Difference between revisions of "BioPortal REST services"

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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.
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NCBO BioPortal v4.0 REST services are documented at: http://data.bioontology.org/documentation
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The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/bioportal/
 
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* '''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. 
 
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* '''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].''
 
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= Overview - Using NCBO Technology in Your Project =
 
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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.
 
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= Code Examples =
 
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*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.
 
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*Code examples for the Annotator and Resources can be found on pages specific for those tools.
 
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= BioPortal Announce Mailing List =
 
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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.
 
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= Services to access ontologies and ontology versions =
 
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== List all the latest version of ontologies ==
 
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* '''Signature''': ./ontologies?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/ontologies?email=example@example.org
 
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==  Get a specific ontology based on a version id ==
 
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* '''Signature''':  ./ontologies/{ontology version id}?email={email_address}
 
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* '''Example''':  http://rest.bioontology.org/bioportal/ontologies/39002?email=example@example.org
 
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==  Download an ontology file ==
 
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* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.
 
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* '''Signature''':  ./ontologies/download/{ontology version id}?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?email=example@example.org
 
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==  Download the latest ontology file ==
 
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* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.
 
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* '''Signature''':  ./virtual/download/{ontology id}?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?email=example@example.org
 
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==  Get all versions of an ontology from a virtual ontology id ==
 
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* '''Signature''': ./ontologies/versions/{ontology id}?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?email=example@example.org
 
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==  Get latest version of an ontology id ==
 
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'''NOTE''': ''This signature will change in BioPortal release 2.2''
 
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* '''Signature''': ./virtual/ontology/{ontology_id}?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?email=example@example.org
 
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−
 
 
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* '''Signature''': ./virtual/{ontology_id}?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/virtual/1104?email=example@example.org
 
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==  List all ontology categories ==
 
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'''NOTE''': ''To be released in BioPortal version 2.2''
 
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* '''Signature''':  ./categories?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/categories
 
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==  List all ontology groups ==
 
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'''NOTE''': ''To be released in BioPortal version 2.2''
 
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* '''Signature''':  ./groups?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/groups
 
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= Services to access ontology views and ontology view versions =
 
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Since all the views on ontologies are ontologies themselves all the services that work on ontologies do
 
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work for ontology views also with the same signature.
 
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For example to get a specific ontology view based on a version id would be possible by using the signature:
 
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'''./ontologies/download/{view version id}?email={email_address}'''
 
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or for getting all view versions of a virtual view can be achieved called using the signature:
 
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'''./ontologies/versions/{view id}?email={email_address}'''
 
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However, there are a couple of services that are special for views:
 
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== List all the latest version of views ==
 
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'''NOTE''': ''To be released in BioPortal version 2.2''
 
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* '''Signature''': ./views?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/views?email=example@example.org
 
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== Get all versions of views from a virtual ontology id ==
 
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'''NOTE''': ''To be released in BioPortal version 2.2''
 
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* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.
 
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* '''Signature''': ./views/versions/{ontology id}?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?email=example@example.org
 
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= Search services =
 
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==  Search BioPortal ==
 
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* '''Signature''': ./search/{query}[?{optional args}]&email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/search/Gene?email=example@example.org
 
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* 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]
 
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* '''Optional arguments:'''
 
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** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)
 
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** isexactmatch=[1/0] – match the entire concept name (default: 0)
 
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** includeproperties=[1/0] – include attributes in the search (default: 0)
 
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** pagesize=<pagesize> - the number of results to display in a single request (default: all)
 
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** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)
 
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** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)
 
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** 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.
 
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* '''Description:'''
 
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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).
 
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In phrase searches (multiple words), the wildcard character is appended to the last word. For example, searching for "cutaneous mela" would return all concepts whose name contains the word "cutaneous", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).
 
