Difference between revisions of "BioPortal REST services"

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This page documents the signatures for NCBO (and, more specifically, BioPortal) REST services. This list may not be exhaustive.
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NCBO BioPortal v4.0 REST services are documented at: http://data.bioontology.org/documentation
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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:bioontology-support@lists.stanford.edu BioPortal Support].''
 
−
 
 
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The '''prefix''' for all service URLs in the table below is http://rest.bioontology.org/bioportal/
 
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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
 
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* '''Example''': http://rest.bioontology.org/bioportal/ontologies
 
−
 
 
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==  Get a specific ontology based on a version id ==
 
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* '''Signature''':  ./ontologies/{ontology version id}
 
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* '''Example''':  http://rest.bioontology.org/bioportal/ontologies/39002
 
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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}
 
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* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002
 
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==  Get all versions of an ontology form a virtual ontology id ==
 
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* '''Signature''': ./ontologies/versions/{ontology id}
 
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* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104
 
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==  Get latest version of an ontology id ==
 
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* '''Signature''':  ./virtual/{ontology_id}
 
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* '''Example''': http://rest.bioontology.org/bioportal/virtual/1104
 
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==  List all ontology categories id ==
 
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* '''Signature''':  ./categories
 
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* '''Example''': http://rest.bioontology.org/bioportal/categories
 
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= Concept services =
 
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==  Get concept id ==
 
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* '''Signature''': ./concepts/{ontology version id}/{concept id}
 
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* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource
 
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==  Get all root concepts for an ontology id ==
 
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* '''Signature''': ./concepts/{ontology version id}/root
 
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* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root
 
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==  Get concept for latest ontology version id ==
 
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* '''Signature''': ./virtual/{ontology id}/{concept id}
 
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* '''Example''': http://rest.bioontology.org/bioportal/virtual/1104/BRO:Resource
 
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= Search services =
 
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==  Search BioPortal ==
 
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* '''Signature''': ./search/{query}[?{optional args}]
 
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* '''Example''': http://rest.bioontology.org/bioportal/search/Gene
 
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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]
 
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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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** '''Example''': http://rest.bioontology.org/bioportal/search/software/?ontologyids=1104&isexactmatch=1
 
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=  Hierarchy Services =
 
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==  Get parents of a given concept in a specific ontology version ==
 
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* '''Signature''': ./concepts/parents/{ontlogyVersionId}/{conceptId}[?{optional args}]
 
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* '''Example''': http://rest.bioontology.org/bioportal/concepts/parents/13578/Melanoma
 
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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
 
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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/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 of a given concept in the latest version of a given ontology ==
 
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* '''Signature''': ./virtual/parents/{ontlogyId}/{conceptId}[?{optional args}]
 
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* '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma
 
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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/virtual/parents/1032/Melanoma?level=1&offset=1&limit=10
 
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* '''Sample Output:'''
 
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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/concepts/parents/13578/Melanoma
 
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</accessedResource>
 
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<accessDate>2009-04-21 10:28:43.964 PDT</accessDate>
 
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<data>
 
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<list>
 
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<classBean>
 
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<ontologyVersionId>13578</ontologyVersionId>
 
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<id>Common_Neoplasm</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>13578</ontologyVersionId>
 
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<id>Diseases_and_Disorders</id>
 
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<relations>
 
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<entry>
 
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<string>Level</string>
 
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<int>4</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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==  Get children of a given concept in a specific ontology version ==
 
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* '''Signature''': ./concepts/children/{ontlogyVersionId}/{conceptId}[?{optional args}]
 
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* '''Example''': http://rest.bioontology.org/bioportal/concepts/children/13578/Melanoma
 
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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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* '''Sample Output:'''
 
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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/concepts/children/13578/Melanoma
 
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</accessedResource>
 
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<accessDate>2009-04-21 11:02:03.238 PDT</accessDate>
 
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<data>
 
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<list>
 
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<classBean>
 
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<ontologyVersionId>13578</ontologyVersionId>
 
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<id>Non-Cutaneous_Melanoma</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>13578</ontologyVersionId>
 
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<id>Recurrent_Melanoma</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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==  Get children of a given concept in the latest version of a given ontology ==
 
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* '''Signature''': ./virtual/children/{ontlogyId}/{conceptId}[?{optional args}]
 
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* '''Example''': http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma
 
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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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* '''Sample Output:'''
 
−
 
 
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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/virtual/children/MSH/C0025202
 
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</accessedResource>
 
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<accessDate>2009-04-21 11:04:26.733 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>C0149722</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>C0206735</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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==  Get paths to root from a concept in a specific ontology version ==
 
−
* '''Signature''': ./concepts/rootpath/{ontologyVersionId}/{conceptId}[?{optional args}]
 
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* '''Example''': http://rest.bioontology.org/bioportal/concepts/rootpath/13578/Melanoma
 
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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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* '''Sample Output:'''
 
−
 
 
−
<?xml version="1.0" encoding="UTF-8" ?>
 
−
<success>
 
−
<accessedResource>
 
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/bioportal/concepts/rootpath/13578/Melanoma
 
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</accessedResource>
 
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<accessDate>2009-04-21 11:06:23.439 PDT</accessDate>
 
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<data>
 
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<list>
 
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<classBean>
 
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<ontologyVersionId>13578</ontologyVersionId>
 
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<id>Melanoma</id>
 
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<relations>
 
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<entry>
 
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<string>Path</string>
 
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<string>
 
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Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Morphology.Melanocytic_Neoplasm
 
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</string>
 
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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>13578</ontologyVersionId>
 
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<id>Melanoma</id>
 
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<relations>
 
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<entry>
 
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<string>Path</string>
 
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<string>
 
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Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Special_Category.Common_Neoplasm
 
