|'''executionBeginning'''
|width="90%"|Specifies Date/Time at which execution started.

|-valign="top"
|width="10%"|'''executionEnd'''
|width="90%"|Specifies Date/Time at which execution ended..

|-valign="top"
|width="10%"|'''executionTime'''
|width="90%"|Time required (in HH:mm:ss format) to complete current execution.

|}

====Resource Executions Service====
Returns the information about workflow executions done for given resource in resource index.

*GET Request Format : ''/executions/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/executions/WP?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All executions represented by ObrExecutionBean.
----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-08-11T09:12:39Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

* Test HTML Page : http://rest.bioontology.org/resource_index/test

* Test HTML Page ('''element per concept(s)''') : http://rest.bioontology.org/resource_index/test/search

* Resources Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoints===
* To retrieve "annotations" either per element or per concept(s) : http://rest.bioontology.org/resource_index/

* To retrieve "element" per concept(s) : http://rest.bioontology.org/resource_index/search

=== POST calls ===

POST your requests at the service endpoints.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotation results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, rdf, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response. RDF and OWL outputs are defined according to a RDFS schema and OWL ontology respectively available here: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs and http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|-valign="top"
|width="10%"|'''rdf'''
|width="90%"| Returns RDF representation of the annotations in ObrResultBean(Detailled). The elements of the result are described as instances in the following ontology: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression. Attention, those values are in number of bytes, not characters e.g., ½ is a two-byte character, thus will count for 2 characters.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Element is a representation of one element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====Virtual Ontology Service with resources indexed ====
Returns the ontology versions in resource index with list of resources for given virtual_ontology_id.

*GET Request Format : ''/virtual/ontology/{virtual_ontology_id}?withresources={true|false}''
*Example: http://rest.bioontology.org/resource_index/virtual/ontology/1032?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : List of ontologies represented by ObrOntologyBean.

====Concept Frequency Service====
Returns the get most used concepts for given resource id.

*GET Request Format : ''/most-used-concepts/{resourceid}?method={counts|score}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/most-used-concepts/AE?method=counts&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource Index Concepts with format ObrConceptFrequencyBean.

'''Response Content: ObrConceptFrequencyBean'''

Following are contents for ObrConceptFrequencyBean:
{| border="2" 
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|ConceptBean is a representation of concept

|-valign="top"
|width="10%"|'''counts'''
|width="90%"|Frequency counts for a concept .

|-valign="top"
|width="10%"|'''score'''
|width="90%"|score for a concept .

|}

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

====All Executions Service====
Returns the information about all workflow executions done in resource index.

*GET Request Format : ''/executions''
*Web Page Request Format : ''/executions/list/''
*Examples:
**http://rest.bioontology.org/resource_index/executions?email=example@bioontology.org&applicationid=NCBOtest
**http://rest.bioontology.org/resource_index/executions/list/?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All executions represented by ObrExecutionBean.

'''Response Content: ObrExecutionBean'''
Following are remaining contents for ObrExecutionBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|Identifier of the resource.

|-valign="top"
|width="10%"|'''dictionaryId'''
|width="90%"|Identifier of the dictionary used for execution.

|-valign="top"
|width="10%"|'''withCompleteDictionary'''
|width="90%"|Specifies if complete dictionary is used for execution or not (true/false).

|-valign="top"
|width="10%"|'''nbElement'''
|width="90%"|Number of elements updated/annotated in execution.

|-valign="top"
|width="10%"|'''firstExecution'''
|width="90%"|Boolean value specifies if execution is first execution.

|-valign="top"
|width="10%"|'''executionBeginning'''
|width="90%"|Specifies Date/Time at which execution started.

|-valign="top"
|width="10%"|'''executionEnd'''
|width="90%"|Specifies Date/Time at which execution ended..

|-valign="top"
|width="10%"|'''executionTime'''
|width="90%"|Time required (in HH:mm:ss format) to complete current execution.

|}

====Resource Executions Service====
Returns the information about workflow executions done for given resource in resource index.

*GET Request Format : ''/executions/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/executions/WP?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All executions represented by ObrExecutionBean.
----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-29T11:14:02Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

* Test HTML Page : http://rest.bioontology.org/resource_index/test

* Test HTML Page ('''element per concept(s)''') : http://rest.bioontology.org/resource_index/test/search

* Resources Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoints===
* To retrieve "annotations" either per element or per concept(s) : http://rest.bioontology.org/resource_index/

* To retrieve "element" per concept(s) : http://rest.bioontology.org/resource_index/search

=== POST calls ===

POST your requests at the service endpoints.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotation results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, rdf, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|-valign="top"
|width="10%"|'''rdf'''
|width="90%"| Returns RDF representation of the annotations in ObrResultBean(Detailled). The elements of the result are described as instances in the following ontology: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression. Attention, those values are in number of bytes, not characters e.g., ½ is a two-byte character, thus will count for 2 characters.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Element is a representation of one element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====Virtual Ontology Service with resources indexed ====
Returns the ontology versions in resource index with list of resources for given virtual_ontology_id.

*GET Request Format : ''/virtual/ontology/{virtual_ontology_id}?withresources={true|false}''
*Example: http://rest.bioontology.org/resource_index/virtual/ontology/1032?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : List of ontologies represented by ObrOntologyBean.

====Concept Frequency Service====
Returns the get most used concepts for given resource id.

*GET Request Format : ''/most-used-concepts/{resourceid}?method={counts|score}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/most-used-concepts/AE?method=counts&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource Index Concepts with format ObrConceptFrequencyBean.

'''Response Content: ObrConceptFrequencyBean'''

Following are contents for ObrConceptFrequencyBean:
{| border="2" 
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|ConceptBean is a representation of concept

|-valign="top"
|width="10%"|'''counts'''
|width="90%"|Frequency counts for a concept .

|-valign="top"
|width="10%"|'''score'''
|width="90%"|score for a concept .

|}

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-23T11:19:30Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

* Test HTML Page : http://rest.bioontology.org/resource_index/test

* Test HTML Page ('''element per concept(s)''') : http://rest.bioontology.org/resource_index/test/search

* Resources Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoints===
* To retrieve "annotations" either per element or per concept(s) : http://rest.bioontology.org/resource_index/

* To retrieve "element" per concept(s) : http://rest.bioontology.org/resource_index/search

=== POST calls ===

POST your requests at the service endpoints.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotation results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Element is a representation of one element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====Virtual Ontology Service with resources indexed ====
Returns the ontology versions in resource index with list of resources for given virtual_ontology_id.

*GET Request Format : ''/virtual/ontology/{virtual_ontology_id}?withresources={true|false}''
*Example: http://rest.bioontology.org/resource_index/virtual/ontology/1032?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : List of ontologies represented by ObrOntologyBean.

====Concept Frequency Service====
Returns the get most used concepts for given resource id.

*GET Request Format : ''/most-used-concepts/{resourceid}?method={counts|score}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/most-used-concepts/AE?method=counts&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource Index Concepts with format ObrConceptFrequencyBean.

'''Response Content: ObrConceptFrequencyBean'''

Following are contents for ObrConceptFrequencyBean:
{| border="2" 
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|ConceptBean is a representation of concept

|-valign="top"
|width="10%"|'''counts'''
|width="90%"|Frequency counts for a concept .

|-valign="top"
|width="10%"|'''score'''
|width="90%"|score for a concept .

|}

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-21T09:47:23Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

* Test HTML Page : http://rest.bioontology.org/resource_index/test

* Test HTML Page ('''element per concept(s)''') : http://rest.bioontology.org/resource_index/test/search

* Resources Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoints===
* To retrieve "annotations" either per element or per concept(s) : http://rest.bioontology.org/resource_index/

* To retrieve "element" per concept(s) : http://rest.bioontology.org/resource_index/search

=== POST calls ===

POST your requests at the service endpoints.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotation results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Element is a representation of one element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-21T07:21:06Z

Optra: /* Parameters */

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotation results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Element is a representation of one element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-21T07:19:49Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotations results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Element is a representation of one element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-16T12:20:42Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{from}/{number}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Element is a representation of one element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-09T07:30:12Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text,tabDelimited, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{from}/{number}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Element details service by elementid ====
Retruns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : element

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-07T12:43:17Z

Optra: /* Parameters */

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text,tabDelimited, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{withContext}/{counts}/{from}/{number}?elementid={elementid}'''
*Example : http://rest.bioontology.org/resource_index/byelement/AE/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-07T08:27:37Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' are applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text,tabDelimited, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{withContext}/{counts}/{from}/{number}?elementid={elementid}'''
*Example : http://rest.bioontology.org/resource_index/byelement/AE/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-07T08:24:22Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''email''' and '''applicationid''' are applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email**'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|A user identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text,tabDelimited, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{withContext}/{counts}/{from}/{number}?elementid={elementid}'''
*Example : http://rest.bioontology.org/resource_index/byelement/AE/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-07T07:58:25Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

'''Attention, this documentation is not currently in sync with the deployed version... we plan to release pretty soon the new API (that goes with this documentation). Please refer to the history of this wiki page for [http://www.bioontology.org/wiki/index.php?title=Resource_Index_REST_Web_Service_User_Guide&oldid=10015, old documentation].'''

----

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note* :''' ''Parameter email and applicationid are applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''email*'''
|width="10%"|{email id}
|width="10%"|default: null
|width="70%"|A user identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding).For example, email=example@example.org or email=example%40example.org as an encoded email.

|-valign="top"
|width="10%"|'''applicationid*'''
|width="10%"|{aplicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service.

