BioPortal REST services

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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

Get a specific ontology based on a version id

Download an ontology file

Get all versions of an ontology form a virtual ontology id

Get latest version of an ontology id

List all ontology categories id

Concept services

Get concept id

Get all root concepts for an ontology id

Get concept for latest ontology version id

Search services

Search BioPortal

Hierarchy Services

Tentative of new page here:

Get parents of a given concept in a specific ontology version

  • Signature: ./concepts/parents/{ontlogyVersionId}/{conceptId}[?{optional args}]
  • Example: http://rest.bioontology.org/bioportal/concepts/parents/13578/Melanoma
  • Optional arguments:
  • 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.
  • 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 of a given concept in the latest version of a given ontology

<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/concepts/parents/13578/Melanoma
	</accessedResource>
	<accessDate>2009-04-21 10:28:43.964 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>13578</ontologyVersionId>
				<id>Common_Neoplasm</id>
				<relations>
					<entry>
						<string>Level</string>
						<int>1</int>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>13578</ontologyVersionId>
				<id>Diseases_and_Disorders</id>
				<relations>
					<entry>
						<string>Level</string>
						<int>4</int>
					</entry>
				</relations>
			</classBean>
		</list>
	</data>
</success>

Get children of a given concept in a specific ontology version

  • Signature: ./concepts/children/{ontlogyVersionId}/{conceptId}[?{optional args}]
  • 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)
  • Description: returns all children of the concept, with the level indicating how far away the child node is from the concept. For instance, direct children have level 1; their direct children have level 2, etc. If no level is specified, the service returns all the levels up to the leaves. If the level is specified, the service returns only the children at that level.
  • Sample Output:
<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/concepts/children/13578/Melanoma
	</accessedResource>
	<accessDate>2009-04-21 11:02:03.238 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>13578</ontologyVersionId>
				<id>Non-Cutaneous_Melanoma</id>
				<relations>
					<entry>
						<string>Level</string>
						<int>1</int>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>13578</ontologyVersionId>
				<id>Recurrent_Melanoma</id>
				<relations>
					<entry>
						<string>Level</string>
						<int>1</int>
					</entry>
				</relations>
			</classBean>
		</list>
	</data>
</success>

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

  • Signature: ./virtual/children/{ontlogyId}/{conceptId}[?{optional args}]
  • Example: http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma
  • Optional arguments:
    • level=<integer> - limits results to a given level in the hierarchy
    • offset=<integer> – results offset (used for pagination)
  • Description: The same as the service to get children for a particular version, but takes an ontology id and returns children from the latest version of that ontology. If the latest version of the ontology is not in our index for hierarchy services, returns an error.
  • Sample Output:
<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/virtual/children/MSH/C0025202
	</accessedResource>
	<accessDate>2009-04-21 11:04:26.733 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>MSH</ontologyVersionId>
				<id>C0149722</id>
				<relations>
					<entry>
						<string>Level</string>
						<int>1</int>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>MSH</ontologyVersionId>
				<id>C0206735</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

<?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

<?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

<?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

<?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

<?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

<?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>