The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold an Introduction and Application of Bio-Ontologies tutorial as part of its [http://www.bioontology.org/wiki/index.php/Meetings_and_Events series of training and dissemination events].

:'''Venue:''' [http://bmir.stanford.edu/ Stanford Center for Biomedical Informatics Research, Stanford University]

:'''Date: Tutorial: March 15, 2012'''

:'''Organization:''' Barry Smith (NCBO / Buffalo), Trish Whetzel (NCBO / Stanford University), and Nigam Shah (NCBO / Stanford University)

:'''Registration:''' Please write to [mailto:phismith@buffalo.edu Barry Smith]

:'''Audience:''' Some background in bioinformatics or medical informatics is required. No knowledge of ontology is presupposed.

----

'''Agenda:'''
* 1:00pm What is an ontology and what is it useful for? (Barry Smith)

This section will provide an introduction to biomedical ontology with a focus on illustrations of success stories in the application of ontologies to supporting specific kinds of research.

* 2:30pm NCBO Web Services and Development of Semantic Applications (Trish Whetzel). Overview presentation of NCBO Web services and how they are being incorporated into software applications.
** Introduction to REST Web services
** [http://bioportal.bioontology.org NCBO BioPortal]
** NCBO REST Web services
*** [http://www.bioontology.org/wiki/index.php/NCBO_REST_services Ontology Web services] - Search, Traverse, Download
*** [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction Web service] - Subset
*** [http://www.bioontology.org/wiki/index.php/Ontology_Notes Notes Web service] - Propose Terms, Comment
*** [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mapping Web services] - Create, Upload, Download
*** [http://www.bioontology.org/wiki/index.php/NCBO_Widgets Widgets] - Tree view, Auto-complete, Graph view
*** [http://www.bioontology.org/wiki/index.php/Annotator_Web_service Annotation] - Ontology Term recognition
*** [http://www.bioontology.org/wiki/index.php/Resource_Index Data Access] - Fetch ontology-indexed data
** [http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal BioPortal SPARQL Endpoint] - Access Ontologies via SPARQL

* 4:00pm Use of ontologies in biomedical research (Nigam Shah)

We will review the use of NCBO components to create an annotation workflow (specifically using the Annotator and Lexicon Builder components). We will then discuss the applications of this workflow to 9.5 million clinical documents--from the electronic health records of approximately one million adult patients from the STRIDE Clinical Data Warehouse, part of Stanford's CTSA Informatics platform--to identify statistically significant patterns of drug use and to conduct drug safety surveillance.

For the patterns of drug use, we validate the usage patterns learned from the data against FDA-approved indications as well as external sources of known off-label use such as Medi-Span. For drug safety surveillance, we show that drug–disease co-occurrences and the temporal ordering of drugs and disease mentions in clinical notes can be examined for statistical enrichment and used to detect potential adverse events.

Introduction and Applications of Bio-Ontologies

2012-02-03T18:24:12Z

Nigam:

2011-07-22T18:16:11Z

Nigam:

[http://www.bioontology.org/wiki/images/f/f6/Tutorial_Slides_-_T18.pdf Tutorial Slides]

'''Sample Links'''

* http://rest.bioontology.org/bioportal/search/Melanoma/?ontologyids=1353
* http://rest.bioontology.org/bioportal/virtual/rootpath/1353/2092003
* http://rest.bioontology.org/bioportal/virtual/rdf/1353/2092003
* http://rest.bioontology.org/bioportal/virtual/ontology/1353/2092003

----

* http://purl.bioontology.org/ontology/SNOMEDCT/2092003
* http://bioportal.bioontology.org/visualize/virtual/1353/2092003
* http://bioportal.bioontology.org/visualize/42789/2092003
* http://bioportal.bioontology.org/visualize/42789/?conceptid=2092003
* http://bioportal.bioontology.org/ontologies/42789#widgets

----

* http://purl.bioontology.org/ontology/MSH/D008545
* http://bioportal.bioontology.org/visualize/39228/DOID:399
* http://rest.bioontology.org/bioportal/virtual/rootpath/1025/MP:0000929

'''Sample user needs'''

* I need to restrict user input to a certain value set

Create a value set with the needed terms, submit to BioPortal and then use the auto complete widget or the search service. If the value set is a subtree of an existing ontology, use the search service restricted to that sub branch.

e.g. http://rest.bioontology.org/bioportal/search/Melanoma?ontologyids=1353&subtreerootconceptid=108369006, searches for Melanoma under 'Neoplasm' in SNOMEDCT.

* I need to extract the disease branch from SNOMEDCT

Use the view extractor service or pick the desired root node and recursively call get child nodes; or pick the desired root node and get all paths to leaf terms from that node.

* I need to identify all terms mapped to UMLS CUI C0151779

Use the search service, search the properties of every term for C0151779.
http://rest.bioontology.org/bioportal/search/C0151779?isexactmatch=1&includeproperties=1

* I need to code/annotate free-text with ontology terms

Use the Annotator service (at BioPortal or as a Virtual Machine at your institution); or make sure to use the auto complete widgets in the web forms at content acquisition time!

API-Key for Tutorial: 24e037b6-54e0-11e0-9d7b-005056aa331[SIX]

Lexicon Builder

2011-02-01T22:53:20Z

Nigam: /* Publication */

== Introduction ==

The LexiconBuilder project has been undertaken for creating a Web service that allows building of custom lexicons from BioPortal ontologies. The custom lexicons built by our system can be used for a variety of natural language processing and other ontology related tasks.

While generating the custom lexicons, several features of our system can be utilized for ease of creation, integration and maintainence of such lexicons. The users can specify ontology mappings in order to identify and retrieve relevant concepts in other ontologies which they might not otherwise know about, in order to assist in enriching the custom lexicons. It also facilitates the interpretation of datasets using the concept mappings between particular datasets. They can also make use of the visualization services provided by NCBO to view and understand the ontology structure retrieved, which otherwise can be a daunting task. Additionally, users can also retrieve identifiers for concepts etc using the lexicon builder and can then utilize the hierarchy services using those ids to identify and visualize the hierarchies(using the visualization service) in the lexicon and can then subsequently make changes to their lexicon building parameters, until they narrow down to their exact requirements. Our system also simplifies the task of performing version management of the custom lexicons. When changes occur to the underlying data, new data is added to the ontologies or old data is changed/deleted, the users can simply retrieve a newer version of their lexicon using our services.