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* '''Example''': http://rest.bioontology.org/bioportal/search/software/?ontologyids=1104&isexactmatch=1&email=example@example.org
 
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* '''Sample Output''':
 
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<pre>
 
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<?xml version="1.0" encoding="UTF-8" ?>
 
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<success>
 
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<accessedResource>
 
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/bioportal/search/cutaneous%20mela
 
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</accessedResource>
 
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<accessDate>2009-05-07 16:17:46.182 PDT</accessDate>
 
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<data>
 
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<page>
 
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<pageNum>1</pageNum>
 
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<numPages>1</numPages>
 
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<pageSize>3</pageSize>
 
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<numResultsPage>3</numResultsPage>
 
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<numResultsTotal>3</numResultsTotal>
 
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<contents
 
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class="org.ncbo.stanford.bean.search.SearchResultListBean">
 
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<searchResultList>
 
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<searchBean>
 
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<ontologyVersionId>39715</ontologyVersionId>
 
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<ontologyId>1136</ontologyId>
 
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<ontologyDisplayLabel>
 
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Experimental Factor Ontology
 
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</ontologyDisplayLabel>
 
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<recordType>
 
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RECORD_TYPE_PREFERRED_NAME
 
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</recordType>
 
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<conceptId>
 
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http://www.ebi.ac.uk/efo/EFO_0000389
 
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</conceptId>
 
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<conceptIdShort>EFO_0000389</conceptIdShort>
 
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<preferredName>
 
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cutaneous melanoma
 
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</preferredName>
 
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<contents>cutaneous melanoma</contents>
 
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</searchBean>
 
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<searchBean>
 
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<ontologyVersionId>39478</ontologyVersionId>
 
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<ontologyId>1032</ontologyId>
 
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<ontologyDisplayLabel>
 
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NCI Thesaurus
 
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</ontologyDisplayLabel>
 
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<recordType>
 
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RECORD_TYPE_PREFERRED_NAME
 
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</recordType>
 
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<conceptId>
 
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http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cutaneous_Melanoma
 
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</conceptId>
 
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<conceptIdShort>
 
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Cutaneous_Melanoma
 
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</conceptIdShort>
 
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<preferredName>
 
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Cutaneous Melanoma
 
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</preferredName>
 
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<contents>Cutaneous Melanoma</contents>
 
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</searchBean>
 
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<searchBean>
 
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<ontologyVersionId>39833</ontologyVersionId>
 
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<ontologyId>1009</ontologyId>
 
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<ontologyDisplayLabel>
 
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Human disease
 
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</ontologyDisplayLabel>
 
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<recordType>
 
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RECORD_TYPE_PREFERRED_NAME
 
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</recordType>
 
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<conceptId>DOID:2418</conceptId>
 
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<conceptIdShort>DOID:2418</conceptIdShort>
 
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<preferredName>
 
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Cutaneous Melanocytic Neoplasm
 
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</preferredName>
 
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<contents>
 
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Cutaneous Melanocytic Neoplasm
 
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</contents>
 
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</searchBean>
 
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</searchResultList>
 
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<ontologyHitList>
 
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<ontologyHitBean>
 
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<ontologyVersionId>39715</ontologyVersionId>
 
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<ontologyId>1136</ontologyId>
 
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<ontologyDisplayLabel>
 
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Experimental Factor Ontology
 
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</ontologyDisplayLabel>
 
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<numHits>1</numHits>
 
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</ontologyHitBean>
 
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<ontologyHitBean>
 
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<ontologyVersionId>39833</ontologyVersionId>
 
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<ontologyId>1009</ontologyId>
 
