Revision as of 16:04, 21 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

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:
- 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
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
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)
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)
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> <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> </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> <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> </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> <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> </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> <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> </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> <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> </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> <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> </success>

@@ Line 194: / Line 194: @@
 ** offset=<integer> – results offset (used for pagination)
 * '''Sample Output:'''
+<pre>
 <?xml version="1.0" encoding="UTF-8" ?>
 <success>
@@ Line 226: / Line 226: @@
 	</data>
 </success>
+</pre>
 ==  Get paths to root from a concept in a specific ontology version ==

Difference between revisions of "BioPortal REST services"