The custom lexicons generated by using our system can help users in a variety of tasks, some exemplified by the users of our system. These lexicons can be used for domain or requirement specific text annotation tasks. e.g. annotation of protein mutations with disease terms. They can also be very useful for ontology related tasks such as ontology learning especially information extraction and also for the task of ontology enrichment. One of our users want to use our service for compiling a disease dictionary, which has actually served as our driving use case. They can also be employed for the purpose of tagging elements for enhancing the user browsing experience for domain specific information e.g. For the task of assisting the user when they are browsing the Web especially for documents related to the biomedical domain we could possible tag elements related to say Tumors and add more context specific information using a Tumor lexicon generated using our system. Another example comes from our user who are using our system to create workflow specific lexicons for concept recognition tasks.

== Code location ==

https://bmir-gforge.stanford.edu/gf/project/lexicon_builder/

Home page: http://labs.bioontology.org/LexiconBuilder/

The Service end point: http://labs.bioontology.org/LexiconBuilderService/

'''Note: The prototype is currently in the development phase and constantly undergoing changes.'''

== Publication ==

The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies
Gautam Kumar Parai, Clement Jonquet, Rong Xu, Mark A. Musen and Nigam H. Shah
AMIA Annu Symp Proc. 2010

[[Media:LexiconBuilder.pdf]]

== Usage ==
===Inclusion Criteria===

'''Ontologies''' [default: all]
(i.e., list of ontologies you want to use to expand separated with comma (without spaces) e.g., SNOMEDCT,NCI,MSH.

'''Parent Concept''' [default: all]
(i.e. localConceptID of the concept to retrieve children concepts.

'''Synonyms''' true false [default: true]
(i.e., do you want the synonyms of the concept too?)

'''Semantic Types For Concepts''' [default: all]
(i.e., list of UMLS semantic types you want to use separated with comma (without spaces) e.g., T000,T047,T048.

'''Mapping Types For Mapped Concepts''' [default: none]
(i.e., list of mapping types you want to use for the mapping expansion component separated with comma (without spaces) e.g., inter-cui,from-mrrel.)

'''MEDLINE Counts''' [default: all]
(i.e., MEDLINE count of the concepts retrieved is greater than the specified count e.g. 10000)

'''Result Offset''' [default: None]
(i.e., Retrieve results starting from this result. If Result Offset and NO Result Count then returns the top 'Result Offset' results)
Result Count [default: None]
(i.e., Number of results you want to retrieve starting from the offset.)
e.g. 'Result Offset' = 0 'Result Count' = 100 For retrieving the top 100 results.

===Exclusion Criteria===

'''stopWords''' [default: empty]
(i.e., list of stop words to use (i.e., not to use for annotation) separated with comma (without spaces) e.g., in,am,be,is.

'''withDefaultStopWords''' true false [default: false]
(i.e., do you want to use our default stop word list available here: /obs/stopwords . This cancel the above one.)

===Output Criteria===

'''Output Columns''' (i.e., the columns you want in the results.)
LocalConceptID
LocalOntologyID
OntologyName
OntologyVersion
OntologyDescription
TermName
LocalSemanticTypeID
LocalSemanticTypeName
MappedLocalConceptID
MappingType

'''Unique Column''' (i.e., the unique column on which to group the results. e.g. using Concept will give one row for each unique concept.)
LocalConceptID
TermName
The 'unique column' parameters are available only if you choose them in the Output Columns section too.

'''Output Format''' (i.e., the format of the results.) [default: asXml]
asXML
asText
asTabDelimited

'''Compressed Output''' (Yes: Dictionary as a compressed ZIP file. No: Dictionary displayed on browser. ) [default: No]
Yes
No

== Workflow ==

[[Image:Example.png]]

File:LexiconBuilder.pdf

2011-02-01T22:53:06Z

Nigam:

Lexicon Builder

2011-02-01T22:52:44Z

Nigam: /* Code location */

== Introduction ==

The LexiconBuilder project has been undertaken for creating a Web service that allows building of custom lexicons from BioPortal ontologies. The custom lexicons built by our system can be used for a variety of natural language processing and other ontology related tasks.

While generating the custom lexicons, several features of our system can be utilized for ease of creation, integration and maintainence of such lexicons. The users can specify ontology mappings in order to identify and retrieve relevant concepts in other ontologies which they might not otherwise know about, in order to assist in enriching the custom lexicons. It also facilitates the interpretation of datasets using the concept mappings between particular datasets. They can also make use of the visualization services provided by NCBO to view and understand the ontology structure retrieved, which otherwise can be a daunting task. Additionally, users can also retrieve identifiers for concepts etc using the lexicon builder and can then utilize the hierarchy services using those ids to identify and visualize the hierarchies(using the visualization service) in the lexicon and can then subsequently make changes to their lexicon building parameters, until they narrow down to their exact requirements. Our system also simplifies the task of performing version management of the custom lexicons. When changes occur to the underlying data, new data is added to the ontologies or old data is changed/deleted, the users can simply retrieve a newer version of their lexicon using our services.

The custom lexicons generated by using our system can help users in a variety of tasks, some exemplified by the users of our system. These lexicons can be used for domain or requirement specific text annotation tasks. e.g. annotation of protein mutations with disease terms. They can also be very useful for ontology related tasks such as ontology learning especially information extraction and also for the task of ontology enrichment. One of our users want to use our service for compiling a disease dictionary, which has actually served as our driving use case. They can also be employed for the purpose of tagging elements for enhancing the user browsing experience for domain specific information e.g. For the task of assisting the user when they are browsing the Web especially for documents related to the biomedical domain we could possible tag elements related to say Tumors and add more context specific information using a Tumor lexicon generated using our system. Another example comes from our user who are using our system to create workflow specific lexicons for concept recognition tasks.

== Code location ==

https://bmir-gforge.stanford.edu/gf/project/lexicon_builder/

Home page: http://labs.bioontology.org/LexiconBuilder/

The Service end point: http://labs.bioontology.org/LexiconBuilderService/

'''Note: The prototype is currently in the development phase and constantly undergoing changes.'''

== Publication ==

The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies
Gautam Kumar Parai, Clement Jonquet, Rong Xu, Mark A. Musen and Nigam H. Shah
AMIA Annu Symp Proc. 2010 [[Media:LexiconBuilder.pdf]]

== Usage ==
===Inclusion Criteria===

'''Ontologies''' [default: all]
(i.e., list of ontologies you want to use to expand separated with comma (without spaces) e.g., SNOMEDCT,NCI,MSH.

'''Parent Concept''' [default: all]
(i.e. localConceptID of the concept to retrieve children concepts.

'''Synonyms''' true false [default: true]
(i.e., do you want the synonyms of the concept too?)

'''Semantic Types For Concepts''' [default: all]
(i.e., list of UMLS semantic types you want to use separated with comma (without spaces) e.g., T000,T047,T048.