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</string>
 
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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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==  Get paths to root from a concept in the latest version of a given ontology  ==
 
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* '''Signature''': ./virtual/rootpath/{ontologyId}/{conceptId}[?{optional args}]
 
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* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma
 
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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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* '''Sample Output:'''
 
−
 
 
−
<?xml version="1.0" encoding="UTF-8" ?>
 
−
<success>
 
−
<accessedResource>
 
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/bioportal/virtual/rootpath/MSH/C0025202
 
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</accessedResource>
 
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<accessDate>2009-04-21 11:08:05.811 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>C0025202</id>
 
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<relations>
 
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<entry>
 
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<string>Path</string>
 
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<string>
 
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C1256739.C1256741.C0012674.C0027651.C0027652.C0206769
 
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</string>
 
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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>C0025202</id>
 
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<relations>
 
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<entry>
 
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<string>Path</string>
 
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<string>
 
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C1256739.C1256741.C0012674.C0027651.C0027652.C0027658.C0206093.C0206754
 
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</string>
 
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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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==  Get paths to leaves from a concept in a specific ontology version ==
 
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* '''Signature''': ./concepts/leafpath/{ontologyVersionId}/{conceptId}[?{optional args}]
 
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* '''Example''': http://rest.bioontology.org/bioportal/concepts/leafpath/13578/Melanoma
 
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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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* '''Sample Output:'''
 
−
 
 
−
<?xml version="1.0" encoding="UTF-8" ?>
 
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<success>
 
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<accessedResource>
 
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/bioportal/concepts/leafpath/13578/Melanoma
 
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</accessedResource>
 
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<accessDate>2009-04-21 11:10:04.386 PDT</accessDate>
 
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<data>
 
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<list>
 
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<classBean>
 
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<ontologyVersionId>13578</ontologyVersionId>
 
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<id>Melanoma</id>
 
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<relations>
 
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<entry>
 
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<string>Path</string>
 
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<string>
 
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Regressing_Non-Cutaneous_Melanoma.Regressing_Melanoma
 
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</string>
 
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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>13578</ontologyVersionId>
 
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<id>Melanoma</id>
 
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<relations>
 
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<entry>
 
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<string>Path</string>
 
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<string>
 
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Regressing_Melanoma_of_the_Skin.Regressing_Melanoma
 
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</string>
 
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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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==  Get paths to leaves from a concept in the latest version of a given ontology  ==
 
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* '''Signature''': ./virtual/leafpath/{ontologyId}/{conceptId}[?{optional args}]
 
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* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma
 
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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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* '''Sample Output:'''
 
−
 
 
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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/virtual/leafpath/MSH/C0025202
 
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</accessedResource>
 
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<accessDate>2009-04-21 11:11:56.348 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>C0025202</id>
 
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<relations>
 
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<entry>
 
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<string>Path</string>
 
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<string>C0025205</string>
 
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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>C0025202</id>
 
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<relations>
 
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<entry>
 
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<string>Path</string>
 
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<string>C0206735</string>
 
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</entry>
 
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</relations>
 
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</classBean>
 
−
</list>
 
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</data>
 
−
</success>
 
−
 
 
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==  Get siblings of a given concept in a specific ontology version ==
 
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* '''Signature''': ./concepts/siblings/{ontlogyVersionId}/{conceptId}?level=<level>[&{optional args}]
 
−
* '''Example''': http://rest.bioontology.org/bioportal/concepts/siblings/13578/Melanoma?level=1
 
−
* '''Required arguments:'''
 
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** level=<integer> - limits results to a given level in the hierarchy
 
−
* '''Optional arguments:'''
 
−
** offset=<integer> – results offset (used for pagination)
 
−
* '''Sample Output:'''
 
−
 
 
−
<?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>
 
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<id>Common_Germ_Cell_Neoplasm</id>
 
−
<relations>
 
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<entry>
 
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<string>Level</string>
 
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<int>1</int>
 
−
</entry>
 
−
</relations>
 
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</classBean>
 
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<classBean>
 
−
<ontologyVersionId>13578</ontologyVersionId>
 
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<id>Common_Hematopoietic_Neoplasm</id>
 
−
<relations>
 
−
<entry>
 
−
<string>Level</string>
 
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<int>1</int>
 
−
</entry>
 
−
</relations>
 
−
</classBean>
 
−
</list>
 
−
</data>
 
−
</success>
 
−
 
−
==  Get siblings of a given concept in the latest version of a given ontology ==
 
−
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>[&{optional args}]
 
−
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1
 
−
* '''Required arguments:'''
 
−
** level=<integer> - limits results to a given level in the hierarchy
 
−
* '''Optional arguments:'''
 
−
** offset=<integer> – results offset (used for pagination)
 
−
* '''Sample Output:'''
 
−
 
 
−
<?xml version="1.0" encoding="UTF-8" ?>
 
−
<success>
 
−
<accessedResource>
 
−
/bioportal/virtual/siblings/MSH/C0206093
 
−
</accessedResource>
 
−
<accessDate>2009-04-21 11:30:12.183 PDT</accessDate>
 
−
<data>
 
−
<list>
 
−
<classBean>
 
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<ontologyVersionId>MSH</ontologyVersionId>
 
−
<id>C0206720</id>
 
−
<relations>
 
−
<entry>
 
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<string>Level</string>
 
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<int>2</int>
 
−
</entry>
 
−
</relations>
 
−
</classBean>
 
−
<classBean>
 
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<ontologyVersionId>MSH</ontologyVersionId>
 
−
<id>C0206727</id>
 
−
<relations>
 
−
<entry>
 
−
<string>Level</string>
 
−
<int>2</int>
 
−
</entry>
 
−
</relations>
 
−
</classBean>
 
−
</list>
 
−
</data>
 
−
</success>
 

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"