BioPortal REST services

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

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

  • Note: All NCBO REST web service calls MUST append a user identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding). For example, email=example@example.org or email=example%40example.org as an encoded email. Please start adding the user identification URL parameter to all your web service invocations. Later in 2009, we may start challenging REST service calls that do not have this parameter.
  • Note: Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. If you have any questions, please contact BioPortal Support.

Overview - Using NCBO Technology in Your Project

See Using NCBO Technology in your Project for general information and widgets available for use.

Code Examples

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

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

NOTE: To be released in BioPortal version 2.2

List all ontology groups

NOTE: To be released in BioPortal version 2.2

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

Get all versions of views from a virtual ontology id

NOTE: To be released in BioPortal version 2.2

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.
  • 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). 

<?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

  • Signature: ./concepts/{ontology version id}/{concept id}?email={email_address}
  • Alt Signature: ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}
    • To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI.
  • Optional arguments:
    • light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children
    • norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.
  • Examples:

http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource?email=example@example.org
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&light=0&email=example@example.org
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&norelations=1&email=example@example.org

  • Sample Output:
<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>/bioportal/concepts/40644/</accessedResource>
	<accessDate>2009-12-16 10:06:10.727 PST</accessDate>
	<data>
		<classBean>
			<id>Melanoma</id>
			<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanoma</fullId>
			<label>Melanoma</label>
			<type>Class</type>
			<synonyms>
				<string>Malignant Melanoma</string>
				<string>Melanoma</string>
				<string>melanoma</string>
			</synonyms>
			<definitions>
				<string>A malignant, usually aggressive tumor composed of atypical,
					neoplastic melanocytes.</string>
			</definitions>
			<relations>
				<entry>
					<string>UMLS_CUI</string>
					<list>
						<string>C0025202</string>
					</list>
				</entry>
				<entry>
					<string>owl:equivalentClass</string>
					<list>
						<string>'Common Neoplasm' and 'Melanocytic Neoplasm' and
							(Disease_Has_Abnormal_Cell only 'Melanoma Cell')</string>
					</list>
				</entry>
				<entry>
					<string>ALT_DEFINITION</string>
					<list>
						<string>
							<def-source>NCI-GLOSS</def-source>
							<def-definition>A form of skin cancer that arises in
								melanocytes, the cells that produce pigment.</def-definition>
						</string>
					</list>
				</entry>
				<entry>
					<string>ICD-O-3_Code</string>
					<list>
						<string>8720/3</string>
					</list>
				</entry>
				<entry>
					<string>Semantic_Type</string>
					<list>
						<string>Neoplastic Process</string>
					</list>
				</entry>
				<entry>
					<string>SubClass</string>
					<list>
						<classBean>
							<id>Non-Cutaneous_Melanoma</id>
							<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Non-Cutaneous_Melanoma</fullId>
							<label>Non-Cutaneous Melanoma</label>
							<type>Class</type>
							<synonyms>
								<string>Extracutaneous Melanoma</string>
								<string>Non-Cutaneous Melanoma</string>
							</synonyms>
							<definitions>
								<string>Melanoma is a malignant tumor of melanocytes,
									cells that are derived from the neural crest.</string>
							</definitions>
							<relations>
								<entry>
									<string>code</string>
									<list>
										<string>C8711</string>
									</list>
								</entry>
							</relations>
						</classBean>
					</list>
				</entry>
			</relations>
		</classBean>
	</data>
</success>

Get all root terms for an ontology version id

Get term for latest ontology version id

NOTE: This signature will change in BioPortal release 2.2


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.

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.

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.

  • 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}]&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)
<?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}]
<?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

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

Get parents/children of a given concept in a specific ontology version

  • Signature: ./concepts/[parents|children]/{ontlogyVersionId}/{conceptId}[?email={email_address}&{optional args}]
<?xml version="1.0" encoding="UTF8" ?>
<success>
	<accessedResource>/bioportal/concepts/parents/42331/Melanoma
	</accessedResource>
	<accessDate>20100408 17:58:14.230 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>42331</ontologyVersionId>
				<id>Common_Neoplasm</id>
				<fullId>
					http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Neoplasm
				</fullId>
				<label>Common Neoplasm</label>
				<synonyms>
					<string>Common Tumor</string>
					<string>Common Neoplasm</string>
				</synonyms>
				<relations>
					<entry>
						<string>Level</string>
						<int>1</int>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>42331</ontologyVersionId>
				<id>Melanocytic_Neoplasm</id>
				<fullId>
					http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanocytic_Neoplasm
				</fullId>
				<label>Melanocytic Neoplasm</label>
				<synonyms>
					<string>Melanocytic Neoplasm</string>
				</synonyms>
				<relations>
					<entry>
						<string>Level</string>
						<int>1</int>
					</entry>
				</relations>
			</classBean>
		</list>
	</data>
</success>

Get parents/children of a given concept in the latest version of a given ontology

Get paths to roots/leaves from a concept in a specific ontology version

<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/concepts/rootpath/40644/Melanoma
	</accessedResource>
	<accessDate>2009-04-21 11:06:23.439 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>40644</ontologyVersionId>
				<id>Melanoma</id>
				<relations>
					<entry>
						<string>Path</string>
						<string>
							Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Morphology.Melanocytic_Neoplasm
						</string>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>40644</ontologyVersionId>
				<id>Melanoma</id>
				<relations>
					<entry>
						<string>Path</string>
						<string>
							Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Special_Category.Common_Neoplasm
						</string>
					</entry>
				</relations>
			</classBean>
		</list>
	</data>
</success>

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

Get siblings of a given concept in a specific ontology version

<?xml version="1.0" encoding="UTF8" ?>
<success>
	<accessedResource>/bioportal/concepts/siblings/42331/Melanoma
	</accessedResource>
	<accessDate>20100408 18:06:16.868 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>42331</ontologyVersionId>
				<id>Common_Germ_Cell_Neoplasm</id>
				<fullId>
					http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Germ_Cell_Neoplasm
				</fullId>
				<label>Common Germ Cell Tumor</label>
				<synonyms>
					<string>Common Germ Cell Tumor</string>
					<string>Common Germ Cell Neoplasm</string>
				</synonyms>
				<relations>
					<entry>
						<string>Level</string>
						<int>1</int>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>42331</ontologyVersionId>
				<id>Common_Hematopoietic_Neoplasm</id>
				<fullId>
					http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Hematopoietic_Neoplasm
				</fullId>
				<label>Common Hematopoietic Neoplasm</label>
				<synonyms>
					<string>Common Hematopoietic Neoplasm</string>
					<string>Common Hematopoietic Tumor</string>
				</synonyms>
				<relations>
					<entry>
						<string>Level</string>
						<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>&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.

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.

Prototypes

RDF Term Service

Coming in late May, 2010! This service allows you to output a snippet of an ontology from BioPortal in the form of an RDF file. 

<?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

Coming in late July, 2010. This service allows you to download an entire ontology from BioPortal in the form of an RDF file.

Notes Service

The prototype notes service has been replaced with a new structured notes service.

Mapping Service

  • Prototype
    • Signature: ./mappings/service/{ontology_id}/{concept_id}
    • Example: http://bioportal.bioontology.org/mappings/service/1083/
    • Required arguments:
      • ontology_id
    • Optional arguments:
      • concept_id=if concept_id is included, the service will return all mappings to and from the given concept
    • Description: returns BioPortal Mappings as XML. This is a prototype web service, for updates subscribe to 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.

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