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

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

• Signature: ./concepts/[parents|children]/{ontlogyVersionId}/{conceptId}[?{optional args}]
• Example: http://rest.bioontology.org/bioportal/concepts/parents/13578/Melanoma
• Example: http://rest.bioontology.org/bioportal/concepts/children/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: returns all parents of the concept, with the level indicating how far away the parent is from the concept. For instance, direct parents have level 1; their direct parents have level 2, etc. If no level is specified, the service returns all the levels up to the root. If the level is specified, the service returns only the parents at that level.
• Note: These services accept UMLS Abbreviated source name (SAB) for ontlogyVersionId and UMLS Unique identifier for concept (CUI) for conceptId.
• 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 parents|children of a given concept in the latest version of a given ontology

• Signature: ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?{optional args}]
• Example: http://rest.bioontology.org/bioportal/virtual/parents/1009/DOID:1909
• Example: http://rest.bioontology.org/bioportal/virtual/children/1009/DOID:1909
• 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/virtual/parents/1009/DOID:1909?level=1&offset=1&limit=3
• Description: The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.

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

• Signature: ./concepts/[rootpath|leafpath]/{ontologyVersionId}/{conceptId}[?{optional args}]
• Example: http://rest.bioontology.org/bioportal/concepts/rootpath/13578/Melanoma
• 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
• Description: return a set of path to the roots (resp. leaves) for a given concept in a specific ontology version. Paths are represented as a list of conceptIds, separated by periods (.) The first one in the list is a root (resp. leaf) in the hierarchy; the last one in the list is the direct parent (resp. direct child) of the concept.
• Note: These services accepts UMLS Abbreviated source name (SAB) for ontlogyVersionId and UMLS Unique identifier for concept (CUI) fro conceptId.
• 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|leaves from a concept in the latest version of a given ontology

• Signature: ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?{optional args}]
• Example: http://rest.bioontology.org/bioportal/virtual/rootpath/1009/DOID:1909
• Example: http://rest.bioontology.org/bioportal/virtual/leafpath/1009/DOID:1909
• Optional arguments:
  • offset=<integer> – results offset (used for pagination)
  • limit=<integer> – limits the number of results
• 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 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)
• Description: returns the set of sibling concepts at the given level (i.e., siblings that have the same direct (level=1), grand-parents (level=2), etc.) for a given concept.
• Note: These services accepts UMLS Abbreviated source name (SAB) for ontlogyVersionId and UMLS Unique identifier for concept (CUI) fro conceptId.
• 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/1009/DOID:1909?level=1
• 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.