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceid identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceid can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text,tabDelimited, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{withContext}/{counts}/{from}/{number}?elementid={elementid}'''
*Example : http://rest.bioontology.org/resource_index/byelement/AE/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-06T12:00:08Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of stop words to use.

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text,tabDelimited, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42693/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{withContext}/{counts}/{from}/{number}?elementid={elementid}'''
*Example : http://rest.bioontology.org/resource_index/byelement/AE/true/false/0/10?elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/42693/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/Melanoma/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/npo:Nanoparticle/resource/AE?conceptid=Melanoma&elementid=E-GEOD-18509&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42693?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-06T11:42:47Z

Optra: /* Resource Element Service */

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of stop words to use.

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text,tabDelimited, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptid=npo%3ANanoparticle&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptid=npo%3ANanoparticle&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptid=npo%3ANanoparticle&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptid=npo%3ANanoparticle&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{withContext}/{counts}/{from}/{number}?elementid={elementid}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementid=6979603&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptid=npo%3ANanoparticle&elementid=6979603&email=example@bioontology.org&applicationid=NCBOtest
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptid=npo%3ANanoparticle&elementid=6979603
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptid=npo%3ANanoparticle&elementid=6979603&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptid=npo%3ANanoparticle&elementid=6979603&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-06T11:42:05Z

Optra: /* Resource Element Service */

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of stop words to use.

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text,tabDelimited, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptid=npo%3ANanoparticle&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptid=npo%3ANanoparticle&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptid=npo%3ANanoparticle&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptid=npo%3ANanoparticle&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{withContext}/{counts}/{from}/{number}?elementid={elementid}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementid=6979603&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptid=npo%3ANanoparticle&elementid=6979603&email=example@bioontology.org&applicationid=NCBOtest
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptid=npo%3ANanoparticle&elementid=6979603
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptid=npo%3ANanoparticle&elementid=6979603&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptid=npo%3ANanoparticle&elementid=6979603&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-06T11:37:46Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of stop words to use.

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text,tabDelimited, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptid=npo%3ANanoparticle&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptid=npo%3ANanoparticle&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptid=npo%3ANanoparticle&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptid=npo%3ANanoparticle&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{withContext}/{counts}/{from}/{number}?elementid={elementid}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementid=6979603&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptid=npo%3ANanoparticle&elementid=6979603&email=example@bioontology.org&applicationid=NCBOtest
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptid=npo%3ANanoparticle&elementid=6979603
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceid}?conceptid={conceptid}&elementid={elementid}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptid=npo%3ANanoparticle&elementid=6979603&email=example@bioontology.org&applicationid=NCBOtest
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptid=npo%3ANanoparticle&elementid=6979603&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO?email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources/{resourceID}
*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-06T10:47:50Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of stop words to use.

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text,tabDelimited, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptid=npo%3ANanoparticle
*Prev Request Format* : /byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptid=npo%3ANanoparticle
*Prev Request Format* : /byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*Old Request Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-07-06T10:34:09Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of stop words to use.

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''resourceid'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text,tabDelimited, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptID=npo%3ANanoparticle

*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*Old Request Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-06-30T10:15:14Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''localConceptIDs'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If localConceptIDs contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''virtual'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''localElementID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The localElementID is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the localElementID type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text,tabDelimited, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptID=npo%3ANanoparticle

*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*Old Request Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?byresource=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true&email=example@bioontology.org&applicationid=NCBOtest

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-06-21T10:34:37Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''localOntologyIDs'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''localConceptIDs'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If localConceptIDs contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''virtual'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''localElementID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The localElementID is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the localElementID type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 1/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{asText ,asTabDelimited, asXML ,asOWL}
|width="10%"|default: asXML
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''OWL'''
|width="90%"| returns OWL representation of the ObrResultBeanDetailled.
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptID=npo%3ANanoparticle

*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*Old Request Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?byresource=true

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-01-25T09:28:00Z

Optra: /* Annotation Details By Resource Element Service */

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''localOntologyIDs'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMin and levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum (resp. maximum) level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMin=1 & levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMin=0 & levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''localConceptIDs'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If localConceptIDs contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''virtual'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''localElementID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The localElementID is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the localElementID type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 1/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{asText ,asTabDelimited, asXML ,asOWL}
|width="10%"|default: asXML
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''OWL'''
|width="90%"| returns OWL representation of the ObrResultBeanDetailled.
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptID=npo%3ANanoparticle

*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*Old Request Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies''
*Example: http://rest.bioontology.org/resource_index/ontologies

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{localOntologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?byresource=true

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-01-22T12:42:28Z

Optra: /* Resources Service with ontologies used for indexing */

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''localOntologyIDs'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMin and levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum (resp. maximum) level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMin=1 & levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMin=0 & levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''localConceptIDs'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If localConceptIDs contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''virtual'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''localElementID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The localElementID is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the localElementID type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 1/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{asText ,asTabDelimited, asXML ,asOWL}
|width="10%"|default: asXML
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''OWL'''
|width="90%"| returns OWL representation of the ObrResultBeanDetailled.
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptID=npo%3ANanoparticle

*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*Old Request Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies''
*Example: http://rest.bioontology.org/resource_index/ontologies

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{localOntologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?byresource=true

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-01-22T12:35:08Z

Optra: /* Resource Statistics Service by ontologies */

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''localOntologyIDs'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMin and levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum (resp. maximum) level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMin=1 & levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMin=0 & levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''localConceptIDs'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If localConceptIDs contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''virtual'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''localElementID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The localElementID is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the localElementID type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 1/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{asText ,asTabDelimited, asXML ,asOWL}
|width="10%"|default: asXML
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''OWL'''
|width="90%"| returns OWL representation of the ObrResultBeanDetailled.
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptID=npo%3ANanoparticle

*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*Old Request Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section Response Content: Resource.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies''
*Example: http://rest.bioontology.org/resource_index/ontologies

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{localOntologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?byresource=true

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----
'''Note* :''' ''Old Request Format not working anymore.''

----

Resource Index REST Web Service User Guide

2010-01-22T12:34:25Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''localOntologyIDs'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMin and levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum (resp. maximum) level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMin=1 & levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMin=0 & levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''localConceptIDs'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If localConceptIDs contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''virtual'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''localElementID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The localElementID is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the localElementID type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 1/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{asText ,asTabDelimited, asXML ,asOWL}
|width="10%"|default: asXML
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''OWL'''
|width="90%"| returns OWL representation of the ObrResultBeanDetailled.
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptID=npo%3ANanoparticle

*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*Old Request Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section Response Content: Resource.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies''
*Example: http://rest.bioontology.org/resource_index/ontologies

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{localOntologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?byresource=true

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Note* :''' ''Old Request Format not working anymore''

----

Resource Index REST Web Service User Guide

2010-01-22T12:31:24Z

Optra: /* Annotation By Resource Element Service */

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''localOntologyIDs'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMin and levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum (resp. maximum) level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMin=1 & levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMin=0 & levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''localConceptIDs'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If localConceptIDs contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''virtual'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''localElementID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The localElementID is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the localElementID type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 1/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{asText ,asTabDelimited, asXML ,asOWL}
|width="10%"|default: asXML
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''OWL'''
|width="90%"| returns OWL representation of the ObrResultBeanDetailled.
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptID=npo%3ANanoparticle

*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*Old Request Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section Response Content: Resource.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies''
*Example: http://rest.bioontology.org/resource_index/ontologies

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{localOntologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?byresource=true

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----

Resource Index REST Web Service User Guide

2010-01-22T11:40:17Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''localOntologyIDs'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMin and levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum (resp. maximum) level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMin=1 & levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMin=0 & levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''localConceptIDs'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If localConceptIDs contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''virtual'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''localElementID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The localElementID is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the localElementID type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 1/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{asText ,asTabDelimited, asXML ,asOWL}
|width="10%"|default: asXML
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''OWL'''
|width="90%"| returns OWL representation of the ObrResultBeanDetailled.
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptID=npo%3ANanoparticle

*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*OldRequest Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section Response Content: Resource.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies''
*Example: http://rest.bioontology.org/resource_index/ontologies

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{localOntologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/40477?byresource=true

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----

Resource Index REST Web Service User Guide

2010-01-22T11:39:17Z

Optra: /* Ontology Service with resources indexed */

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''localOntologyIDs'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMin and levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum (resp. maximum) level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMin=1 & levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMin=0 & levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''localConceptIDs'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If localConceptIDs contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''virtual'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''localElementID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The localElementID is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the localElementID type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 1/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{asText ,asTabDelimited, asXML ,asOWL}
|width="10%"|default: asXML
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''OWL'''
|width="90%"| returns OWL representation of the ObrResultBeanDetailled.
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptID=npo%3ANanoparticle

*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*OldRequest Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section Response Content: Resource.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies''
*Example: http://rest.bioontology.org/resource_index/ontologies

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{localOntologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies/40477

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/1083

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/1083?byresource=true

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----

Resource Index REST Web Service User Guide

2010-01-22T11:38:34Z

Optra: /* Ontology Service with resources indexed */

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''localOntologyIDs'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMin and levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum (resp. maximum) level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMin=1 & levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMin=0 & levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''localConceptIDs'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If localConceptIDs contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''virtual'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''localElementID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The localElementID is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the localElementID type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 1/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{asText ,asTabDelimited, asXML ,asOWL}
|width="10%"|default: asXML
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''OWL'''
|width="90%"| returns OWL representation of the ObrResultBeanDetailled.
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptID=npo%3ANanoparticle