'''Mapping Types For Mapped Concepts''' [default: none]
(i.e., list of mapping types you want to use for the mapping expansion component separated with comma (without spaces) e.g., inter-cui,from-mrrel.)

'''MEDLINE Counts''' [default: all]
(i.e., MEDLINE count of the concepts retrieved is greater than the specified count e.g. 10000)

'''Result Offset''' [default: None]
(i.e., Retrieve results starting from this result. If Result Offset and NO Result Count then returns the top 'Result Offset' results)
Result Count [default: None]
(i.e., Number of results you want to retrieve starting from the offset.)
e.g. 'Result Offset' = 0 'Result Count' = 100 For retrieving the top 100 results.

===Exclusion Criteria===

'''stopWords''' [default: empty]
(i.e., list of stop words to use (i.e., not to use for annotation) separated with comma (without spaces) e.g., in,am,be,is.

'''withDefaultStopWords''' true false [default: false]
(i.e., do you want to use our default stop word list available here: /obs/stopwords . This cancel the above one.)

===Output Criteria===

'''Output Columns''' (i.e., the columns you want in the results.)
LocalConceptID
LocalOntologyID
OntologyName
OntologyVersion
OntologyDescription
TermName
LocalSemanticTypeID
LocalSemanticTypeName
MappedLocalConceptID
MappingType

'''Unique Column''' (i.e., the unique column on which to group the results. e.g. using Concept will give one row for each unique concept.)
LocalConceptID
TermName
The 'unique column' parameters are available only if you choose them in the Output Columns section too.

'''Output Format''' (i.e., the format of the results.) [default: asXml]
asXML
asText
asTabDelimited

'''Compressed Output''' (Yes: Dictionary as a compressed ZIP file. No: Dictionary displayed on browser. ) [default: No]
Yes
No

== Workflow ==

[[Image:Example.png]]

Main Page

2011-01-15T01:10:32Z

Nigam: /* Research projects and Prototypes */

Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, dissemination events conducted by the NCBO and publically shared materials from the NCBO.
Please visit our [http://www.bioontology.org Main Site] for more information and materials.

{| class="wikitable"
|-
! style="background:#efefef;" | NCBO Links
! style="background:#efefef;" | Shared Materials
! style="background:#efefef;" | NCBC Links
|-
| [http://www.bioontology.org/ Home page]
| [[Public Requirements Redirect|Public Requirements]]
| [http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]
|-
| [http://www.bioontology.org/wiki/index.php/NCBO_FAQ FAQ]
| [[Shared Materials]]
| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]
|-
| [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination]
|-
| [http://www.bioontology.org/wiki/index.php/News_Events_Publications News, Events and Publications]
| [[Evaluation Activities]]
| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]
|}

=== Ontology Development Area ===

Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki

*[[BRO:Main_Page]] - Biomedical Resource Ontology
*[[PATO:Main_Page]] - An ontology of phenotypic qualities
*[[RO:Main_Page]] - OBO Relations ontology
*[[CARO:Main_Page]] - Reference anatomical ontology
*[[CL:Main_Page]] - OBO Cell ontology
*[[SO:Main_Page]] - Sequence Ontology
*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders
*[[OCI:Main_Page]] - Ontology of Clinical Investigation
*[[NPO:Main_Page]] - NanoParticle Ontology

Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.

=== Software ===

*[http://bioportal.bioontology.org Bioportal:Main_Page] - Main page for accessing Bioportal
*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.

=== How to's ===

* [[NCBO REST services]] - Documentation on how to use BioPortal functionality as Web services
* [[BioPortal UI URLs]] - Documentation on how to link back to BioPortal UI pages
* [http://www.bioontology.org/wiki/index.php/SampleCodeCookbook Code samples] - Sample code for common tasks with BioPortal Web services
* [[Annotator Web service]] - Documentation & information about the NCBO Annotator
* [[Resource Index]] - Documentation & information about the annotation-based NCBO biomedical Resources Index
* ''Retired'' -> See [[BioPortal REST services]] for access to UMLS content. [[UMLS_REST_Services]] - Documentation on how to use our ''prototype'' UMLS services (NetKernel)

=== Research projects and Prototypes ===

*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores (Nipun Bhatia)
*[[Path to Root]] - Project for consuming the path to root and other OBS rest services (Nipun Bhatia)
*[[PURL Server]] - Instructions on how to set-up a PURL server and create Master-Slave architecture for redundancy (Nipun Bhatia)
*[[Ontology Recommender Web service]] - Documentation & information about the NCBO Ontology Recommender (Clement Jonquet)
*[[Annotation Summarizer]] - Project utilizing OBS REST services to derive information from datasets referencing ontologies in BioPortal (Rob Tirrell)
*[[Lexicon Builder]] - Project for creating a service that allows building of custom lexicons from bioportal ontologies. (Gautam Parai)
*[[Medline Analysis]] - Project for applying natural language processing methods on Medline to analyze the frequency and syntactic type distribution of ontology terms. (Rong Xu)
*[[MetaMap Installation]] - Project to install a custom MetaMap using the NCBO data in order to integrate it in the [[Annotator Web service]] workflow. (Tejaswi Tenneti)

Mining Grants and Publications

2011-01-12T23:22:59Z

Nigam: New page: Page for Yi's project

Page for Yi's project

Main Page

2011-01-12T23:15:54Z

Nigam:

2010-11-13T15:21:30Z

Nigam: New page: Sample Links * http://rest.bioontology.org/bioportal/search/Melanoma/?ontologyids=1353 * http://rest.bioontology.org/bioportal/virtual/rootpath/1353/2092003 * http://rest.bioontology.org/...

BioPortal REST services

2010-11-03T22:40:07Z

Nigam:

This page documents BioPortal Web Service signatures. The list below contains commonly accessed BioPortal Web services and is not intended to be an exhaustive list. If a feature you are interested in is not in the list below, please contact [mailto:support@bioontology.org BioPortal Support] to request the service or ask for more details on the full list of services.

The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/bioportal/

* '''Note''': All NCBO REST web service calls MUST append 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. Please start adding the user identification URL parameter to all your web service invocations. Later in 2009, we may start challenging REST service calls that do not have this parameter.

* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. If you have any questions, please contact [mailto:support@bioontology.org BioPortal Support].''

= Overview - Using NCBO Technology in Your Project =
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.

= Code Examples =
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.

*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] can be found on pages specific for those tools.

= BioPortal Announce Mailing List =
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.

