BioPortal REST services

This page documents the signatures for NCBO (and, more specifically, BioPortal) REST services. This list may not be exhaustive.

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.

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

Services to access ontologies and ontology versions

List all the latest version of ontologies

• Signature: ./ontologies
• Example: http://rest.bioontology.org/bioportal/ontologies

Get a specific ontology based on a version id

• Signature: ./ontologies/{ontology version id}
• Example: http://rest.bioontology.org/bioportal/ontologies/39002

Download an ontology file

• Description: Download the file (.obo, .owl) corresponding to the given ontology version ID.
• Signature: ./ontologies/download/{ontology version id}
• Example: http://rest.bioontology.org/bioportal/ontologies/download/39002

Get all versions of an ontology form a virtual ontology id

• Signature: ./ontologies/versions/{ontology id}
• Example: http://rest.bioontology.org/bioportal/ontologies/versions/1104

Get latest version of an ontology id

• Signature: ./virtual/{ontology_id}
• Example: http://rest.bioontology.org/bioportal/virtual/1104

List all ontology categories id

• Signature: ./categories
• Example: http://rest.bioontology.org/bioportal/categories

Concept services

Get concept id

• Signature: ./concepts/{ontology version id}/{concept id}
• Example: http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource

Get all root concepts for an ontology id

• Signature: ./concepts/{ontology version id}/root
• Example: http://rest.bioontology.org/bioportal/concepts/39002/root

Get concept for latest ontology version id

• Signature: ./virtual/{ontology id}/{concept id}
• Example: http://rest.bioontology.org/bioportal/virtual/1104/BRO:Resource

Search services

Search BioPortal

• Signature: ./search/{query}[?{optional args}]
• Example: http://rest.bioontology.org/bioportal/search/Gene
• You can use multiple query terms, separated by a space, for example: http://rest.bioontology.org/bioportal/search/lung disease
• 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)
  • Example: http://rest.bioontology.org/bioportal/search/software/?ontologyids=1104&isexactmatch=1

Hierarchy Services

Those services accepts 3 kinds of ontologyId:

• BioPortal ontology version id
• BioPortal ontology virtual id. In that case the latest version of the ontology is used (If the latest version of the ontology is not in our index for hierarchy services, returns an error).
• UMLS Abbreviated source name (SAB). In that case the conceptId must be a UMLS Unique identifier for concept (CUI) defined in that SAB.

Get parents|children of a given concept

• Signature: ./concepts/[parents|children]/{ontlogyId}/{conceptId}[?{optional args}]
• Example: http://rest.bioontology.org/bioportal/concepts/parents/13578/Melanoma
• Optional arguments:
  • level=<integer> - limits results to a given level in the hierarchy
  • offset=<integer> – results offset (used for pagination)
  • limit=<integer> – limits the number of results
  • Example: http://rest.bioontology.org/bioportal/concepts/parents/13578/Melanoma?level=1&offset=1&limit=10
• Description: return all parents (resp. children) of the concept, with the level indicating how far away the parent (child) is from the concept. For instance, direct parents have level 1; their direct parents have level 2, etc. If no level is specified, the services return all the parents (resp. children) up to the ontology roots (resp. down to the ontology leaves). If the level is specified, the service returns only the parents (resp. children) at that level.
• Sample Output:

<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/virtual/parents/MSH/C0025202
	</accessedResource>
	<accessDate>2009-04-21 10:55:33.494 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>MSH</ontologyVersionId>
				<id>C0206769</id>
				<relations>
					<entry>
						<string>Level</string>
						<int>1</int>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>MSH</ontologyVersionId>
				<id>C0206754</id>
				<relations>
					<entry>
						<string>Level</string>
						<int>1</int>
					</entry>
				</relations>
			</classBean>
		</list>
	</data>
</success>

Get paths to root from a concept in a specific ontology version

• Signature: ./concepts/rootpath/{ontologyVersionId}/{conceptId}[?{optional args}]
• Example: http://rest.bioontology.org/bioportal/concepts/rootpath/13578/Melanoma
• Optional arguments:
  • offset=<integer> – results offset (used for pagination)
  • limit=<integer> – limits the number of results
• Sample Output:

<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/concepts/rootpath/13578/Melanoma
	</accessedResource>
	<accessDate>2009-04-21 11:06:23.439 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>13578</ontologyVersionId>
				<id>Melanoma</id>
				<relations>
					<entry>
						<string>Path</string>
						<string>
							Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Morphology.Melanocytic_Neoplasm
						</string>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>13578</ontologyVersionId>
				<id>Melanoma</id>
				<relations>
					<entry>
						<string>Path</string>
						<string>
							Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Special_Category.Common_Neoplasm
						</string>
					</entry>
				</relations>
			</classBean>
		</list>
	</data>
</success>