*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*OldRequest Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section Response Content: Resource.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies''
*Example: http://rest.bioontology.org/resource_index/ontologies

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies?ontologyID={localOntologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies?ontologyID=40477

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/1083

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/1083?byresource=true

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----

Resource Index REST Web Service User Guide

2010-01-22T11:19:35Z

Optra: /* Ontologies Service with resources indexed */

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''localOntologyIDs'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMin and levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum (resp. maximum) level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMin=1 & levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMin=0 & levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''localConceptIDs'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If localConceptIDs contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''virtual'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''localElementID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The localElementID is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the localElementID type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 1/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{asText ,asTabDelimited, asXML ,asOWL}
|width="10%"|default: asXML
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''OWL'''
|width="90%"| returns OWL representation of the ObrResultBeanDetailled.
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptID=npo%3ANanoparticle

*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*OldRequest Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section Response Content: Resource.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies''
*Example: http://rest.bioontology.org/resource_index/ontologies

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies?ontologyID={localOntologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies?ontologyID=1083

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/1083

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/1083?byresource=true

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----

Resource Index REST Web Service User Guide

2010-01-22T11:18:12Z

Optra:

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

===Sample HTTP Client for the Resource Index REST Web Service===

Test HTML Page : http://rest.bioontology.org/resource_index/test

Resources Service Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoint===

http://rest.bioontology.org/resource_index/

=== POST calls ===

POST your requests at the service endpoint.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''localOntologyIDs'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, SNOMEDCT,NCI,MSH.
|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.
|-valign="top"
|width="10%"|'''levelMin and levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum (resp. maximum) level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMin=1 & levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMin=0 & levelMax=0 is equivalent to disable the is_a transitive closure expansion step.
|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, from-mrrel,Human.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.

|-valign="top"
|width="10%"|'''localConceptIDs'''
|width="10%"|{localConceptID1,...,localConceptIDN}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If localConceptIDs contains only one element then the mode parameter can be ignored.The values are separated with comma (without spaces).
* For example, NCI/C0025202,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''virtual'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology IDs or UMLS ontologies.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter localConceptIDs). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified localConceptID. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''localElementID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The localElementID is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the localElementID type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceID'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resource_identifier used for this parameter identify a resource in the OBR index. They are defined in section Resource identifiers.The list of resourceID can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not.If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned (which implies score=true)

|-valign="top"
|width="10%"|'''from and number'''
|width="10%"|{real_number}
|width="10%"|default: 1/10 respectively
|width="70%"|Specifies an offset of annotations defined by from and number.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{asText ,asTabDelimited, asXML ,asOWL}
|width="10%"|default: asXML
|width="70%"|Specifies the desired format of the response.

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''xml'''
|width="90%"| returns XML representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''text'''
|width="90%"| returns plain text representation of the ObrResultBeanDetailled.

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''OWL'''
|width="90%"| returns OWL representation of the ObrResultBeanDetailled.
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailled'''

Response ObrResultBeanDetailled contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailled :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| ObrAnnotationBean is a representation of one annotation.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultID'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''statistics'''
|width="90%"| Statistics contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and nbAnnotation is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ObrAnnotationBean/ObrAnnotationBeanDetailled is a representation of one annotation. If ''elementDetails'' parameter is true the service return response of type ObrAnnotationBean ,otherwise ObrAnnotationBeanDetailled. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailled contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailled :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementID'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementID'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
|}
|}

|-valign="top"
|width="10%"|'''localElementID localConceptIDs mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptID.

*GET Request Format : '''/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/false/true/0/10?conceptID=npo%3ANanoparticle

*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled. If request parameter withContext is true, then returns representation of the ObrResultBeanDetailled and if request parameter withContext is false, then returns representation of the ObrResultBean.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID for given resourceID.

*GET Request Format : '''/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/40477/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : /byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptID using BioPortal virtual ontology ID and using particular resourceID.

*GET Request Format : '''/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1083/CANANO/false/true/0/10?conceptID=npo%3ANanoparticle
*Old Request Format* : byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementID for all the concepts.

*GET Request Format : '''/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}'''
*Example : http://rest.bioontology.org/resource_index/byelement/CANANO/true/false/0/10?elementID=6979603
*OldRequest Format* : /byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ObrResultBean/ObrResultBeanDetailled.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementID for given conceptID

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example1 : http://rest.bioontology.org/resource_index/details/false/concept/40477/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : /details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementID for given conceptID of BioPortal virtual ontologyID

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}'''
*Example1 : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Example2 : http://rest.bioontology.org/resource_index/details/false/virtual/concept/1083/npo:Nanoparticle/resource/CANANO?conceptID=npo%3ANanoparticle&elementID=6979603
*Old Request Format* : ''/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}''

*Response Content : ObrAnnotationBeanDetailled if elementDetails is true otherwise ObrAnnotationBean.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIDs'''
|width="90%"|map contain ontologyIDs for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resourceID and information related to it.

*GET Request Format : ''/resources/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/resources/CANANO

*Response Content : Resource.

====Resource Element Service ====
Service returns elementURL for given localElementID and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceID}?element={localElementID}''
*Example: http://rest.bioontology.org/resource_index/element/AE?element=E-GEOD-9118

*Response Content : Web page containing details of the element.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withOntologies=true

*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section Response Content: Resource.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyID'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceID}?withOntologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/GEO?withOntologies=true

*Response Content : Resource is represented by ObrResourceBean.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies''
*Example: http://rest.bioontology.org/resource_index/ontologies

*Response Content : Each Ontology is represented by ObrOntologyBean.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each resource is of type Resource.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies?ontologyID={localOntologyID}''
*Example: http://rest.bioontology.org/resource_index/ontologies?ontologyID=1083

*Response Content : Ontology is represented by ObrOntologyBean.

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all

*Response Content : All annotations represented by ObrStatisticsBean.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''indexedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/1083

*Response Content : Ontology statistics with format ObrOntologyStatisticsBean.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceID'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{localOnotlogyID}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/1083?byresource=true

*Response Content : ObrOntologyStatisticsBean

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceID}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyID'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceID}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?byontology=true

*Response Content : Resource statistics with format ObrResourceStatisticsBean.

----

Resource Index REST Web Service User Guide

2010-01-22T10:20:40Z

Optra:

Resource Index REST Web Service User Guide

2010-01-22T10:15:51Z

Optra:

Resource Index REST Web Service User Guide

2010-01-22T09:28:03Z

Optra:

Resource Index REST Web Service User Guide

2010-01-22T09:09:34Z

Optra: /* Annotation by Concept Service */

Processing OBR Resources

2009-12-02T12:53:05Z

Optra: /* OBR workflow execution history */

This wiki page describes the status of the OBR index.

= Execution of the OBR worklow & maintenance of the OBR index =

== Technical documentation ==
[[Image:PopulationOBRtables.png|thumb|Population of the OBR tables]]
* '''Population And Maintenance Of The OBR Index'''
Population of OBR and OBS tables is described in document [http://www.bioontology.org/wiki/images/5/5f/Population_And_Maintenance_Of_The_OBR_Index.doc Population_And_Maintenance_Of_The_OBR_Index]

* '''Technical Instructions for Configuring OBR Workflow'''
Population of OBR and OBS tables using properties files and shell script is described in document [http://www.bioontology.org/wiki/images/4/47/Technical_Instructions_for_Configuring_OBR_Workflow.doc Technical_Instructions_for_Configuring_OBR_Workflow]

RAT Start Date End Date Database Type of workflow execution
PCM Sunday, Oct 04, 2009 10:47 PM
Monday, Oct 05, 2009 06:11 PM
Obsdb1.obs_stage Resource update + OBR execution with full dictionary of the new delta of resources

== Headline text ==

== OBR workflow execution history ==

{| class="wikitable" border="1" cellspacing="0" cellpadding="1" width="150%"
|-
! RAT
! Date first processed
! Date last processed
! Database/schema
! Executed by
! Type of work flow execution
|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Tuesday Dec 01, 2009 11:23 PM
| valign="top" width="25%" |Tuesday Dec 01, 2009 11:38 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |MICAD
| valign="top" width="25%" |Monday Nov 09, 2009 05:29 AM
| valign="top" width="25%" |Monday Nov 09, 2009 04:08 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 04:14 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |DBK
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PCM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |AE
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GEO
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:38 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:34 PM
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:38 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:39 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 05:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Monday Oct 26, 2009 05:24 AM
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Wednesday Oct 14, 2009 10:47 PM
| valign="top" width="25%" |Wednesday Oct 14, 2009 11:00 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources

|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="25%" |Monday Oct 12, 2009 08:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |RXRD
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | DBK
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CT
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | BSM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | AE
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GAP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | WP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GEO
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGGE
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDI
| valign="top" width="25%" |Monday Oct 05, 2009 11:44 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CDD
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | UPKB
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:44 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDR
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | OMIM
| valign="top" width="25%" | Monday Oct 05, 2009 10:32 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | PCM
| valign="top" width="25%" | Sunday, Oct 04, 2009 10:47 PM
| valign="top" width="25%" | Monday, Oct 05, 2009 06:11 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" | Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" | Sunday, Aug 23, 2009 10:44 PM
| valign="top" width="25%" | Monday, Aug 24, 2009 04:40 AM
| valign="top" width="10%" |obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |SMD, DBK
| valign="top" width="25%" | Monday, Aug 03, 2009 11:28 PM
| valign="top" width="25%" | Tuesday, Aug 04, 2009 02:12 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Monday, July 27, 2009 11:19 PM
| valign="top" width="25%" | Wednesday, July 29, 2009 02:42 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" | Monday, July 13, 2009 02:45 AM
| valign="top" width="25%" | Tuesday, July 21, 2009 03:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip/Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Wednesday, June 17, 2009 3:45 AM
| valign="top" width="25%" | Wednesday, June 17, 2009 10:04 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip
| valign="top" |Contexts Populated : name, description, species
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | June 8, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |End of execution of the OBR workflow & switch of OBR API to the obsdb1.obs_stage schema
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | May 22, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources
|-
| valign="top" width="5%" | RXRD
| valign="top" width="25%" |
| valign="top" width="25%" | May 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Adrien
| valign="top" |Execution of the OBR index on RXRD independently
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | March 2009
| valign="top" width="10%" |
| valign="top" width="10%" |Clement
| valign="top" |DB schema use right now: ncbodb2.obs
|}

== Resources logs ==
* '''Execution of the OBR workflow log files'''
Log files are available here : [https://bmir-gforge.stanford.edu/gf/project/obs/docman/?subdir=58 /project/obs/docman/logs]

= Resources Access Tools (RATs) development and update =

This page is for keeping track of Resources Access Tools (RATs) developement.