= Services to access ontologies and ontology versions =

== List all the latest version of ontologies ==

* '''Signature''': ./ontologies?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?email=example@example.org

== Get a specific ontology based on a version id ==
* '''Signature''': ./ontologies/{ontology version id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?email=example@example.org

== Download an ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?email=example@example.org

== Download the latest ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?email=example@example.org

== Get all versions of an ontology from a virtual ontology id ==
* '''Signature''': ./ontologies/versions/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?email=example@example.org

== Get latest version of an ontology id ==
* '''Signature''': ./virtual/ontology/{ontology_id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?email=example@example.org

== List all ontology categories ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./categories?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/categories

== List all ontology groups ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./groups?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/groups

= Services to access ontology views and ontology view versions =

Since all the views on ontologies are ontologies themselves all the services that work on ontologies do
work for ontology views also with the same signature.

For example to get a specific ontology view based on a version id would be possible by using the signature:

'''./ontologies/download/{view version id}?email={email_address}'''

or for getting all view versions of a virtual view can be achieved called using the signature:

'''./ontologies/versions/{view id}?email={email_address}'''

However, there are a couple of services that are special for views:

== List all the latest version of views ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./views?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/views?email=example@example.org

== Get all versions of views from a virtual ontology id ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.
* '''Signature''': ./views/versions/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?email=example@example.org

= Search services =

== Search BioPortal ==
* '''Signature''': ./search/{query}[?{optional args}]&email={email_address}
* '''Alt Signature''': ./search/?query={uri-encoded query}[&{optional args}]&email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/search/Gene?email=example@example.org
* You can use multiple query terms, separated by a space, for example: [http://rest.bioontology.org/bioportal/search/lung%20disease http://rest.bioontology.org/bioportal/search/lung disease?email=example@example.org]
* '''Optional arguments:'''
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)
** isexactmatch=[1/0] – match the entire concept name (default: 0)
** includeproperties=[1/0] – include attributes in the search (default: 0)
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.
* '''Description:'''
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).

In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).

* '''Example''': http://rest.bioontology.org/bioportal/search/software/?ontologyids=1104&isexactmatch=1&email=example@example.org
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8" ?>
<success>
<accessedResource>
/bioportal/search/cutaneous%20mela
</accessedResource>
<accessDate>2009-05-07 16:17:46.182 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>1</numPages>
<pageSize>3</pageSize>
<numResultsPage>3</numResultsPage>
<numResultsTotal>3</numResultsTotal>
<contents
class="org.ncbo.stanford.bean.search.SearchResultListBean">
<searchResultList>
<searchBean>
<ontologyVersionId>39715</ontologyVersionId>
<ontologyId>1136</ontologyId>
<ontologyDisplayLabel>
Experimental Factor Ontology
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>
http://www.ebi.ac.uk/efo/EFO_0000389
</conceptId>
<conceptIdShort>EFO_0000389</conceptIdShort>
<preferredName>
cutaneous melanoma
</preferredName>
<contents>cutaneous melanoma</contents>
</searchBean>
<searchBean>
<ontologyVersionId>39478</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>
NCI Thesaurus
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cutaneous_Melanoma
</conceptId>
<conceptIdShort>
Cutaneous_Melanoma
</conceptIdShort>
<preferredName>
Cutaneous Melanoma
</preferredName>
<contents>Cutaneous Melanoma</contents>
</searchBean>
<searchBean>
<ontologyVersionId>39833</ontologyVersionId>
<ontologyId>1009</ontologyId>
<ontologyDisplayLabel>
Human disease
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>DOID:2418</conceptId>
<conceptIdShort>DOID:2418</conceptIdShort>
<preferredName>
Cutaneous Melanocytic Neoplasm
</preferredName>
<contents>
Cutaneous Melanocytic Neoplasm
</contents>
</searchBean>
</searchResultList>
<ontologyHitList>
<ontologyHitBean>
<ontologyVersionId>39715</ontologyVersionId>
<ontologyId>1136</ontologyId>
<ontologyDisplayLabel>
Experimental Factor Ontology
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
<ontologyHitBean>
<ontologyVersionId>39833</ontologyVersionId>
<ontologyId>1009</ontologyId>
<ontologyDisplayLabel>
Human disease
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
<ontologyHitBean>
<ontologyVersionId>39478</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>
NCI Thesaurus
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
</ontologyHitList>
</contents>
</page>
</data>
</success>
</pre>

= Term services =
(formerly referred to as Concept services)

== Get term ==
* '''Signature''': ./concepts/{ontology version id}/{concept id}?email={email_address}
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI.
* '''Optional arguments:'''
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.
* '''Examples''':
http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource?email=example@example.org 
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&light=0&email=example@example.org 
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&norelations=1&email=example@example.org
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8" ?>
<success>
<accessedResource>/bioportal/concepts/40644/</accessedResource>
<accessDate>2009-12-16 10:06:10.727 PST</accessDate>
<data>
<classBean>
<id>Melanoma</id>
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanoma</fullId>
<label>Melanoma</label>
<type>Class</type>
<synonyms>
<string>Malignant Melanoma</string>
<string>Melanoma</string>
<string>melanoma</string>
</synonyms>
<definitions>
<string>A malignant, usually aggressive tumor composed of atypical,
neoplastic melanocytes.</string>
</definitions>
<relations>
<entry>
<string>UMLS_CUI</string>
<list>
<string>C0025202</string>
</list>
</entry>
<entry>
<string>owl:equivalentClass</string>
<list>
<string>'Common Neoplasm' and 'Melanocytic Neoplasm' and
(Disease_Has_Abnormal_Cell only 'Melanoma Cell')</string>
</list>
</entry>
<entry>
<string>ALT_DEFINITION</string>
<list>
<string>
<def-source>NCI-GLOSS</def-source>
<def-definition>A form of skin cancer that arises in
melanocytes, the cells that produce pigment.</def-definition>
</string>
</list>
</entry>
<entry>
<string>ICD-O-3_Code</string>
<list>
<string>8720/3</string>
</list>
</entry>
<entry>
<string>Semantic_Type</string>
<list>
<string>Neoplastic Process</string>
</list>
</entry>
<entry>
<string>SubClass</string>
<list>
<classBean>
<id>Non-Cutaneous_Melanoma</id>
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Non-Cutaneous_Melanoma</fullId>
<label>Non-Cutaneous Melanoma</label>
<type>Class</type>
<synonyms>
<string>Extracutaneous Melanoma</string>
<string>Non-Cutaneous Melanoma</string>
</synonyms>
<definitions>
<string>Melanoma is a malignant tumor of melanocytes,
cells that are derived from the neural crest.</string>
</definitions>
<relations>
<entry>
<string>code</string>
<list>
<string>C8711</string>
</list>
</entry>
</relations>
</classBean>
</list>
</entry>
</relations>
</classBean>
</data>
</success>
</pre>

== Get all root terms for an ontology version id ==
* '''Signature''': ./concepts/{ontology version id}/root?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?email=example@example.org

== Get a path between two terms ==
* '''Signature''': ./path/{ontology_id}/?source={concept1_id}&target={concept2_id}
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=Tissue

<del> == Get a path between a term and the root == </del>

<del>* '''Signature''': ./path/{ontology_id}/?source={concept1_id}&target=root </del>

<del>* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root </del>

== Get all terms using the specific ontology version id ==

'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.

* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&email=example@example.org
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&email=example@example.org
* '''Arguments:'''
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
** '''pagenum:''' An integer indicating which page of results to return.

== Get all terms using the virtual ontology id ==

'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.

* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&email=example@example.org
* '''Arguments:'''
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
** '''pagenum:''' An integer indicating which page of results to return.

== Changes to the Get all terms service ==

Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.

* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500

* '''Signature'''
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
*** '''pagenum:''' An integer indicating which page of results to return.

* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.

= View Extraction Service =
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details.

= Instance Services =

== Get all direct instances for a given term ==
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&email={email_address}
* '''Optional arguments:'''
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)

* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=1&pagenum=1&email=example@example.org
* '''Description''': returns all direct instances for a given term.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/instances/38801
</accessedResource>
<accessDate>20100408 18:17:21.226 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>5</numPages>
<pageSize>1</pageSize>
<numResultsPage>1</numResultsPage>
<numResultsTotal>5</numResultsTotal>
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean">
<list>
<instanceBean>
<id>unknown_substrate_type</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</fullId>
<label>unknown_substrate_type</label>
<relations>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>

<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_484</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>

<list>
<string>SubstrateType of unknown type.</string>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</contents>
</page>
</data>
</success>
</pre>

== Get an instance and its property/value pairs ==
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&email={email_address}]

* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&email=example@example.org
* '''Description''': returns information about an instance and a list of property/value pairs.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/instance/38801
</accessedResource>
<accessDate>20100408 18:10:48.760 PDT</accessDate>
<data>
<instanceBean>
<id>glass</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</fullId>
<label>glass</label>
<relations>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_742</string>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>
<list>
<string>The array is made on a glass slide.</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</data>
</success>
</pre>

= Hierarchy Services =

The Hierarchy Services only work on the latest version of the ontology (the "virtual ontology").

'''NOTE: To see which ontology versions have been processed for use with the Hierarchy Services, see http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''

== Get parents/children of a given concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?email={email_address}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma?email=example@example.org
* '''Optional arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
** '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?level=1&offset=1&limit=3&email=example@example.org
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.

== Get paths to root/leaves from a concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?email={email_address}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?email=example@example.org
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.

== Get siblings of a given concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&email=example@example.org
* '''Required arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology.

= Bio2RDF Dump Service =

This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.

* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?email=example@example.org

= Annotator Service =

The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others.

The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.

= Resource Index Service =

The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.

= Prototypes =

== RDF Term Service ==
'''Coming in late May, 2010!''' This service allows you to output a snippet of an ontology from BioPortal in the form of an RDF file.
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?email=example@example.org
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_spatial:NEMO_0000024?email=example@example.org
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_spatial:NEMO_0000023?email=example@example.org
* '''Required arguments:'''
** ontology version id
** concept id
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki>
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki>
* '''Sample Output:'''
<pre>
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf#"

...

<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf">
<bioportal:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</bioportal:description>
<bioportal:abbreviation>NEMO</bioportal:abbreviation>
<bioportal:format>OWL</bioportal:format>
<bioportal:date>Wed May 19 09:56:21 PDT 2010</bioportal:date>
<bioportal:uri>http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf</bioportal:uri>
<bioportal:displayLabel>Neural ElectroMagnetic Ontologies</bioportal:displayLabel>
<bioportal:versionNumber>.95</bioportal:versionNumber>
<bioportal:id>42743</bioportal:id>
<bioportal:ontologyId>1321</bioportal:ontologyId>
</owl:Ontology>

...

<owl:Class rdf:about="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000023">
<rdfs:label>right_parietal_scalp_surface_region</rdfs:label>
<rdfs:subClassOf rdf:resource="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000006"/>
<skos:broader>NEMO_spatial:NEMO_0000006</skos:broader>
<skos:notation>NEMO_spatial:NEMO_0000023</skos:notation>
<skos:prefLabel>right_parietal_scalp_surface_region</skos:prefLabel>
</owl:Class>
</rdf:RDF>


</pre>

== RDF Download Service ==
'''Coming in late July, 2010.''' This service allows you to download an entire ontology from BioPortal in the form of an RDF file.
* '''Signature''': ./bioportal/rdf/download/{ontology version id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/download/{ontology id}?email=example@example.org
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/download/1321?email=example@example.org
** http://rest.bioontology.org/bioportal/rdf/download/42743?email=example@example.org
* '''Required arguments:'''
** ontology version id
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}

== Notes Service ==
The prototype notes service has been replaced with a new [[Ontology_Notes|structured notes service]].

== Mapping Service ==
* '''Prototype'''
** '''Signature''': ./mappings/service/{ontology_id}/{concept_id}
** '''Example''': http://bioportal.bioontology.org/mappings/service/1083/
** '''Required arguments:'''
*** ontology_id
** '''Optional arguments:'''
*** concept_id=if concept_id is included, the service will return all mappings to and from the given concept
** '''Description''': returns BioPortal Mappings as XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]
** '''Example Code:''' [http://www.bioontology.org/wiki/index.php/ExtractMappings Extract Mappings]
** '''Sample Output:'''
<pre>
<hash>
<mapping-from type="array">
<mapping-from>
<comment nil="true"></comment>
<map-type>Human</map-type>
<created-at>2008-05-09 08:25:23</created-at>
<updated-at>2008-08-05 17:26:06</updated-at>

<source-name>Carbon</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>CHEBI:27594</destination-id>
<id>98216</id>
<user-id>38139</user-id>
<relationship-type nil="true"></relationship-type>

<destination-ont-name>Chemical entities of biological interest</destination-ont-name>
<destination-name>Carbon</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1007</destination-ont>
<source-id>Carbon</source-id>
<destination-version-id>38377</destination-version-id>

<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-from>
<mapping-from>
<comment nil="true"></comment>
<map-type>Human</map-type>
<created-at>2008-05-09 08:27:05</created-at>

<updated-at>2008-08-05 17:26:06</updated-at>
<source-name>Gold</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>CHEBI:29287</destination-id>
<id>98218</id>
<user-id>38139</user-id>

