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?apikey={YourAPIKey}
Example: http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey

Get a specific ontology based on a version id

Signature: ./ontologies/{ontology version id}?apikey={YourAPIKey}
Example: http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey

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?apikey=YourAPIKey

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?apikey=YourAPIKey

Get all versions of an ontology from a virtual ontology id

Signature: ./ontologies/versions/{ontology id}?apikey={YourAPIKey}
Example: http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey

Get latest version of an ontology id

Signature: ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}
Example: http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey

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}?apikey={YourAPIKey}

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

./ontologies/versions/{view id}?apikey={YourAPIKey}

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?apikey={YourAPIKey}
Example: http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey

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}?apikey={YourAPIKey}
Example: http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey

Search services

Search BioPortal

Signature: ./search/{query}[?{optional args}]&apikey={YourAPIKey}
Alt Signature: ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}
Example: http://rest.bioontology.org/bioportal/search/Gene?apikey=YourAPIKey
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&apikey=YourAPIKey
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}?apikey={YourAPIKey}
Alt Signature: ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}
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&apikey=YourAPIKey

http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey

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?apikey={YourAPIKey}
Example: http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey

Get a path between two terms

Signature: ./path/{ontology_id}/?source={concept1_id}&target={concept2_id}&apikey=YourAPIKey
Example: http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=Tissue&apikey=YourAPIKey

Get a path between a term and the root

Signature: ./path/{ontology_id}/?source={concept1_id}&target=root&apikey=YourAPIKey

Example: http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey

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}&apikey={YourAPIKey}
Examples:
- http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey
- http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey
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}&apikey={YourAPIKey}
Example: http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey
Arguments:
- pagesize: An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
- pagenum: An integer indicating which page of results to return.

Changes to the Get all terms service

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

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

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

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

View Extraction Service

This web service can be used to extract a subtree from an ontology. See 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}]&apikey={YourAPIKey}
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&apikey=YourAPIKey
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}&apikey={YourAPIKey}]

Example: http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey
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 provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure.

NOTE: To see which ontology versions have been processed for use with the Hierarchy Services, check 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}[?apikey={YourAPIKey}&{optional args}]
Example: http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey
Example: http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey
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>&apikey={YourAPIKey}&[&{optional args}]
Example: http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&apikey=YourAPIKey
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}?apikey={YourAPIKey}
Example: http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey

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}?apikey=YourAPIKey
Alt Signature: ./bioportal/virtual/rdf/{ontology id}/{concept id}?apikey=YourAPIKey
Alt Signature: ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?apikey=YourAPIKey
Examples:
- http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_spatial:NEMO_0000024?apikey=YourAPIKey
- http://rest.bioontology.org/bioportal/rdf/42743/NEMO_spatial:NEMO_0000023?apikey=YourAPIKey
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}
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}?apikey=YourAPIKey
Alt Signature: ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey
Examples:
- http://rest.bioontology.org/bioportal/ontologies/rdf/download/44016?apikey=YourAPIKey
- http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1054?apikey=YourAPIKey

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}

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.

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.

@@ Line 851: / Line 851: @@
 * ''' 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 [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]
-** '''Example Code:''' [http://www.bioontology.org/wiki/index.php/ExtractMappings Extract Mappings]
-** '''Sample Output:'''
-<pre>
-<hash>
-  <mapping-from type="array">
-    <mapping-from>
-      <comment nil="true"></comment>
-      <map-type>Human</map-type>
-      <created-at>2008-05-09 08:25:23</created-at>
-      <updated-at>2008-08-05 17:26:06</updated-at>
-      <source-name>Carbon</source-name>
-      <source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
-      <destination-id>CHEBI:27594</destination-id>
-      <id>98216</id>
-      <user-id>38139</user-id>
-      <relationship-type nil="true"></relationship-type>
-      <destination-ont-name>Chemical entities of biological interest</destination-ont-name>
-      <destination-name>Carbon</destination-name>
-      <map-source nil="true"></map-source>
-      <destination-ont>1007</destination-ont>
-      <source-id>Carbon</source-id>
-      <destination-version-id>38377</destination-version-id>
-      <source-version-id>29531</source-version-id>
-      <source-ont>1083</source-ont>
-    </mapping-from>
-    <mapping-from>
-      <comment nil="true"></comment>
-      <map-type>Human</map-type>
-      <created-at>2008-05-09 08:27:05</created-at>
-      <updated-at>2008-08-05 17:26:06</updated-at>
-      <source-name>Gold</source-name>
-      <source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
-      <destination-id>CHEBI:29287</destination-id>
-      <id>98218</id>
-      <user-id>38139</user-id>
-      <relationship-type nil="true"></relationship-type>
-      <destination-ont-name>Chemical entities of biological interest</destination-ont-name>
-      <destination-name>Gold</destination-name>
-      <map-source nil="true"></map-source>
-      <destination-ont>1007</destination-ont>
-      <source-id>Gold</source-id>
-      <destination-version-id>38377</destination-version-id>
-      <source-version-id>29531</source-version-id>
-      <source-ont>1083</source-ont>
-    </mapping-from>
-  </mapping-from>
-  <mapping-to type="array">
-    <mapping-to>
-      <comment nil="true"></comment>
-      <map-type>Human</map-type>
-      <created-at>2008-05-09 08:35:27</created-at>
-      <updated-at>2008-08-05 17:26:06</updated-at>
-      <source-name>Carbohydrate</source-name>
-      <source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
-      <destination-id>Carbohydrate</destination-id>
-      <id>98219</id>
-      <user-id>38139</user-id>
-      <relationship-type nil="true"></relationship-type>
-      <destination-ont-name>NanoParticle Ontology (NPO)</destination-ont-name>
-      <destination-name>Carbohydrate</destination-name>
-      <map-source nil="true"></map-source>
-      <destination-ont>1083</destination-ont>
-      <source-id>Carbohydrate</source-id>
-      <destination-version-id>29531</destination-version-id>
-      <source-version-id>29531</source-version-id>
-      <source-ont>1083</source-ont>
-    </mapping-to>
-  </mapping-to>
-</hash>
-</pre>

Difference between revisions of "BioPortal REST services"

Revision as of 21:51, 24 April 2011

Overview - Using NCBO Technology in Your Project

Code Examples

BioPortal Announce Mailing List

Services to access ontologies and ontology versions

List all the latest version of ontologies

Get a specific ontology based on a version id

Download an ontology file

Download the latest ontology file

Get all versions of an ontology from a virtual ontology id

Get latest version of an ontology id

List all ontology categories

List all ontology groups

Services to access ontology views and ontology view versions

List all the latest version of views

Get all versions of views from a virtual ontology id

Search services

Search BioPortal

Term services

Get term, including its properties, subclasses, and superclasses

Get all root terms for an ontology version id

Get a path between two terms

Get a path between a term and the root

Get all terms using the specific ontology version id

Get all terms using the virtual ontology id

Changes to the Get all terms service

View Extraction Service

Instance Services

Get all direct instances for a given term

Get an instance and its property/value pairs

Hierarchy Services

Get paths to root/leaves from a concept in the latest version of a given ontology

Get siblings of a given concept in the latest version of a given ontology

Bio2RDF Dump Service

Annotator Service

Resource Index Service

RDF Term Service

RDF Download Service

Notes Service

Mapping Service

XML Schema Definitions for the REST services

Navigation menu

Search