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<ontologyDisplayLabel>
 
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Human disease
 
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</ontologyDisplayLabel>
 
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<numHits>1</numHits>
 
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</ontologyHitBean>
 
−
<ontologyHitBean>
 
−
<ontologyVersionId>39478</ontologyVersionId>
 
−
<ontologyId>1032</ontologyId>
 
−
<ontologyDisplayLabel>
 
−
NCI Thesaurus
 
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</ontologyDisplayLabel>
 
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<numHits>1</numHits>
 
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</ontologyHitBean>
 
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</ontologyHitList>
 
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</contents>
 
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</page>
 
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</data>
 
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</success>
 
−
</pre>
 
−
 
 
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= Concept services =
 
−
 
 
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==  Get concept  ==
 
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* '''Signature''': ./concepts/{ontology version id}/{concept id}?email={email_address}
 
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* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}
 
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* '''Optional arguments:'''
 
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** 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
 
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* '''Examples''':
 
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http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource?email=example@example.org<br/>
 
−
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&light=false&email=example@example.org
 
−
 
 
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==  Get all root concepts for an ontology version id ==
 
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* '''Signature''': ./concepts/{ontology version id}/root?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?email=example@example.org
 
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==  Get concept for latest ontology version id ==
 
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'''NOTE''': ''This signature will change in BioPortal release 2.2''
 
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* '''New Signature''': ./virtual/ontology/{ontology id}/{concept id}?email={email_address}
 
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* '''New Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/BRO:Resource?email=example@example.org
 
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−
 
 
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* '''Signature''': ./virtual/{ontology id}/{concept id}?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/virtual/1104/BRO:Resource?email=example@example.org
 
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==  Get all concepts using the specific ontology version id ==
 
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* '''Signature''': ./concepts/{ontology version id}/all?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/concepts/13578/all?email=example@example.org
 
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* '''Optional arguments:'''
 
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** offset=<integer> – results offset (used for pagination)
 
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** limit=<integer> – limits the number of results
 
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** '''Example''': http://rest.bioontology.org/bioportal/concepts/13578/all?offset=1&limit=10&email=example@example.org
 
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*** This call will return 10 concepts, starting from position 1.
 
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==  Get all concepts using the virtual ontology id ==
 
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* '''Signature''': ./virtual/ontology/{ontology id}/all?email={email_address}
 
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* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?email=example@example.org
 
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* '''Optional arguments:'''
 
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** offset=<integer> – results offset (used for pagination)
 
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** limit=<integer> – limits the number of results
 
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** '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?offset=1&limit=10&email=example@example.org
 
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*** This call will return 10 concepts, starting from position 1.
 
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=  Hierarchy Services =
 
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'''NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies'''
 
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==  Get parents/children of a given concept in a specific ontology version ==
 
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* '''Signature''': ./concepts/[parents|children]/{ontlogyVersionId}/{conceptId}[?email={email_address}&{optional args}]
 
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* '''Example''': http://rest.bioontology.org/bioportal/concepts/parents/13578/Melanoma?email=example@example.org
 
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* '''Example''': http://rest.bioontology.org/bioportal/concepts/children/13578/Melanoma?email=example@example.org
 
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* '''Optional arguments:'''
 
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** level=<integer> - limits results to a given level in the hierarchy
 
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** offset=<integer> – results offset (used for pagination)
 
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** limit=<integer> – limits the number of results
 
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** '''Example''': http://rest.bioontology.org/bioportal/concepts/parents/13578/Melanoma?level=1&offset=1&limit=10&email=example@example.org
 
−
* '''Description''': returns all parents of the concept, with the level indicating how far away the parent is from the concept. For instance, direct parents have level 1; their direct parents have level 2, etc. If no level is specified, the service returns all the levels up to the root. If the level is specified, the service returns only the parents at that level.
 
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* '''Note:''' These services accept UMLS Abbreviated source name (SAB) for ontologyVersionId and UMLS Unique identifier for concept (CUI) for conceptId.
 