<relationship-type nil="true"></relationship-type>
<destination-ont-name>Chemical entities of biological interest</destination-ont-name>
<destination-name>Gold</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1007</destination-ont>
<source-id>Gold</source-id>
<destination-version-id>38377</destination-version-id>

<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-from>
</mapping-from>
<mapping-to type="array">
<mapping-to>
<comment nil="true"></comment>
<map-type>Human</map-type>

<created-at>2008-05-09 08:35:27</created-at>
<updated-at>2008-08-05 17:26:06</updated-at>
<source-name>Carbohydrate</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>Carbohydrate</destination-id>
<id>98219</id>

<user-id>38139</user-id>
<relationship-type nil="true"></relationship-type>
<destination-ont-name>NanoParticle Ontology (NPO)</destination-ont-name>
<destination-name>Carbohydrate</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1083</destination-ont>
<source-id>Carbohydrate</source-id>

<destination-version-id>29531</destination-version-id>
<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-to>
</mapping-to>
</hash>

</pre>



= XML Schema Definitions for the REST services =

XML Schema for [[#Term_services|concept]] and [[#Hierarchy_Services|hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.

BioPortal REST services

2010-11-03T22:39:07Z

Nigam:

This page documents BioPortal Web Service signatures. The list below contains commonly accessed BioPortal Web services and is not intended to be an exhaustive list. If a feature you are interested in is not in the list below, please contact [mailto:support@bioontology.org BioPortal Support] to request the service or ask for more details on the full list of services.

The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/bioportal/

* '''Note''': All NCBO REST web service calls MUST append 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. Please start adding the user identification URL parameter to all your web service invocations. Later in 2009, we may start challenging REST service calls that do not have this parameter.

* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. If you have any questions, please contact [mailto:support@bioontology.org BioPortal Support].''

= Overview - Using NCBO Technology in Your Project =
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.

= Code Examples =
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.

*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] can be found on pages specific for those tools.

= BioPortal Announce Mailing List =
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.

= Services to access ontologies and ontology versions =

== List all the latest version of ontologies ==

* '''Signature''': ./ontologies?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?email=example@example.org

== Get a specific ontology based on a version id ==
* '''Signature''': ./ontologies/{ontology version id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?email=example@example.org

== Download an ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?email=example@example.org

== Download the latest ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?email=example@example.org

== Get all versions of an ontology from a virtual ontology id ==
* '''Signature''': ./ontologies/versions/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?email=example@example.org

== Get latest version of an ontology id ==
* '''Signature''': ./virtual/ontology/{ontology_id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?email=example@example.org

== List all ontology categories ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./categories?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/categories

== List all ontology groups ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./groups?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/groups

= Services to access ontology views and ontology view versions =

Since all the views on ontologies are ontologies themselves all the services that work on ontologies do
work for ontology views also with the same signature.

For example to get a specific ontology view based on a version id would be possible by using the signature:

'''./ontologies/download/{view version id}?email={email_address}'''

or for getting all view versions of a virtual view can be achieved called using the signature:

'''./ontologies/versions/{view id}?email={email_address}'''

However, there are a couple of services that are special for views:

== List all the latest version of views ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./views?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/views?email=example@example.org

== Get all versions of views from a virtual ontology id ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.
* '''Signature''': ./views/versions/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?email=example@example.org

= Search services =

== Search BioPortal ==
* '''Signature''': ./search/{query}[?{optional args}]&email={email_address}
* '''Alt Signature''': ./search/?query={uri-encoded query}[&{optional args}]&email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/search/Gene?email=example@example.org
* You can use multiple query terms, separated by a space, for example: [http://rest.bioontology.org/bioportal/search/lung%20disease http://rest.bioontology.org/bioportal/search/lung disease?email=example@example.org]
* '''Optional arguments:'''
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)
** isexactmatch=[1/0] – match the entire concept name (default: 0)
** includeproperties=[1/0] – include attributes in the search (default: 0)
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.
* '''Description:'''
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).

In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).

* '''Example''': http://rest.bioontology.org/bioportal/search/software/?ontologyids=1104&isexactmatch=1&email=example@example.org
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8" ?>
<success>
<accessedResource>
/bioportal/search/cutaneous%20mela
</accessedResource>
<accessDate>2009-05-07 16:17:46.182 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>1</numPages>
<pageSize>3</pageSize>
<numResultsPage>3</numResultsPage>
<numResultsTotal>3</numResultsTotal>
<contents
class="org.ncbo.stanford.bean.search.SearchResultListBean">
<searchResultList>
<searchBean>
<ontologyVersionId>39715</ontologyVersionId>
<ontologyId>1136</ontologyId>
<ontologyDisplayLabel>
Experimental Factor Ontology
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>
http://www.ebi.ac.uk/efo/EFO_0000389
</conceptId>
<conceptIdShort>EFO_0000389</conceptIdShort>
<preferredName>
cutaneous melanoma
</preferredName>
<contents>cutaneous melanoma</contents>
</searchBean>
<searchBean>
<ontologyVersionId>39478</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>
NCI Thesaurus
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cutaneous_Melanoma
</conceptId>
<conceptIdShort>
Cutaneous_Melanoma
</conceptIdShort>
<preferredName>
Cutaneous Melanoma
</preferredName>
<contents>Cutaneous Melanoma</contents>
</searchBean>
<searchBean>
<ontologyVersionId>39833</ontologyVersionId>
<ontologyId>1009</ontologyId>
<ontologyDisplayLabel>
Human disease
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>DOID:2418</conceptId>
<conceptIdShort>DOID:2418</conceptIdShort>
<preferredName>
Cutaneous Melanocytic Neoplasm
</preferredName>
<contents>
Cutaneous Melanocytic Neoplasm
</contents>
</searchBean>
</searchResultList>
<ontologyHitList>
<ontologyHitBean>
<ontologyVersionId>39715</ontologyVersionId>
<ontologyId>1136</ontologyId>
<ontologyDisplayLabel>
Experimental Factor Ontology
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
<ontologyHitBean>
<ontologyVersionId>39833</ontologyVersionId>
<ontologyId>1009</ontologyId>
<ontologyDisplayLabel>
Human disease
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
<ontologyHitBean>
<ontologyVersionId>39478</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>
NCI Thesaurus
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
</ontologyHitList>
</contents>
</page>
</data>
</success>
</pre>

= Term services =
(formerly referred to as Concept services)