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

• Signature: ./virtual/rootpath/{ontologyId}/{conceptId}[?{optional args}]
• Example: http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma
• Optional arguments:
  • offset=<integer> – results offset (used for pagination)
  • limit=<integer> – limits the number of results
• Sample Output:

<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/virtual/rootpath/MSH/C0025202
	</accessedResource>
	<accessDate>2009-04-21 11:08:05.811 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>MSH</ontologyVersionId>
				<id>C0025202</id>
				<relations>
					<entry>
						<string>Path</string>
						<string>
							C1256739.C1256741.C0012674.C0027651.C0027652.C0206769
						</string>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>MSH</ontologyVersionId>
				<id>C0025202</id>
				<relations>
					<entry>
						<string>Path</string>
						<string>
							C1256739.C1256741.C0012674.C0027651.C0027652.C0027658.C0206093.C0206754
						</string>
					</entry>
				</relations>
			</classBean>
		</list>
	</data>
</success>

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

• Signature: ./concepts/leafpath/{ontologyVersionId}/{conceptId}[?{optional args}]
• Example: http://rest.bioontology.org/bioportal/concepts/leafpath/13578/Melanoma
• Optional arguments:
  • offset=<integer> – results offset (used for pagination)
  • limit=<integer> – limits the number of results
• Sample Output:

<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/concepts/leafpath/13578/Melanoma
	</accessedResource>
	<accessDate>2009-04-21 11:10:04.386 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>13578</ontologyVersionId>
				<id>Melanoma</id>
				<relations>
					<entry>
						<string>Path</string>
						<string>
							Regressing_Non-Cutaneous_Melanoma.Regressing_Melanoma
						</string>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>13578</ontologyVersionId>
				<id>Melanoma</id>
				<relations>
					<entry>
						<string>Path</string>
						<string>
							Regressing_Melanoma_of_the_Skin.Regressing_Melanoma
						</string>
					</entry>
				</relations>
			</classBean>
		</list>
	</data>
</success>

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

• Signature: ./virtual/leafpath/{ontologyId}/{conceptId}[?{optional args}]
• Example: http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma
• Optional arguments:
  • offset=<integer> – results offset (used for pagination)
  • limit=<integer> – limits the number of results
• Sample Output:

<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/virtual/leafpath/MSH/C0025202
	</accessedResource>
	<accessDate>2009-04-21 11:11:56.348 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>MSH</ontologyVersionId>
				<id>C0025202</id>
				<relations>
					<entry>
						<string>Path</string>
						<string>C0025205</string>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>MSH</ontologyVersionId>
				<id>C0025202</id>
				<relations>
					<entry>
						<string>Path</string>
						<string>C0206735</string>
					</entry>
				</relations>
			</classBean>
		</list>
	</data>
</success>

Get siblings of a given concept in a specific ontology version

• Signature: ./concepts/siblings/{ontlogyVersionId}/{conceptId}?level=<level>[&{optional args}]
• Example: http://rest.bioontology.org/bioportal/concepts/siblings/13578/Melanoma?level=1
• Required arguments:
  • level=<integer> - limits results to a given level in the hierarchy
• Optional arguments:
  • offset=<integer> – results offset (used for pagination)
• Sample Output:

<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/concepts/siblings/13578/Melanoma
	</accessedResource>
	<accessDate>2009-04-21 11:15:13.427 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>13578</ontologyVersionId>
				<id>Common_Germ_Cell_Neoplasm</id>
				<relations>
					<entry>
						<string>Level</string>
						<int>1</int>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>13578</ontologyVersionId>
				<id>Common_Hematopoietic_Neoplasm</id>
				<relations>
					<entry>
						<string>Level</string>
						<int>1</int>
					</entry>
				</relations>
			</classBean>
		</list>
	</data>
</success>

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

• Signature: ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>[&{optional args}]
• Example: http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1
• Required arguments:
  • level=<integer> - limits results to a given level in the hierarchy
• Optional arguments:
  • offset=<integer> – results offset (used for pagination)
• Sample Output:

<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/virtual/siblings/MSH/C0206093
	</accessedResource>
	<accessDate>2009-04-21 11:30:12.183 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>MSH</ontologyVersionId>
				<id>C0206720</id>
				<relations>
					<entry>
						<string>Level</string>
						<int>2</int>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>MSH</ontologyVersionId>
				<id>C0206727</id>
				<relations>
					<entry>
						<string>Level</string>
						<int>2</int>
					</entry>
				</relations>
			</classBean>
		</list>
	</data>
</success>