=== How to write Resources Access Tools ===
How to write a resource access tool is described in this [http://www.stanford.edu/~coulet/obr_tutorial_to_add_new_resources.pdf tutorial] by Adrien Coulet.

=== Available resources ===

Resources fully functional and available in the OBR index are available here: [http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources /obr/resources]

=== On development resources ===
* PubMed (PM)
* Stanford Microarray Database (SMD)
* Pathway Commons
* CaNanoLab

Others in queue

* ChemSpider
* Human Gene Mutation Database

=== Development history ===

1. Resource: Clinicaltrials.gov
*Person responsible: Kuladip Yadav(Optra),Sanjay Jadhav(Optra).
*Notes: Fixed issue of authentication, fixed other xml related issues.
*Status:
Changes done as per suggestions :
1. Decrease request delay from 1000 ms to 800ms.
2. Implement log4j logger mechanism.

2. Resource: GEO
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Modified GEO resource access tool to get data from both GSE and GDS database.
*Status:
Changes done as per suggestions :
1. Implement log4j logger mechanism.

3. Resource: Pubmed
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Built a new resource access tool from existing PubMedAccessTool to populate data from eutils and pubmed xml files .
*Status:
Changes done as per suggestions :
1. Remove direct database call from PubMed RAT.
2. Implement mapStringsToLocalConceptIDs method into ObsOntologiesAccessTool and TermTable.
3. Implement log4j logger in related classes.
4. Code changes pushed in SVN.

= Migration to a production architecture & framework =

No yet started

Processing OBR Resources

2009-12-02T12:52:02Z

Optra: /* OBR workflow execution history */

This wiki page describes the status of the OBR index.

= Execution of the OBR worklow & maintenance of the OBR index =

== Technical documentation ==
[[Image:PopulationOBRtables.png|thumb|Population of the OBR tables]]
* '''Population And Maintenance Of The OBR Index'''
Population of OBR and OBS tables is described in document [http://www.bioontology.org/wiki/images/5/5f/Population_And_Maintenance_Of_The_OBR_Index.doc Population_And_Maintenance_Of_The_OBR_Index]

* '''Technical Instructions for Configuring OBR Workflow'''
Population of OBR and OBS tables using properties files and shell script is described in document [http://www.bioontology.org/wiki/images/4/47/Technical_Instructions_for_Configuring_OBR_Workflow.doc Technical_Instructions_for_Configuring_OBR_Workflow]

RAT Start Date End Date Database Type of workflow execution
PCM Sunday, Oct 04, 2009 10:47 PM
Monday, Oct 05, 2009 06:11 PM
Obsdb1.obs_stage Resource update + OBR execution with full dictionary of the new delta of resources

== Headline text ==

== OBR workflow execution history ==

{| class="wikitable" border="1" cellspacing="0" cellpadding="1" width="150%"
|-
! RAT
! Date first processed
! Date last processed
! Database/schema
! Executed by
! Type of work flow execution
|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Tuesday Dec 01, 2009 11:23 PM
| valign="top" width="25%" |Tuesday Dec 01, 2009 11:38 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |MICAD
| valign="top" width="25%" |Monday Nov 09, 2009 05:29 AM
| valign="top" width="25%" |Monday Nov 09, 2009 04:08 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 04:14 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |DBK
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PCM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |AE
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GEO
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:38 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:34 PM
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:38 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:39 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 05:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Monday Oct 26, 2009 05:24 AM
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Wednesday Oct 14, 2009 10:47 PM
| valign="top" width="25%" |Wednesday Oct 14, 2009 11:00 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources

|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="25%" |Monday Oct 12, 2009 08:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |RXRD
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | DBK
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CT
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | BSM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | AE
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GAP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | WP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GEO
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGGE
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDI
| valign="top" width="25%" |Monday Oct 05, 2009 11:44 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CDD
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | UPKB
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:44 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDR
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | OMIM
| valign="top" width="25%" | Monday Oct 05, 2009 10:32 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | PCM
| valign="top" width="25%" | Sunday, Oct 04, 2009 10:47 PM
| valign="top" width="25%" | Monday, Oct 05, 2009 06:11 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" | Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" | Sunday, Aug 23, 2009 10:44 PM
| valign="top" width="25%" | Monday, Aug 24, 2009 04:40 AM
| valign="top" width="10%" |obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |SMD, DBK
| valign="top" width="25%" | Monday, Aug 03, 2009 11:28 PM
| valign="top" width="25%" | Tuesday, Aug 04, 2009 02:12 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Monday, July 27, 2009 11:19 PM
| valign="top" width="25%" | Wednesday, July 29, 2009 02:42 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" | Monday, July 13, 2009 02:45 AM
| valign="top" width="25%" | Tuesday, July 21, 2009 03:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip/Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Wednesday, June 17, 2009 3:45 AM
| valign="top" width="25%" | Wednesday, June 17, 2009 10:04 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip
| valign="top" |Contexts Populated : name, description, species
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | June 8, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |End of execution of the OBR workflow & switch of OBR API to the obsdb1.obs_stage schema
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | May 22, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources
|-
| valign="top" width="5%" | RXRD
| valign="top" width="25%" |
| valign="top" width="25%" | May 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Adrien
| valign="top" |Execution of the OBR index on RXRD independently
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | March 2009
| valign="top" width="10%" |
| valign="top" width="10%" |Clement
| valign="top" |DB schema use right now: ncbodb2.obs
|}

== Resources logs ==
* '''Execution of the OBR workflow log files'''
Log files are available here : [https://bmir-gforge.stanford.edu/gf/project/obs/docman/?subdir=58 /project/obs/docman/logs]

= Resources Access Tools (RATs) development and update =

This page is for keeping track of Resources Access Tools (RATs) developement.

=== How to write Resources Access Tools ===
How to write a resource access tool is described in this [http://www.stanford.edu/~coulet/obr_tutorial_to_add_new_resources.pdf tutorial] by Adrien Coulet.

=== Available resources ===

Resources fully functional and available in the OBR index are available here: [http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources /obr/resources]

=== On development resources ===
* PubMed (PM)
* Stanford Microarray Database (SMD)
* Pathway Commons
* CaNanoLab

Others in queue

* ChemSpider
* Human Gene Mutation Database

=== Development history ===

1. Resource: Clinicaltrials.gov
*Person responsible: Kuladip Yadav(Optra),Sanjay Jadhav(Optra).
*Notes: Fixed issue of authentication, fixed other xml related issues.
*Status:
Changes done as per suggestions :
1. Decrease request delay from 1000 ms to 800ms.
2. Implement log4j logger mechanism.

2. Resource: GEO
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Modified GEO resource access tool to get data from both GSE and GDS database.
*Status:
Changes done as per suggestions :
1. Implement log4j logger mechanism.

3. Resource: Pubmed
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Built a new resource access tool from existing PubMedAccessTool to populate data from eutils and pubmed xml files .
*Status:
Changes done as per suggestions :
1. Remove direct database call from PubMed RAT.
2. Implement mapStringsToLocalConceptIDs method into ObsOntologiesAccessTool and TermTable.
3. Implement log4j logger in related classes.
4. Code changes pushed in SVN.

= Migration to a production architecture & framework =

No yet started

Processing OBR Resources

2009-11-10T09:27:52Z

Optra: /* OBR workflow execution history */

This wiki page describes the status of the OBR index.