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* '''Sample Output:'''
 
−
<pre>
 
−
<?xml version="1.0" encoding="UTF-8" ?>
 
−
<success>
 
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<accessedResource>
 
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/bioportal/virtual/parents/MSH/C0025202
 
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</accessedResource>
 
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<accessDate>2009-04-21 10:55:33.494 PDT</accessDate>
 
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<data>
 
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<list>
 
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<classBean>
 
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<ontologyVersionId>MSH</ontologyVersionId>
 
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<id>C0206769</id>
 
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<relations>
 
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<entry>
 
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<string>Level</string>
 
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<int>1</int>
 
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</entry>
 
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</relations>
 
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</classBean>
 
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<classBean>
 
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<ontologyVersionId>MSH</ontologyVersionId>
 
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<id>C0206754</id>
 
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<relations>
 
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<entry>
 
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<string>Level</string>
 
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<int>1</int>
 
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</entry>
 
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</relations>
 
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</classBean>
 
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</list>
 
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</data>
 
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</success>
 
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</pre>
 
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−
==  Get parents/children of a given concept in the latest version of a given ontology ==
 
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* '''Signature''': ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?email={email_address}&{optional args}]
 
−
* '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1009/DOID:1909?email=example@example.org
 
−
* '''Example''': http://rest.bioontology.org/bioportal/virtual/children/1009/DOID:1909?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/1009/DOID:1909?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 roots/leaves from a concept in a specific ontology version ==
 
−
* '''Signature''': ./concepts/[rootpath|leafpath]/{ontologyVersionId}/{conceptId}[?email={email_address}&{optional args}]
 
−
**NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs_hibernate/ontologies
 
−
* '''Example''': http://rest.bioontology.org/bioportal/concepts/rootpath/13578/Melanoma?email=example@example.org
 
−
* '''Example''': http://rest.bioontology.org/bioportal/concepts/leafpath/13578/Melanoma?email=example@example.org
 
−
* '''Optional arguments:'''
 
−
** offset=<integer> – results offset (used for pagination)
 
−
** limit=<integer> – limits the number of results
 
−
* '''Description''': return a set of path to the roots (resp. leaves) for a given concept in a specific ontology version. Paths are represented as a list of conceptIds, separated by periods (.) The first one in the list is a root (resp. leaf) in the hierarchy; the last one in the list is the direct parent (resp. direct child) of the concept.
 
−
* '''Note:''' These services accepts UMLS Abbreviated source name (SAB) for ontlogyVersionId and UMLS Unique identifier for concept (CUI) fro conceptId.
 
−
* '''Sample Output:'''
 
−
<pre>
 
−
<?xml version="1.0" encoding="UTF-8" ?>
 
−
<success>
 
−
<accessedResource>
 
−
/bioportal/concepts/rootpath/13578/Melanoma
 
−
</accessedResource>
 
−
<accessDate>2009-04-21 11:06:23.439 PDT</accessDate>
 
−
<data>
 
−
<list>
 
−
<classBean>
 
−
<ontologyVersionId>13578</ontologyVersionId>
 
−
<id>Melanoma</id>
 
−
<relations>
 
−
<entry>
 
−
<string>Path</string>
 
−
<string>
 
−
Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Morphology.Melanocytic_Neoplasm
 
−
</string>
 
−
</entry>
 
−
</relations>
 
−
</classBean>
 
−
<classBean>
 
−
<ontologyVersionId>13578</ontologyVersionId>
 
−
<id>Melanoma</id>
 
−
<relations>
 
−
<entry>
 
−
<string>Path</string>
 
−
<string>
 
−
Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Special_Category.Common_Neoplasm
 
−
</string>
 
−
</entry>
 
−
</relations>
 
−
</classBean>
 
−
</list>
 
−
</data>
 
−
</success>
 
−
</pre>
 
−
 
 
−
==  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/1009/DOID:1909?email=example@example.org
 
−
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1009/DOID:1909?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 a specific ontology version ==
 
−
* '''Signature''': ./concepts/siblings/{ontlogyVersionId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]
 
−
**NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs_hibernate/ontologies
 
−
* '''Example''': http://rest.bioontology.org/bioportal/concepts/siblings/13578/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''': returns the set of sibling concepts at the given level (i.e., siblings that have the same direct (level=1), grand-parents (level=2), etc.) for a given concept.
 
