Difference between revisions of "BioPortal REST services"
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* '''Signature''': ./ontologies?email={email_address} | * '''Signature''': ./ontologies?email={email_address} | ||
| − | * '''Example''': http:// | + | * '''Example''': http://stagerest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey |
== Get a specific ontology based on a version id == | == Get a specific ontology based on a version id == | ||
Revision as of 20:35, 24 April 2011
The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact Support.
The prefix for all production service URLs in the table below is http://rest.bioontology.org/
- Note: All NCBO REST Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email 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.
Overview - Using NCBO Technology in Your Project
See 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 Test User Interface that has been set-up using the FlexViz code.
- Examples of using the Web services in sample code can be found here
- Sample code is located within the NCBO Gforge repository and can be checked out via anonymous SVN access
- Code examples for the Annotator and Resource Index is located on the pages documenting these Web services
BioPortal Announce Mailing List
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the bioportal-annouce list.
Services to access ontologies and ontology versions
List all the latest version of ontologies
- Signature: ./ontologies?email={email_address}
- Example: http://stagerest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey
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 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.
- objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.
- 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:
<?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>
Term services
(formerly referred to as Concept services)
Get term, including its properties, subclasses, and superclasses
- Signature: ./concepts/{ontology version id}/{concept id}?email={email_address}
- Alt Signature: ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}
- Virtual Signature (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}
- Alt Virtual Signature (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}
- 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/44103?conceptid=O80-O84.9&email=example@example.org
- Sample Output:
<?xml version="1.0" encoding="UTF-8"?>
<success>
<accessedResource>/bioportal/concepts/44103</accessedResource>
<accessDate>2010-12-08 16:57:43.763 PST</accessDate>
<data>
<classBean>
<id>O80-O84.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId>
<label>Delivery</label>
<type>Class</type>
<relations>
<entry>
<string>SubClass</string>
<list>
<classBean>
<id>O84</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId>
<label>Multiple delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>5</int>
</entry>
</relations>
</classBean>
<classBean>
<id>O83</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId>
<label>Other assisted single delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>7</int>
</entry>
</relations>
</classBean>
<classBean>
<id>O82</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId>
<label>Single delivery by caesarean section</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>5</int>
</entry>
</relations>
</classBean>
<classBean>
<id>O81</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId>
<label>Single delivery by forceps and vacuum extractor</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>6</int>
</entry>
</relations>
</classBean>
<classBean>
<id>O80</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId>
<label>Single spontaneous delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>4</int>
</entry>
</relations>
</classBean>
</list>
</entry>
<entry>
<string>PAR</string>
<list>
<classBean>
<id>O00-O99.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId>
<label>Pregnancy, childbirth and the puerperium</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>8</int>
</entry>
</relations>
</classBean>
</list>
</entry>
<entry>
<string>ChildCount</string>
<int>5</int>
</entry>
<entry>
<string>Semantic_Type</string>
<list>
<string>Therapeutic or Preventive Procedure</string>
</list>
</entry>
<entry>
<string>TUI</string>
<list>
<string>T061</string>
</list>
</entry>
<entry>
<string>UMLS_CUI</string>
<list>
<string>C0011209</string>
</list>
</entry>
<entry>
<string>SuperClass</string>
<list>
<classBean>
<id>O00-O99.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId>
<label>Pregnancy, childbirth and the puerperium</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>8</int>
</entry>
</relations>
</classBean>
</list>
</entry>
</relations>
</classBean>
</data>
</success>
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
Get a path between a term and the root
- Signature: ./path/{ontology_id}/?source={concept1_id}&target=root
- Example: http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root
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:
- 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:
- 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.
- New parameters: Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:
- 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 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=10&pagenum=1&email=example@example.org
- Description: returns all direct instances for a given term.
- Sample Output:
<?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>
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:
<?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>
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 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
- delim=<string> – use a custom delimiter between returned terms. Default is a period (.).
- 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 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 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.
RDF Term Service
- 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:
- 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 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/{ACRONYM}/{ID}
- OBO: http://purl.obolibrary.org/{IDSPACE}_{LOCALID}
- The RDF dump will use URIs that are based on which format the ontology is in:
- Sample Output:
<?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>
<!-- Generated by the OWL API (version 3.0.0.1447) http://owlapi.sourceforge.net -->
RDF Download Service
- Signature: ./bioportal/ontologies/rdf/download/{ontology version id}?email=example@example.org
- Alt Signature: ./bioportal/virtual/ontology/rdf/download/{ontology id}?email=example@example.org
- Examples:
NOTE: If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files.
- Required arguments:
- ontology version id
- Description: returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to 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}
- The RDF dump will use URIs that are based on which format the ontology is in:
Notes Service
See structured notes service for more details on the Notes web service.
Mapping Service
- Production Mapping Web Service
- The production Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. Example Web service signatures are included for testing code updates.
- 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 bioportal-announce
- Example Code: Extract Mappings
- Sample Output:
<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>
XML Schema Definitions for the REST services
XML Schema for concept and hierarchy services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.