= Execution of the OBR worklow & maintenance of the OBR index =

== Technical documentation ==
[[Image:PopulationOBRtables.png|thumb|Population of the OBR tables]]
* '''Population And Maintenance Of The OBR Index'''
Population of OBR and OBS tables is described in document [http://www.bioontology.org/wiki/images/5/5f/Population_And_Maintenance_Of_The_OBR_Index.doc Population_And_Maintenance_Of_The_OBR_Index]

* '''Technical Instructions for Configuring OBR Workflow'''
Population of OBR and OBS tables using properties files and shell script is described in document [http://www.bioontology.org/wiki/images/4/47/Technical_Instructions_for_Configuring_OBR_Workflow.doc Technical_Instructions_for_Configuring_OBR_Workflow]

RAT Start Date End Date Database Type of workflow execution
PCM Sunday, Oct 04, 2009 10:47 PM
Monday, Oct 05, 2009 06:11 PM
Obsdb1.obs_stage Resource update + OBR execution with full dictionary of the new delta of resources

== Headline text ==

== OBR workflow execution history ==

{| class="wikitable" border="1" cellspacing="0" cellpadding="1" width="150%"
|-
! RAT
! Date first processed
! Date last processed
! Database/schema
! Executed by
! Type of work flow execution
|-
| valign="top" width="5%" |MICAD
| valign="top" width="25%" |Monday Nov 09, 2009 05:29 AM
| valign="top" width="25%" |Monday Nov 09, 2009 04:08 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 04:14 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |DBK
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PCM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |AE
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 AM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GEO
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:38 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:34 PM
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:38 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:39 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 05:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Monday Oct 26, 2009 05:24 AM
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Wednesday Oct 14, 2009 10:47 PM
| valign="top" width="25%" |Wednesday Oct 14, 2009 11:00 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources

|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="25%" |Monday Oct 12, 2009 08:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |RXRD
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | DBK
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CT
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | BSM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | AE
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GAP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | WP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GEO
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGGE
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDI
| valign="top" width="25%" |Monday Oct 05, 2009 11:44 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CDD
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | UPKB
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:44 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDR
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | OMIM
| valign="top" width="25%" | Monday Oct 05, 2009 10:32 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | PCM
| valign="top" width="25%" | Sunday, Oct 04, 2009 10:47 PM
| valign="top" width="25%" | Monday, Oct 05, 2009 06:11 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" | Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" | Sunday, Aug 23, 2009 10:44 PM
| valign="top" width="25%" | Monday, Aug 24, 2009 04:40 AM
| valign="top" width="10%" |obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |SMD, DBK
| valign="top" width="25%" | Monday, Aug 03, 2009 11:28 PM
| valign="top" width="25%" | Tuesday, Aug 04, 2009 02:12 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Monday, July 27, 2009 11:19 PM
| valign="top" width="25%" | Wednesday, July 29, 2009 02:42 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" | Monday, July 13, 2009 02:45 AM
| valign="top" width="25%" | Tuesday, July 21, 2009 03:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip/Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Wednesday, June 17, 2009 3:45 AM
| valign="top" width="25%" | Wednesday, June 17, 2009 10:04 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip
| valign="top" |Contexts Populated : name, description, species
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | June 8, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |End of execution of the OBR workflow & switch of OBR API to the obsdb1.obs_stage schema
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | May 22, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources
|-
| valign="top" width="5%" | RXRD
| valign="top" width="25%" |
| valign="top" width="25%" | May 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Adrien
| valign="top" |Execution of the OBR index on RXRD independently
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | March 2009
| valign="top" width="10%" |
| valign="top" width="10%" |Clement
| valign="top" |DB schema use right now: ncbodb2.obs
|}

== Resources logs ==
* '''Execution of the OBR workflow log files'''
Log files are available here : [https://bmir-gforge.stanford.edu/gf/project/obs/docman/?subdir=58 /project/obs/docman/logs]

= Resources Access Tools (RATs) development and update =

This page is for keeping track of Resources Access Tools (RATs) developement.

=== How to write Resources Access Tools ===
How to write a resource access tool is described in this [http://www.stanford.edu/~coulet/obr_tutorial_to_add_new_resources.pdf tutorial] by Adrien Coulet.

=== Available resources ===

Resources fully functional and available in the OBR index are available here: [http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources /obr/resources]

=== On development resources ===
* PubMed (PM)
* Stanford Microarray Database (SMD)
* Pathway Commons
* CaNanoLab

Others in queue

* ChemSpider
* Human Gene Mutation Database

=== Development history ===

1. Resource: Clinicaltrials.gov
*Person responsible: Kuladip Yadav(Optra),Sanjay Jadhav(Optra).
*Notes: Fixed issue of authentication, fixed other xml related issues.
*Status:
Changes done as per suggestions :
1. Decrease request delay from 1000 ms to 800ms.
2. Implement log4j logger mechanism.

2. Resource: GEO
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Modified GEO resource access tool to get data from both GSE and GDS database.
*Status:
Changes done as per suggestions :
1. Implement log4j logger mechanism.

3. Resource: Pubmed
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Built a new resource access tool from existing PubMedAccessTool to populate data from eutils and pubmed xml files .
*Status:
Changes done as per suggestions :
1. Remove direct database call from PubMed RAT.
2. Implement mapStringsToLocalConceptIDs method into ObsOntologiesAccessTool and TermTable.
3. Implement log4j logger in related classes.
4. Code changes pushed in SVN.

= Migration to a production architecture & framework =

No yet started

Processing OBR Resources

2009-11-10T05:36:12Z

Optra: /* OBR workflow execution history */

This wiki page describes the status of the OBR index.

= Execution of the OBR worklow & maintenance of the OBR index =

== Technical documentation ==
[[Image:PopulationOBRtables.png|thumb|Population of the OBR tables]]
* '''Population And Maintenance Of The OBR Index'''
Population of OBR and OBS tables is described in document [http://www.bioontology.org/wiki/images/5/5f/Population_And_Maintenance_Of_The_OBR_Index.doc Population_And_Maintenance_Of_The_OBR_Index]

* '''Technical Instructions for Configuring OBR Workflow'''
Population of OBR and OBS tables using properties files and shell script is described in document [http://www.bioontology.org/wiki/images/4/47/Technical_Instructions_for_Configuring_OBR_Workflow.doc Technical_Instructions_for_Configuring_OBR_Workflow]

RAT Start Date End Date Database Type of workflow execution
PCM Sunday, Oct 04, 2009 10:47 PM
Monday, Oct 05, 2009 06:11 PM
Obsdb1.obs_stage Resource update + OBR execution with full dictionary of the new delta of resources

== Headline text ==

== OBR workflow execution history ==

{| class="wikitable" border="1" cellspacing="0" cellpadding="1" width="150%"
|-
! RAT
! Date first processed
! Date last processed
! Database/schema
! Executed by
! Type of work flow execution
|-
| valign="top" width="5%" |MICAD
| valign="top" width="25%" |Monday Nov 09, 2009 05:29 AM
| valign="top" width="25%" |Monday Nov 09, 2009 04:08 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 04:14 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |DBK
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PCM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |AE
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GEO
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:38 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:34 PM
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:38 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:39 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 05:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Monday Oct 26, 2009 05:24 AM
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Wednesday Oct 14, 2009 10:47 PM
| valign="top" width="25%" |Wednesday Oct 14, 2009 11:00 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources

|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="25%" |Monday Oct 12, 2009 08:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |RXRD
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | DBK
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CT
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | BSM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | AE
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GAP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | WP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GEO
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGGE
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDI
| valign="top" width="25%" |Monday Oct 05, 2009 11:44 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CDD
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | UPKB
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:44 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDR
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | OMIM
| valign="top" width="25%" | Monday Oct 05, 2009 10:32 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | PCM
| valign="top" width="25%" | Sunday, Oct 04, 2009 10:47 PM
| valign="top" width="25%" | Monday, Oct 05, 2009 06:11 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" | Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" | Sunday, Aug 23, 2009 10:44 PM
| valign="top" width="25%" | Monday, Aug 24, 2009 04:40 AM
| valign="top" width="10%" |obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |SMD, DBK
| valign="top" width="25%" | Monday, Aug 03, 2009 11:28 PM
| valign="top" width="25%" | Tuesday, Aug 04, 2009 02:12 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Monday, July 27, 2009 11:19 PM
| valign="top" width="25%" | Wednesday, July 29, 2009 02:42 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" | Monday, July 13, 2009 02:45 AM
| valign="top" width="25%" | Tuesday, July 21, 2009 03:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip/Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Wednesday, June 17, 2009 3:45 AM
| valign="top" width="25%" | Wednesday, June 17, 2009 10:04 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip
| valign="top" |Contexts Populated : name, description, species
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | June 8, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |End of execution of the OBR workflow & switch of OBR API to the obsdb1.obs_stage schema
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | May 22, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources
|-
| valign="top" width="5%" | RXRD
| valign="top" width="25%" |
| valign="top" width="25%" | May 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Adrien
| valign="top" |Execution of the OBR index on RXRD independently
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | March 2009
| valign="top" width="10%" |
| valign="top" width="10%" |Clement
| valign="top" |DB schema use right now: ncbodb2.obs
|}

== Resources logs ==
* '''Execution of the OBR workflow log files'''
Log files are available here : [https://bmir-gforge.stanford.edu/gf/project/obs/docman/?subdir=58 /project/obs/docman/logs]

= Resources Access Tools (RATs) development and update =

This page is for keeping track of Resources Access Tools (RATs) developement.

=== How to write Resources Access Tools ===
How to write a resource access tool is described in this [http://www.stanford.edu/~coulet/obr_tutorial_to_add_new_resources.pdf tutorial] by Adrien Coulet.

=== Available resources ===

Resources fully functional and available in the OBR index are available here: [http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources /obr/resources]

=== On development resources ===
* PubMed (PM)
* Stanford Microarray Database (SMD)
* Pathway Commons
* CaNanoLab

Others in queue

* ChemSpider
* Human Gene Mutation Database

=== Development history ===

1. Resource: Clinicaltrials.gov
*Person responsible: Kuladip Yadav(Optra),Sanjay Jadhav(Optra).
*Notes: Fixed issue of authentication, fixed other xml related issues.
*Status:
Changes done as per suggestions :
1. Decrease request delay from 1000 ms to 800ms.
2. Implement log4j logger mechanism.