−
* '''Note:''' These services accepts UMLS Abbreviated source name (SAB) for ontlogyVersionId and UMLS Unique identifier for concept (CUI) fro conceptId.
 
−
* '''Sample Output:'''
 
−
<pre>
 
−
<?xml version="1.0" encoding="UTF-8" ?>
 
−
<success>
 
−
<accessedResource>
 
−
/bioportal/concepts/siblings/13578/Melanoma
 
−
</accessedResource>
 
−
<accessDate>2009-04-21 11:15:13.427 PDT</accessDate>
 
−
<data>
 
−
<list>
 
−
<classBean>
 
−
<ontologyVersionId>13578</ontologyVersionId>
 
−
<id>Common_Germ_Cell_Neoplasm</id>
 
−
<relations>
 
−
<entry>
 
−
<string>Level</string>
 
−
<int>1</int>
 
−
</entry>
 
−
</relations>
 
−
</classBean>
 
−
<classBean>
 
−
<ontologyVersionId>13578</ontologyVersionId>
 
−
<id>Common_Hematopoietic_Neoplasm</id>
 
−
<relations>
 
−
<entry>
 
−
<string>Level</string>
 
−
<int>1</int>
 
−
</entry>
 
−
</relations>
 
−
</classBean>
 
−
</list>
 
−
</data>
 
−
</success>
 
−
</pre>
 
−
 
 
−
==  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/1009/DOID:1909?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.
 
−
 
 
−
= 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 =
 
−
 
 
−
== Notes Service ==
 
−
* '''Signature''': ./notes/ont/{ontology_id}
 
−
* '''Example''': http://bioportal.bioontology.org/notes/ont/1104
 
−
* '''Required arguments:'''
 
−
** ontology_id
 
−
* '''Description''': returns BioPortal Notes as XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]
 
−
* '''Sample Output:'''
 
−
<pre>
 
−
<records type="array">
 
−
  <record>
 
−
    <comment>
 
−
    I note that clinical data is specifically defined not to include clinical trial data. So is anyone already thinking about where at a high level subtrees might be added to deal with clinical trial data and clinical trial management systems? Or is it premature to do that? This is for the CTSAs.
 
−
    </comment>
 
−
    <created-at>2008-08-07 11:21:00</created-at>
 
−
    <ontology-id>1104</ontology-id>
 
−
    <updated-at>2008-08-07 11:21:00</updated-at>
 
−
    <mapping-id nil="true"/>
 
−
    <subject>Including clinical trial data as clinical data</subject>
 
−
    <id>75</id>
 
−
    <user-id>38143</user-id>
 
−
    <parent-id nil="true"/>
 
−
    <ontology-version-id>38407</ontology-version-id>
 
−
    <concept-id>BRO:Clinical_Data</concept-id>
 
−
    <note-type>Question</note-type>
 
−
  </record>
 
−
  <record>
 
−
    <comment> Not sure I follow the argument here.&nbsp; Clinical trial data is covered under PHI so no distinction there.&nbsp; Data generated in the course of delivering routine standard of care may be needed in the course of a clinical trial.&nbsp; Does this make clinical trial data an overlapping superset of clinical data?
 
