Revision as of 13:46, 23 April 2009

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.
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: 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

Signature: ./virtual/parents/{ontlogyId}/{conceptId}[?{optional args}]
Example: http://rest.bioontology.org/bioportal/virtual/parents/1032/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/virtual/parents/1032/Melanoma?level=1&offset=1&limit=10
Description: The same as the service to get parents for a particular version, but takes an ontology id and returns parents 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/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

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>

Difference between revisions of "BioPortal REST services"