2. Resource: GEO
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Modified GEO resource access tool to get data from both GSE and GDS database.
*Status:
Changes done as per suggestions :
1. Implement log4j logger mechanism.

3. Resource: Pubmed
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Built a new resource access tool from existing PubMedAccessTool to populate data from eutils and pubmed xml files .
*Status:
Changes done as per suggestions :
1. Remove direct database call from PubMed RAT.
2. Implement mapStringsToLocalConceptIDs method into ObsOntologiesAccessTool and TermTable.
3. Implement log4j logger in related classes.
4. Code changes pushed in SVN.

= Migration to a production architecture & framework =

No yet started

Processing OBR Resources

2009-11-06T05:35:54Z

Optra: /* OBR workflow execution history */

This wiki page describes the status of the OBR index.

= Execution of the OBR worklow & maintenance of the OBR index =

== Technical documentation ==
[[Image:PopulationOBRtables.png|thumb|Population of the OBR tables]]
* '''Population And Maintenance Of The OBR Index'''
Population of OBR and OBS tables is described in document [http://www.bioontology.org/wiki/images/5/5f/Population_And_Maintenance_Of_The_OBR_Index.doc Population_And_Maintenance_Of_The_OBR_Index]

* '''Technical Instructions for Configuring OBR Workflow'''
Population of OBR and OBS tables using properties files and shell script is described in document [http://www.bioontology.org/wiki/images/4/47/Technical_Instructions_for_Configuring_OBR_Workflow.doc Technical_Instructions_for_Configuring_OBR_Workflow]

RAT Start Date End Date Database Type of workflow execution
PCM Sunday, Oct 04, 2009 10:47 PM
Monday, Oct 05, 2009 06:11 PM
Obsdb1.obs_stage Resource update + OBR execution with full dictionary of the new delta of resources

== Headline text ==

== OBR workflow execution history ==

{| class="wikitable" border="1" cellspacing="0" cellpadding="1" width="150%"
|-
! RAT
! Date first processed
! Date last processed
! Database/schema
! Executed by
! Type of work flow execution
|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 04:14 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |DBK
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PCM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |AE
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GEO
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:38 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:34 PM
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:38 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:39 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 05:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Monday Oct 26, 2009 05:24 AM
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Wednesday Oct 14, 2009 10:47 PM
| valign="top" width="25%" |Wednesday Oct 14, 2009 11:00 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources

|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="25%" |Monday Oct 12, 2009 08:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |RXRD
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | DBK
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CT
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | BSM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | AE
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GAP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | WP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GEO
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGGE
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDI
| valign="top" width="25%" |Monday Oct 05, 2009 11:44 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CDD
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | UPKB
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:44 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDR
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | OMIM
| valign="top" width="25%" | Monday Oct 05, 2009 10:32 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | PCM
| valign="top" width="25%" | Sunday, Oct 04, 2009 10:47 PM
| valign="top" width="25%" | Monday, Oct 05, 2009 06:11 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" | Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" | Sunday, Aug 23, 2009 10:44 PM
| valign="top" width="25%" | Monday, Aug 24, 2009 04:40 AM
| valign="top" width="10%" |obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |SMD, DBK
| valign="top" width="25%" | Monday, Aug 03, 2009 11:28 PM
| valign="top" width="25%" | Tuesday, Aug 04, 2009 02:12 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Monday, July 27, 2009 11:19 PM
| valign="top" width="25%" | Wednesday, July 29, 2009 02:42 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" | Monday, July 13, 2009 02:45 AM
| valign="top" width="25%" | Tuesday, July 21, 2009 03:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip/Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Wednesday, June 17, 2009 3:45 AM
| valign="top" width="25%" | Wednesday, June 17, 2009 10:04 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip
| valign="top" |Contexts Populated : name, description, species
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | June 8, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |End of execution of the OBR workflow & switch of OBR API to the obsdb1.obs_stage schema
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | May 22, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources
|-
| valign="top" width="5%" | RXRD
| valign="top" width="25%" |
| valign="top" width="25%" | May 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Adrien
| valign="top" |Execution of the OBR index on RXRD independently
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | March 2009
| valign="top" width="10%" |
| valign="top" width="10%" |Clement
| valign="top" |DB schema use right now: ncbodb2.obs
|}

== Resources logs ==
* '''Execution of the OBR workflow log files'''
Log files are available here : [https://bmir-gforge.stanford.edu/gf/project/obs/docman/?subdir=58 /project/obs/docman/logs]

= Resources Access Tools (RATs) development and update =

This page is for keeping track of Resources Access Tools (RATs) developement.

=== How to write Resources Access Tools ===
How to write a resource access tool is described in this [http://www.stanford.edu/~coulet/obr_tutorial_to_add_new_resources.pdf tutorial] by Adrien Coulet.

=== Available resources ===

Resources fully functional and available in the OBR index are available here: [http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources /obr/resources]

=== On development resources ===
* PubMed (PM)
* Stanford Microarray Database (SMD)
* Pathway Commons
* CaNanoLab

Others in queue

* ChemSpider
* Human Gene Mutation Database

=== Development history ===

1. Resource: Clinicaltrials.gov
*Person responsible: Kuladip Yadav(Optra),Sanjay Jadhav(Optra).
*Notes: Fixed issue of authentication, fixed other xml related issues.
*Status:
Changes done as per suggestions :
1. Decrease request delay from 1000 ms to 800ms.
2. Implement log4j logger mechanism.

2. Resource: GEO
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Modified GEO resource access tool to get data from both GSE and GDS database.
*Status:
Changes done as per suggestions :
1. Implement log4j logger mechanism.

3. Resource: Pubmed
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Built a new resource access tool from existing PubMedAccessTool to populate data from eutils and pubmed xml files .
*Status:
Changes done as per suggestions :
1. Remove direct database call from PubMed RAT.
2. Implement mapStringsToLocalConceptIDs method into ObsOntologiesAccessTool and TermTable.
3. Implement log4j logger in related classes.
4. Code changes pushed in SVN.

= Migration to a production architecture & framework =

No yet started

Processing OBR Resources

2009-11-06T05:30:13Z

Optra: /* OBR workflow execution history */

This wiki page describes the status of the OBR index.

= Execution of the OBR worklow & maintenance of the OBR index =

== Technical documentation ==
[[Image:PopulationOBRtables.png|thumb|Population of the OBR tables]]
* '''Population And Maintenance Of The OBR Index'''
Population of OBR and OBS tables is described in document [http://www.bioontology.org/wiki/images/5/5f/Population_And_Maintenance_Of_The_OBR_Index.doc Population_And_Maintenance_Of_The_OBR_Index]

* '''Technical Instructions for Configuring OBR Workflow'''
Population of OBR and OBS tables using properties files and shell script is described in document [http://www.bioontology.org/wiki/images/4/47/Technical_Instructions_for_Configuring_OBR_Workflow.doc Technical_Instructions_for_Configuring_OBR_Workflow]

RAT Start Date End Date Database Type of workflow execution
PCM Sunday, Oct 04, 2009 10:47 PM
Monday, Oct 05, 2009 06:11 PM
Obsdb1.obs_stage Resource update + OBR execution with full dictionary of the new delta of resources

== Headline text ==

== OBR workflow execution history ==

{| class="wikitable" border="1" cellspacing="0" cellpadding="1" width="150%"
|-
! RAT
! Date first processed
! Date last processed
! Database/schema
! Executed by
! Type of work flow execution
|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 04:14 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |DBK
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PCM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |AE
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GEO
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:383 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:39 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 05:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Monday Oct 26, 2009 05:24 AM
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Wednesday Oct 14, 2009 10:47 PM
| valign="top" width="25%" |Wednesday Oct 14, 2009 11:00 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources

|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="25%" |Monday Oct 12, 2009 08:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |RXRD
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | DBK
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CT
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | BSM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | AE
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GAP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | WP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GEO
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGGE
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDI
| valign="top" width="25%" |Monday Oct 05, 2009 11:44 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CDD
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | UPKB
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:44 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDR
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | OMIM
| valign="top" width="25%" | Monday Oct 05, 2009 10:32 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | PCM
| valign="top" width="25%" | Sunday, Oct 04, 2009 10:47 PM
| valign="top" width="25%" | Monday, Oct 05, 2009 06:11 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" | Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" | Sunday, Aug 23, 2009 10:44 PM
| valign="top" width="25%" | Monday, Aug 24, 2009 04:40 AM
| valign="top" width="10%" |obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |SMD, DBK
| valign="top" width="25%" | Monday, Aug 03, 2009 11:28 PM
| valign="top" width="25%" | Tuesday, Aug 04, 2009 02:12 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Monday, July 27, 2009 11:19 PM
| valign="top" width="25%" | Wednesday, July 29, 2009 02:42 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" | Monday, July 13, 2009 02:45 AM
| valign="top" width="25%" | Tuesday, July 21, 2009 03:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip/Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Wednesday, June 17, 2009 3:45 AM
| valign="top" width="25%" | Wednesday, June 17, 2009 10:04 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip
| valign="top" |Contexts Populated : name, description, species
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | June 8, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |End of execution of the OBR workflow & switch of OBR API to the obsdb1.obs_stage schema
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | May 22, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources
|-
| valign="top" width="5%" | RXRD
| valign="top" width="25%" |
| valign="top" width="25%" | May 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Adrien
| valign="top" |Execution of the OBR index on RXRD independently
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | March 2009
| valign="top" width="10%" |
| valign="top" width="10%" |Clement
| valign="top" |DB schema use right now: ncbodb2.obs
|}

== Resources logs ==
* '''Execution of the OBR workflow log files'''
Log files are available here : [https://bmir-gforge.stanford.edu/gf/project/obs/docman/?subdir=58 /project/obs/docman/logs]

= Resources Access Tools (RATs) development and update =

This page is for keeping track of Resources Access Tools (RATs) developement.