== Get term ==
* '''Signature''': ./concepts/{ontology version id}/{concept id}?email={email_address}
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI.
* '''Optional arguments:'''
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.
* '''Examples''':
http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource?email=example@example.org 
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&light=0&email=example@example.org 
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&norelations=1&email=example@example.org
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8" ?>
<success>
<accessedResource>/bioportal/concepts/40644/</accessedResource>
<accessDate>2009-12-16 10:06:10.727 PST</accessDate>
<data>
<classBean>
<id>Melanoma</id>
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanoma</fullId>
<label>Melanoma</label>
<type>Class</type>
<synonyms>
<string>Malignant Melanoma</string>
<string>Melanoma</string>
<string>melanoma</string>
</synonyms>
<definitions>
<string>A malignant, usually aggressive tumor composed of atypical,
neoplastic melanocytes.</string>
</definitions>
<relations>
<entry>
<string>UMLS_CUI</string>
<list>
<string>C0025202</string>
</list>
</entry>
<entry>
<string>owl:equivalentClass</string>
<list>
<string>'Common Neoplasm' and 'Melanocytic Neoplasm' and
(Disease_Has_Abnormal_Cell only 'Melanoma Cell')</string>
</list>
</entry>
<entry>
<string>ALT_DEFINITION</string>
<list>
<string>
<def-source>NCI-GLOSS</def-source>
<def-definition>A form of skin cancer that arises in
melanocytes, the cells that produce pigment.</def-definition>
</string>
</list>
</entry>
<entry>
<string>ICD-O-3_Code</string>
<list>
<string>8720/3</string>
</list>
</entry>
<entry>
<string>Semantic_Type</string>
<list>
<string>Neoplastic Process</string>
</list>
</entry>
<entry>
<string>SubClass</string>
<list>
<classBean>
<id>Non-Cutaneous_Melanoma</id>
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Non-Cutaneous_Melanoma</fullId>
<label>Non-Cutaneous Melanoma</label>
<type>Class</type>
<synonyms>
<string>Extracutaneous Melanoma</string>
<string>Non-Cutaneous Melanoma</string>
</synonyms>
<definitions>
<string>Melanoma is a malignant tumor of melanocytes,
cells that are derived from the neural crest.</string>
</definitions>
<relations>
<entry>
<string>code</string>
<list>
<string>C8711</string>
</list>
</entry>
</relations>
</classBean>
</list>
</entry>
</relations>
</classBean>
</data>
</success>
</pre>

== Get all root terms for an ontology version id ==
* '''Signature''': ./concepts/{ontology version id}/root?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?email=example@example.org

== Get a path between two terms ==
* '''Signature''': ./path/{ontology_id}/?source={concept1_id}&target={concept2_id}
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=Tissue

<del>Get a path between a term and the root </del>
<del>* '''Signature''': ./path/{ontology_id}/?source={concept1_id}&target=root </del>
<del>* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root </del>

== Get all terms using the specific ontology version id ==

'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.

* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&email=example@example.org
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&email=example@example.org
* '''Arguments:'''
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
** '''pagenum:''' An integer indicating which page of results to return.

== Get all terms using the virtual ontology id ==

'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.

* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&email=example@example.org
* '''Arguments:'''
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
** '''pagenum:''' An integer indicating which page of results to return.

== Changes to the Get all terms service ==

Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.

* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500

* '''Signature'''
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
*** '''pagenum:''' An integer indicating which page of results to return.

* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.

= View Extraction Service =
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details.

= Instance Services =

== Get all direct instances for a given term ==
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&email={email_address}
* '''Optional arguments:'''
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)

* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=1&pagenum=1&email=example@example.org
* '''Description''': returns all direct instances for a given term.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/instances/38801
</accessedResource>
<accessDate>20100408 18:17:21.226 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>5</numPages>
<pageSize>1</pageSize>
<numResultsPage>1</numResultsPage>
<numResultsTotal>5</numResultsTotal>
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean">
<list>
<instanceBean>
<id>unknown_substrate_type</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</fullId>
<label>unknown_substrate_type</label>
<relations>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>

<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_484</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>

<list>
<string>SubstrateType of unknown type.</string>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</contents>
</page>
</data>
</success>
</pre>

== Get an instance and its property/value pairs ==
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&email={email_address}]

* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&email=example@example.org
* '''Description''': returns information about an instance and a list of property/value pairs.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/instance/38801
</accessedResource>
<accessDate>20100408 18:10:48.760 PDT</accessDate>
<data>
<instanceBean>
<id>glass</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</fullId>
<label>glass</label>
<relations>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_742</string>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>
<list>
<string>The array is made on a glass slide.</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</data>
</success>
</pre>

= Hierarchy Services =

The Hierarchy Services only work on the latest version of the ontology (the "virtual ontology").

'''NOTE: To see which ontology versions have been processed for use with the Hierarchy Services, see http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''

== Get parents/children of a given concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?email={email_address}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma?email=example@example.org
* '''Optional arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
** '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?level=1&offset=1&limit=3&email=example@example.org
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.

== Get paths to root/leaves from a concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?email={email_address}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?email=example@example.org
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.

== Get siblings of a given concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&email=example@example.org
* '''Required arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology.

= Bio2RDF Dump Service =

This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.

* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?email=example@example.org

= Annotator Service =

The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others.

The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.

= Resource Index Service =

The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.

= Prototypes =

== RDF Term Service ==
'''Coming in late May, 2010!''' This service allows you to output a snippet of an ontology from BioPortal in the form of an RDF file.
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?email=example@example.org
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_spatial:NEMO_0000024?email=example@example.org
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_spatial:NEMO_0000023?email=example@example.org
* '''Required arguments:'''
** ontology version id
** concept id
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki>
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki>
* '''Sample Output:'''
<pre>
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf#"

...

<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf">
<bioportal:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</bioportal:description>
<bioportal:abbreviation>NEMO</bioportal:abbreviation>
<bioportal:format>OWL</bioportal:format>
<bioportal:date>Wed May 19 09:56:21 PDT 2010</bioportal:date>
<bioportal:uri>http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf</bioportal:uri>
<bioportal:displayLabel>Neural ElectroMagnetic Ontologies</bioportal:displayLabel>
<bioportal:versionNumber>.95</bioportal:versionNumber>
<bioportal:id>42743</bioportal:id>
<bioportal:ontologyId>1321</bioportal:ontologyId>
</owl:Ontology>

...