−
    </comment>
 
−
    <created-at>2008-08-07 11:24:04</created-at>
 
−
    <ontology-id>1104</ontology-id>
 
−
    <updated-at>2008-08-07 11:24:04</updated-at>
 
−
    <mapping-id nil="true"/>
 
−
    <subject>RE:Including clinical trial data as clinical data</subject>
 
−
    <id>76</id>
 
−
    <user-id>38144</user-id>
 
−
    <parent-id>75</parent-id>
 
−
    <ontology-version-id>38407</ontology-version-id>
 
−
    <concept-id>BRO:Clinical_Data</concept-id>
 
−
    <note-type>Comment</note-type>
 
−
  </record>
 
−
</records>
 
−
</pre>
 
−
 
 
−
== Mapping Service ==
 
−
* '''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]
 
−
* '''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>
 
−
 
 
−
 
 
−
<!--
 
−
= Usage Logging =
 
−
* '''Signature''': ./usage?{args}
 
−
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org
 
−
* '''Required arguments:'''
 
−
** none specifically, but at least one optional argument is required
 
−
* '''Optional arguments:'''
 
−
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are:
 
−
<pre>
 
−
  /categories
 
−
  /concepts/{ontology version id}/{concept id}
 
−
  /concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}
 
−
  /diffs/{virtual id}
 
−
  /ontologies/{ontology version id}
 
−
  /ontologies/download/{ontology version id}
 
−
  /ontologies/versions/{ontology virtual id}
 
−
  /path/{ontology version id}/{concept id}
 
−
  /search/{search terms}
 
−
  /virtual/{virtual id}
 
−
  /virtual/ontology/{virtual id}/{concept id}
 
−
  /virtual/rootpath/{virtual id}/{concept id}
 
−
  /virtual/siblings/{virtual id}/{concept id}
 
−
</pre>
 
−
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".
 
−
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)
 
−
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)
 
−
* '''Description''': returns BioPortal REST services usage data as XML.
 
−
* '''Sample Output:'''
 
−
<pre>
 
−
<?xml version="1.0" encoding="UTF-8" ?>
 
−
<success>
 
−
<accessedResource>/bioportal/usage</accessedResource>
 
−
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate>
 
−
<data>
 
−
<list>
 
−
<usageLoggingBean>
 
−
<requestUrl>
 
−
/search/Certain infectious and parasitic diseases/
 
−
</requestUrl>
 
−
<httpMethod>GET</httpMethod>
 
−
<resourceParameters>
 
−
query=Certain%20infectious%20and%20parasitic%20diseases
 
−
</resourceParameters>
 
−
<requestParameters>
 
−
pagenum=1&ontologyids=1265&pagesize=20
 
−
</requestParameters>
 
−
<hitCount>1</hitCount>
 
−
<dateAccessed class="sql-timestamp">
 
−
2009-07-27 00:00:00.0
 
−
</dateAccessed>
 
−
</usageLoggingBean>
 
−
<usageLoggingBean>
 
−
<requestUrl>/search/Hypertension/</requestUrl>
 
−
<httpMethod>GET</httpMethod>
 
−
<resourceParameters>
 
−
query=Hypertension
 
−
</resourceParameters>
 
−
<requestParameters>
 
−
pagenum=1&ontologyids=1265&pagesize=20
 
−
</requestParameters>
 
−
<hitCount>2</hitCount>
 
−
<dateAccessed class="sql-timestamp">
 
−
2009-07-27 00:00:00.0
 
−
</dateAccessed>
 
−
</usageLoggingBean>
 
−
<usageLoggingBean>
 
−
<requestUrl>/search/Melanoma/</requestUrl>
 
−
<httpMethod>GET</httpMethod>
 
−
<resourceParameters>query=Melanoma</resourceParameters>
 
−
<requestParameters>
 
−
pagenum=1&ontologyids=1265&pagesize=20
 
−
</requestParameters>
 
−
<hitCount>3</hitCount>
 
−
<dateAccessed class="sql-timestamp">
 
−
2009-07-27 00:00:00.0
 
−
</dateAccessed>
 
−
</usageLoggingBean>
 
−
</list>
 
−
</data>
 
−
</success>
 
−
</pre>
 
−
-->
 

Latest revision as of 22:00, 16 July 2016

NCBO BioPortal v4.0 REST services are documented at: http://data.bioontology.org/documentation

Retrieved from "https://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&oldid=12848"