=== How to write Resources Access Tools ===
How to write a resource access tool is described in this [http://www.stanford.edu/~coulet/obr_tutorial_to_add_new_resources.pdf tutorial] by Adrien Coulet.

=== Available resources ===

Resources fully functional and available in the OBR index are available here: [http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources /obr/resources]

=== On development resources ===
* PubMed (PM)
* Stanford Microarray Database (SMD)
* Pathway Commons
* CaNanoLab

Others in queue

* ChemSpider
* Human Gene Mutation Database

=== Development history ===

1. Resource: Clinicaltrials.gov
*Person responsible: Kuladip Yadav(Optra),Sanjay Jadhav(Optra).
*Notes: Fixed issue of authentication, fixed other xml related issues.
*Status:
Changes done as per suggestions :
1. Decrease request delay from 1000 ms to 800ms.
2. Implement log4j logger mechanism.

2. Resource: GEO
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Modified GEO resource access tool to get data from both GSE and GDS database.
*Status:
Changes done as per suggestions :
1. Implement log4j logger mechanism.

3. Resource: Pubmed
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Built a new resource access tool from existing PubMedAccessTool to populate data from eutils and pubmed xml files .
*Status:
Changes done as per suggestions :
1. Remove direct database call from PubMed RAT.
2. Implement mapStringsToLocalConceptIDs method into ObsOntologiesAccessTool and TermTable.
3. Implement log4j logger in related classes.
4. Code changes pushed in SVN.

= Migration to a production architecture & framework =

No yet started

Processing OBR Resources

2009-11-06T05:29:07Z

Optra: /* OBR workflow execution history */

This wiki page describes the status of the OBR index.

= Execution of the OBR worklow & maintenance of the OBR index =

== Technical documentation ==
[[Image:PopulationOBRtables.png|thumb|Population of the OBR tables]]
* '''Population And Maintenance Of The OBR Index'''
Population of OBR and OBS tables is described in document [http://www.bioontology.org/wiki/images/5/5f/Population_And_Maintenance_Of_The_OBR_Index.doc Population_And_Maintenance_Of_The_OBR_Index]

* '''Technical Instructions for Configuring OBR Workflow'''
Population of OBR and OBS tables using properties files and shell script is described in document [http://www.bioontology.org/wiki/images/4/47/Technical_Instructions_for_Configuring_OBR_Workflow.doc Technical_Instructions_for_Configuring_OBR_Workflow]

RAT Start Date End Date Database Type of workflow execution
PCM Sunday, Oct 04, 2009 10:47 PM
Monday, Oct 05, 2009 06:11 PM
Obsdb1.obs_stage Resource update + OBR execution with full dictionary of the new delta of resources

== Headline text ==

== OBR workflow execution history ==

{| class="wikitable" border="1" cellspacing="0" cellpadding="1" width="150%"
|-
! RAT
! Date first processed
! Date last processed
! Database/schema
! Executed by
! Type of work flow execution
|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 04:14 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |DBK
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PCM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |AE
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GAP 2009-11-05 00:17.........2009-11-05 00:19
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GEO
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:383 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGDI 2009-11-03 01:13......2009-11-03 01:19
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:39 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 05:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Monday Oct 26, 2009 05:24 AM
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Wednesday Oct 14, 2009 10:47 PM
| valign="top" width="25%" |Wednesday Oct 14, 2009 11:00 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources

|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="25%" |Monday Oct 12, 2009 08:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |RXRD
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | DBK
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CT
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | BSM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | AE
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GAP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | WP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GEO
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGGE
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDI
| valign="top" width="25%" |Monday Oct 05, 2009 11:44 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CDD
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | UPKB
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:44 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDR
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | OMIM
| valign="top" width="25%" | Monday Oct 05, 2009 10:32 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | PCM
| valign="top" width="25%" | Sunday, Oct 04, 2009 10:47 PM
| valign="top" width="25%" | Monday, Oct 05, 2009 06:11 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" | Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" | Sunday, Aug 23, 2009 10:44 PM
| valign="top" width="25%" | Monday, Aug 24, 2009 04:40 AM
| valign="top" width="10%" |obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |SMD, DBK
| valign="top" width="25%" | Monday, Aug 03, 2009 11:28 PM
| valign="top" width="25%" | Tuesday, Aug 04, 2009 02:12 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Monday, July 27, 2009 11:19 PM
| valign="top" width="25%" | Wednesday, July 29, 2009 02:42 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" | Monday, July 13, 2009 02:45 AM
| valign="top" width="25%" | Tuesday, July 21, 2009 03:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip/Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Wednesday, June 17, 2009 3:45 AM
| valign="top" width="25%" | Wednesday, June 17, 2009 10:04 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip
| valign="top" |Contexts Populated : name, description, species
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | June 8, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |End of execution of the OBR workflow & switch of OBR API to the obsdb1.obs_stage schema
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | May 22, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources
|-
| valign="top" width="5%" | RXRD
| valign="top" width="25%" |
| valign="top" width="25%" | May 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Adrien
| valign="top" |Execution of the OBR index on RXRD independently
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | March 2009
| valign="top" width="10%" |
| valign="top" width="10%" |Clement
| valign="top" |DB schema use right now: ncbodb2.obs
|}

== Resources logs ==
* '''Execution of the OBR workflow log files'''
Log files are available here : [https://bmir-gforge.stanford.edu/gf/project/obs/docman/?subdir=58 /project/obs/docman/logs]

= Resources Access Tools (RATs) development and update =

This page is for keeping track of Resources Access Tools (RATs) developement.

=== How to write Resources Access Tools ===
How to write a resource access tool is described in this [http://www.stanford.edu/~coulet/obr_tutorial_to_add_new_resources.pdf tutorial] by Adrien Coulet.

=== Available resources ===

Resources fully functional and available in the OBR index are available here: [http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources /obr/resources]

=== On development resources ===
* PubMed (PM)
* Stanford Microarray Database (SMD)
* Pathway Commons
* CaNanoLab

Others in queue

* ChemSpider
* Human Gene Mutation Database

=== Development history ===

1. Resource: Clinicaltrials.gov
*Person responsible: Kuladip Yadav(Optra),Sanjay Jadhav(Optra).
*Notes: Fixed issue of authentication, fixed other xml related issues.
*Status:
Changes done as per suggestions :
1. Decrease request delay from 1000 ms to 800ms.
2. Implement log4j logger mechanism.

2. Resource: GEO
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Modified GEO resource access tool to get data from both GSE and GDS database.
*Status:
Changes done as per suggestions :
1. Implement log4j logger mechanism.

3. Resource: Pubmed
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Built a new resource access tool from existing PubMedAccessTool to populate data from eutils and pubmed xml files .
*Status:
Changes done as per suggestions :
1. Remove direct database call from PubMed RAT.
2. Implement mapStringsToLocalConceptIDs method into ObsOntologiesAccessTool and TermTable.
3. Implement log4j logger in related classes.
4. Code changes pushed in SVN.

= Migration to a production architecture & framework =

No yet started

Processing OBR Resources

2009-11-06T05:28:42Z

Optra: /* OBR workflow execution history */

This wiki page describes the status of the OBR index.

= Execution of the OBR worklow & maintenance of the OBR index =

== Technical documentation ==
[[Image:PopulationOBRtables.png|thumb|Population of the OBR tables]]
* '''Population And Maintenance Of The OBR Index'''
Population of OBR and OBS tables is described in document [http://www.bioontology.org/wiki/images/5/5f/Population_And_Maintenance_Of_The_OBR_Index.doc Population_And_Maintenance_Of_The_OBR_Index]

* '''Technical Instructions for Configuring OBR Workflow'''
Population of OBR and OBS tables using properties files and shell script is described in document [http://www.bioontology.org/wiki/images/4/47/Technical_Instructions_for_Configuring_OBR_Workflow.doc Technical_Instructions_for_Configuring_OBR_Workflow]

RAT Start Date End Date Database Type of workflow execution
PCM Sunday, Oct 04, 2009 10:47 PM
Monday, Oct 05, 2009 06:11 PM
Obsdb1.obs_stage Resource update + OBR execution with full dictionary of the new delta of resources