<owl:Class rdf:about="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000023">
<rdfs:label>right_parietal_scalp_surface_region</rdfs:label>
<rdfs:subClassOf rdf:resource="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000006"/>
<skos:broader>NEMO_spatial:NEMO_0000006</skos:broader>
<skos:notation>NEMO_spatial:NEMO_0000023</skos:notation>
<skos:prefLabel>right_parietal_scalp_surface_region</skos:prefLabel>
</owl:Class>
</rdf:RDF>


</pre>

== RDF Download Service ==
'''Coming in late July, 2010.''' This service allows you to download an entire ontology from BioPortal in the form of an RDF file.
* '''Signature''': ./bioportal/rdf/download/{ontology version id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/download/{ontology id}?email=example@example.org
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/download/1321?email=example@example.org
** http://rest.bioontology.org/bioportal/rdf/download/42743?email=example@example.org
* '''Required arguments:'''
** ontology version id
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}

== Notes Service ==
The prototype notes service has been replaced with a new [[Ontology_Notes|structured notes service]].

== Mapping Service ==
* '''Prototype'''
** '''Signature''': ./mappings/service/{ontology_id}/{concept_id}
** '''Example''': http://bioportal.bioontology.org/mappings/service/1083/
** '''Required arguments:'''
*** ontology_id
** '''Optional arguments:'''
*** concept_id=if concept_id is included, the service will return all mappings to and from the given concept
** '''Description''': returns BioPortal Mappings as XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]
** '''Example Code:''' [http://www.bioontology.org/wiki/index.php/ExtractMappings Extract Mappings]
** '''Sample Output:'''
<pre>
<hash>
<mapping-from type="array">
<mapping-from>
<comment nil="true"></comment>
<map-type>Human</map-type>
<created-at>2008-05-09 08:25:23</created-at>
<updated-at>2008-08-05 17:26:06</updated-at>

<source-name>Carbon</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>CHEBI:27594</destination-id>
<id>98216</id>
<user-id>38139</user-id>
<relationship-type nil="true"></relationship-type>

<destination-ont-name>Chemical entities of biological interest</destination-ont-name>
<destination-name>Carbon</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1007</destination-ont>
<source-id>Carbon</source-id>
<destination-version-id>38377</destination-version-id>

<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-from>
<mapping-from>
<comment nil="true"></comment>
<map-type>Human</map-type>
<created-at>2008-05-09 08:27:05</created-at>

<updated-at>2008-08-05 17:26:06</updated-at>
<source-name>Gold</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>CHEBI:29287</destination-id>
<id>98218</id>
<user-id>38139</user-id>

<relationship-type nil="true"></relationship-type>
<destination-ont-name>Chemical entities of biological interest</destination-ont-name>
<destination-name>Gold</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1007</destination-ont>
<source-id>Gold</source-id>
<destination-version-id>38377</destination-version-id>

<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-from>
</mapping-from>
<mapping-to type="array">
<mapping-to>
<comment nil="true"></comment>
<map-type>Human</map-type>

<created-at>2008-05-09 08:35:27</created-at>
<updated-at>2008-08-05 17:26:06</updated-at>
<source-name>Carbohydrate</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>Carbohydrate</destination-id>
<id>98219</id>

<user-id>38139</user-id>
<relationship-type nil="true"></relationship-type>
<destination-ont-name>NanoParticle Ontology (NPO)</destination-ont-name>
<destination-name>Carbohydrate</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1083</destination-ont>
<source-id>Carbohydrate</source-id>

<destination-version-id>29531</destination-version-id>
<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-to>
</mapping-to>
</hash>

</pre>



= XML Schema Definitions for the REST services =

XML Schema for [[#Term_services|concept]] and [[#Hierarchy_Services|hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.

Main Page

2010-10-01T19:11:17Z

Nigam:

Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, dissemination events conducted by the NCBO and publically shared materials from the NCBO.
Please visit our [http://www.bioontology.org Main Site] for more information and materials.

{| class="wikitable"
|-
! style="background:#efefef;" | NCBO Links
! style="background:#efefef;" | Shared Materials
! style="background:#efefef;" | NCBC Links
|-
| [http://www.bioontology.org/ Home page]
| [[Public Requirements Redirect|Public Requirements]]
| [http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]
|-
| [http://www.bioontology.org/wiki/index.php/NCBO_FAQ FAQ]
| [[Shared Materials]]
| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]
|-
| [http://www.bioontology.org/wiki/index.php/News_Events_Publications News, Events and Publications]
| [[Evaluation Activities]]
| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]
|}

=== Ontology Development Area ===

Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki

*[[BRO:Main_Page]] - Biomedical Resource Ontology
*[[PATO:Main_Page]] - An ontology of phenotypic qualities
*[[RO:Main_Page]] - OBO Relations ontology
*[[CARO:Main_Page]] - Reference anatomical ontology
*[[CL:Main_Page]] - OBO Cell ontology
*[[SO:Main_Page]] - Sequence Ontology
*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders
*[[OCI:Main_Page]] - Ontology of Clinical Investigation
*[[NPO:Main_Page]] - NanoParticle Ontology

Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.

=== Software ===

*[http://bioportal.bioontology.org Bioportal:Main_Page] - Main page for accessing Bioportal
*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.

=== How to's ===

* [[NCBO REST services]] - Documentation on how to use BioPortal functionality as Web services
* [[BioPortal UI URLs]] - Documentation on how to link back to BioPortal UI pages
* [http://www.bioontology.org/wiki/index.php/SampleCodeCookbook Code samples] - Sample code for common tasks with BioPortal Web services
* [[Annotator Web service]] - Documentation & information about the NCBO Annotator
* [[Resource Index]] - Documentation & information about the annotation-based NCBO biomedical Resources Index
* ''Retired'' -> See [[BioPortal REST services]] for access to UMLS content. [[UMLS_REST_Services]] - Documentation on how to use our ''prototype'' UMLS services (NetKernel)

=== Research projects and Prototypes ===

*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores
*[[Path to Root]] - Project for consuming the path to root and other OBS rest services
*[[Annotation Summarizer]] - Project utilizing OBS REST services to derive information from datasets referencing ontologies in BioPortal
*[[PURL Server]] - Instructions on how to set-up a PURL server and create Master-Slave architecture for redudancy
*[[Lexicon Builder]] - Project for creating a service that allows building of custom lexicons from bioportal ontologies.
*[[Medline Analysis]] - Project for applying natural language processing methods on Medline to analyze the frequency and syntactic type distribution of ontology terms.
*[[MetaMap Installation]] - Project to install a custom MetaMap using the NCBO data in order to integrate it in the [[Annotator Web service]] workflow.
* [[Ontology Recommender Web service]] - Documentation & information about the NCBO Ontology Recommender

BioPortaul UI URLs

2010-09-29T22:22:07Z

Nigam: BioPortaul UI URLs moved to BioPortal UI URLs: Title was misspelt as BioPortaul

#REDIRECT [[BioPortal UI URLs]]