== Headline text ==

== OBR workflow execution history ==

{| class="wikitable" border="1" cellspacing="0" cellpadding="1" width="150%"
|-
! RAT
! Date first processed
! Date last processed
! Database/schema
! Executed by
! Type of work flow execution
|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 04:14 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |REAC 2009-11-05 02:01.........2009-11-05 03:23
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |DBK
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PCM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |AE
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |GAP 2009-11-05 00:17.........2009-11-05 00:19
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GEO
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:383 PM
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |PGDI 2009-11-03 01:13......2009-11-03 01:19
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:19 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:39 AM
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 05:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Monday Oct 26, 2009 05:24 AM
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Wednesday Oct 14, 2009 10:47 PM
| valign="top" width="25%" |Wednesday Oct 14, 2009 11:00 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources

|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="25%" |Monday Oct 12, 2009 08:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |RXRD
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | DBK
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CT
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | BSM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | AE
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GAP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | WP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GEO
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGGE
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDI
| valign="top" width="25%" |Monday Oct 05, 2009 11:44 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CDD
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | UPKB
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:44 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDR
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | OMIM
| valign="top" width="25%" | Monday Oct 05, 2009 10:32 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | PCM
| valign="top" width="25%" | Sunday, Oct 04, 2009 10:47 PM
| valign="top" width="25%" | Monday, Oct 05, 2009 06:11 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" | Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" | Sunday, Aug 23, 2009 10:44 PM
| valign="top" width="25%" | Monday, Aug 24, 2009 04:40 AM
| valign="top" width="10%" |obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |SMD, DBK
| valign="top" width="25%" | Monday, Aug 03, 2009 11:28 PM
| valign="top" width="25%" | Tuesday, Aug 04, 2009 02:12 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Monday, July 27, 2009 11:19 PM
| valign="top" width="25%" | Wednesday, July 29, 2009 02:42 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" | Monday, July 13, 2009 02:45 AM
| valign="top" width="25%" | Tuesday, July 21, 2009 03:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip/Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Wednesday, June 17, 2009 3:45 AM
| valign="top" width="25%" | Wednesday, June 17, 2009 10:04 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip
| valign="top" |Contexts Populated : name, description, species
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | June 8, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |End of execution of the OBR workflow & switch of OBR API to the obsdb1.obs_stage schema
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | May 22, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources
|-
| valign="top" width="5%" | RXRD
| valign="top" width="25%" |
| valign="top" width="25%" | May 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Adrien
| valign="top" |Execution of the OBR index on RXRD independently
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | March 2009
| valign="top" width="10%" |
| valign="top" width="10%" |Clement
| valign="top" |DB schema use right now: ncbodb2.obs
|}

== Resources logs ==
* '''Execution of the OBR workflow log files'''
Log files are available here : [https://bmir-gforge.stanford.edu/gf/project/obs/docman/?subdir=58 /project/obs/docman/logs]

= Resources Access Tools (RATs) development and update =

This page is for keeping track of Resources Access Tools (RATs) developement.

=== How to write Resources Access Tools ===
How to write a resource access tool is described in this [http://www.stanford.edu/~coulet/obr_tutorial_to_add_new_resources.pdf tutorial] by Adrien Coulet.

=== Available resources ===

Resources fully functional and available in the OBR index are available here: [http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources /obr/resources]

=== On development resources ===
* PubMed (PM)
* Stanford Microarray Database (SMD)
* Pathway Commons
* CaNanoLab

Others in queue

* ChemSpider
* Human Gene Mutation Database

=== Development history ===

1. Resource: Clinicaltrials.gov
*Person responsible: Kuladip Yadav(Optra),Sanjay Jadhav(Optra).
*Notes: Fixed issue of authentication, fixed other xml related issues.
*Status:
Changes done as per suggestions :
1. Decrease request delay from 1000 ms to 800ms.
2. Implement log4j logger mechanism.

2. Resource: GEO
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Modified GEO resource access tool to get data from both GSE and GDS database.
*Status:
Changes done as per suggestions :
1. Implement log4j logger mechanism.

3. Resource: Pubmed
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Built a new resource access tool from existing PubMedAccessTool to populate data from eutils and pubmed xml files .
*Status:
Changes done as per suggestions :
1. Remove direct database call from PubMed RAT.
2. Implement mapStringsToLocalConceptIDs method into ObsOntologiesAccessTool and TermTable.
3. Implement log4j logger in related classes.
4. Code changes pushed in SVN.

= Migration to a production architecture & framework =

No yet started

Processing OBR Resources

2009-10-27T12:14:10Z

Optra: /* OBR workflow execution history */

This wiki page describes the status of the OBR index.

= Execution of the OBR worklow & maintenance of the OBR index =

== Technical documentation ==
[[Image:PopulationOBRtables.png|thumb|Population of the OBR tables]]
* '''Population And Maintenance Of The OBR Index'''
Population of OBR and OBS tables is described in document [http://www.bioontology.org/wiki/images/5/5f/Population_And_Maintenance_Of_The_OBR_Index.doc Population_And_Maintenance_Of_The_OBR_Index]

* '''Technical Instructions for Configuring OBR Workflow'''
Population of OBR and OBS tables using properties files and shell script is described in document [http://www.bioontology.org/wiki/images/4/47/Technical_Instructions_for_Configuring_OBR_Workflow.doc Technical_Instructions_for_Configuring_OBR_Workflow]

RAT Start Date End Date Database Type of workflow execution
PCM Sunday, Oct 04, 2009 10:47 PM
Monday, Oct 05, 2009 06:11 PM
Obsdb1.obs_stage Resource update + OBR execution with full dictionary of the new delta of resources

== Headline text ==

== OBR workflow execution history ==

{| class="wikitable" border="1" cellspacing="0" cellpadding="1" width="150%"
|-
! RAT
! Date first processed
! Date last processed
! Database/schema
! Executed by
! Type of work flow execution
|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 05:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |BSM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |WP
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGGE
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDI
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |UPKB
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |CDD
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PGDR
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |OMIM
| valign="top" width="25%" |Monday Oct 26, 2009 05:24 AM
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |PC
| valign="top" width="25%" |Wednesday Oct 14, 2009 10:47 PM
| valign="top" width="25%" |Wednesday Oct 14, 2009 11:00 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources

|-
| valign="top" width="5%" |SMD
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="25%" |Monday Oct 12, 2009 08:06 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |GM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |REAC
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" |RXRD
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | DBK
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CT
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | BSM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | AE
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GAP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | WP
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | GEO
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGGE
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDI
| valign="top" width="25%" |Monday Oct 05, 2009 11:44 PM
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | CDD
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | UPKB
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM
| valign="top" width="25%" | Monday Oct 05, 2009 11:44 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources

|-
| valign="top" width="5%" | PGDR
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | OMIM
| valign="top" width="25%" | Monday Oct 05, 2009 10:32 PM
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
|-
| valign="top" width="5%" | PCM
| valign="top" width="25%" | Sunday, Oct 04, 2009 10:47 PM
| valign="top" width="25%" | Monday, Oct 05, 2009 06:11 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" | Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |GAP
| valign="top" width="25%" | Sunday, Aug 23, 2009 10:44 PM
| valign="top" width="25%" | Monday, Aug 24, 2009 04:40 AM
| valign="top" width="10%" |obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" |SMD, DBK
| valign="top" width="25%" | Monday, Aug 03, 2009 11:28 PM
| valign="top" width="25%" | Tuesday, Aug 04, 2009 02:12 PM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Monday, July 27, 2009 11:19 PM
| valign="top" width="25%" | Wednesday, July 29, 2009 02:42 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" | Monday, July 13, 2009 02:45 AM
| valign="top" width="25%" | Tuesday, July 21, 2009 03:46 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip/Palani
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
|-
| valign="top" width="5%" | AE
| valign="top" width="25%" | Wednesday, June 17, 2009 3:45 AM
| valign="top" width="25%" | Wednesday, June 17, 2009 10:04 AM
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Kuladip
| valign="top" |Contexts Populated : name, description, species
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | June 8, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |End of execution of the OBR workflow & switch of OBR API to the obsdb1.obs_stage schema
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | May 22, 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Clement
| valign="top" |OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources
|-
| valign="top" width="5%" | RXRD
| valign="top" width="25%" |
| valign="top" width="25%" | May 2009
| valign="top" width="10%" | obsdb1.obs_stage
| valign="top" width="10%" |Adrien
| valign="top" |Execution of the OBR index on RXRD independently
|-
| valign="top" width="5%" | (All)
| valign="top" width="25%" |
| valign="top" width="25%" | March 2009
| valign="top" width="10%" |
| valign="top" width="10%" |Clement
| valign="top" |DB schema use right now: ncbodb2.obs
|}

== Resources logs ==
* '''Execution of the OBR workflow log files'''
Log files are available here : [https://bmir-gforge.stanford.edu/gf/project/obs/docman/?subdir=58 /project/obs/docman/logs]

= Resources Access Tools (RATs) development and update =

This page is for keeping track of Resources Access Tools (RATs) developement.

=== How to write Resources Access Tools ===
How to write a resource access tool is described in this [http://www.stanford.edu/~coulet/obr_tutorial_to_add_new_resources.pdf tutorial] by Adrien Coulet.

=== Available resources ===

Resources fully functional and available in the OBR index are available here: [http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources /obr/resources]

=== On development resources ===
* PubMed (PM)
* Stanford Microarray Database (SMD)
* Pathway Commons
* CaNanoLab

Others in queue

* ChemSpider
* Human Gene Mutation Database

=== Development history ===

1. Resource: Clinicaltrials.gov
*Person responsible: Kuladip Yadav(Optra),Sanjay Jadhav(Optra).
*Notes: Fixed issue of authentication, fixed other xml related issues.
*Status:
Changes done as per suggestions :
1. Decrease request delay from 1000 ms to 800ms.
2. Implement log4j logger mechanism.

2. Resource: GEO
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Modified GEO resource access tool to get data from both GSE and GDS database.
*Status:
Changes done as per suggestions :
1. Implement log4j logger mechanism.

3. Resource: Pubmed
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
*Notes:Built a new resource access tool from existing PubMedAccessTool to populate data from eutils and pubmed xml files .
*Status:
Changes done as per suggestions :
1. Remove direct database call from PubMed RAT.
2. Implement mapStringsToLocalConceptIDs method into ObsOntologiesAccessTool and TermTable.
3. Implement log4j logger in related classes.
4. Code changes pushed in SVN.

= Migration to a production architecture & framework =

No yet started