Difference between revisions of "BioPortal REST services"

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* '''Signature''': ./concepts/{ontology version id}/all?email={email_address}
 
* '''Signature''': ./concepts/{ontology version id}/all?email={email_address}
−
* '''Example''': http://rest.bioontology.org/bioportal/concepts/40644/all?email=example@example.org
+
* '''Example''': http://rest.bioontology.org/bioportal/concepts/42331/all?email=example@example.org
 
* '''Optional arguments:'''  
 
* '''Optional arguments:'''  
 
** offset=<integer> – results offset (used for pagination)
 
** offset=<integer> – results offset (used for pagination)

Revision as of 17:10, 1 March 2010

This page documents BioPortal Web Service signatures. The list below contains commonly accessed BioPortal Web services and is not intended to be an exhaustive list. If a feature you are interested in is not in the list below, please contact BioPortal Support to request the service or ask for more details on the full list of services.

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

  • Note: All NCBO REST web service calls MUST append a user identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding). For example, email=example@example.org or email=example%40example.org as an encoded email. Please start adding the user identification URL parameter to all your web service invocations. Later in 2009, we may start challenging REST service calls that do not have this parameter.
  • 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.

Overview - Using NCBO Technology in Your Project

See Using NCBO Technology in your Project for general information and widgets available for use.

Code Examples

  • Code examples for the Annotator and Resource Index can be found on pages specific for those tools.

BioPortal Announce Mailing List

To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the bioportal-annouce list.

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

Download the latest ontology file

Get all versions of an ontology from a virtual ontology id

Get latest version of an ontology id

List all ontology categories

NOTE: To be released in BioPortal version 2.2

List all ontology groups

NOTE: To be released in BioPortal version 2.2

Services to access ontology views and ontology view versions

Since all the views on ontologies are ontologies themselves all the services that work on ontologies do work for ontology views also with the same signature.

For example to get a specific ontology view based on a version id would be possible by using the signature:

./ontologies/download/{view version id}?email={email_address}

or for getting all view versions of a virtual view can be achieved called using the signature:

./ontologies/versions/{view id}?email={email_address}

However, there are a couple of services that are special for views:

List all the latest version of views

NOTE: To be released in BioPortal version 2.2

Get all versions of views from a virtual ontology id

NOTE: To be released in BioPortal version 2.2

Search services

Search BioPortal

  • Signature: ./search/{query}[?{optional args}]&email={email_address}
  • Example: http://rest.bioontology.org/bioportal/search/Gene?email=example@example.org
  • You can use multiple query terms, separated by a space, for example: http://rest.bioontology.org/bioportal/search/lung disease?email=example@example.org
  • 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)
    • maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)
    • subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.
  • Description:

The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).

In phrase searches (multiple words), the wildcard character is appended to the last word. For example, searching for "cutaneous mela" would return all concepts whose name contains the word "cutaneous", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc). 

<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/search/cutaneous%20mela
	</accessedResource>
	<accessDate>2009-05-07 16:17:46.182 PDT</accessDate>
	<data>
		<page>
			<pageNum>1</pageNum>
			<numPages>1</numPages>
			<pageSize>3</pageSize>
			<numResultsPage>3</numResultsPage>
			<numResultsTotal>3</numResultsTotal>
			<contents
				class="org.ncbo.stanford.bean.search.SearchResultListBean">
				<searchResultList>
					<searchBean>
						<ontologyVersionId>39715</ontologyVersionId>
						<ontologyId>1136</ontologyId>
						<ontologyDisplayLabel>
							Experimental Factor Ontology
						</ontologyDisplayLabel>
						<recordType>
							RECORD_TYPE_PREFERRED_NAME
						</recordType>
						<conceptId>
							http://www.ebi.ac.uk/efo/EFO_0000389
						</conceptId>
						<conceptIdShort>EFO_0000389</conceptIdShort>
						<preferredName>
							cutaneous melanoma
						</preferredName>
						<contents>cutaneous melanoma</contents>
					</searchBean>
					<searchBean>
						<ontologyVersionId>39478</ontologyVersionId>
						<ontologyId>1032</ontologyId>
						<ontologyDisplayLabel>
							NCI Thesaurus
						</ontologyDisplayLabel>
						<recordType>
							RECORD_TYPE_PREFERRED_NAME
						</recordType>
						<conceptId>
							http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cutaneous_Melanoma
						</conceptId>
						<conceptIdShort>
							Cutaneous_Melanoma
						</conceptIdShort>
						<preferredName>
							Cutaneous Melanoma
						</preferredName>
						<contents>Cutaneous Melanoma</contents>
					</searchBean>
					<searchBean>
						<ontologyVersionId>39833</ontologyVersionId>
						<ontologyId>1009</ontologyId>
						<ontologyDisplayLabel>
							Human disease
						</ontologyDisplayLabel>
						<recordType>
							RECORD_TYPE_PREFERRED_NAME
						</recordType>
						<conceptId>DOID:2418</conceptId>
						<conceptIdShort>DOID:2418</conceptIdShort>
						<preferredName>
							Cutaneous Melanocytic Neoplasm
						</preferredName>
						<contents>
							Cutaneous Melanocytic Neoplasm
						</contents>
					</searchBean>
				</searchResultList>
				<ontologyHitList>
					<ontologyHitBean>
						<ontologyVersionId>39715</ontologyVersionId>
						<ontologyId>1136</ontologyId>
						<ontologyDisplayLabel>
							Experimental Factor Ontology
						</ontologyDisplayLabel>
						<numHits>1</numHits>
					</ontologyHitBean>
					<ontologyHitBean>
						<ontologyVersionId>39833</ontologyVersionId>
						<ontologyId>1009</ontologyId>
						<ontologyDisplayLabel>
							Human disease
						</ontologyDisplayLabel>
						<numHits>1</numHits>
					</ontologyHitBean>
					<ontologyHitBean>
						<ontologyVersionId>39478</ontologyVersionId>
						<ontologyId>1032</ontologyId>
						<ontologyDisplayLabel>
							NCI Thesaurus
						</ontologyDisplayLabel>
						<numHits>1</numHits>
					</ontologyHitBean>
				</ontologyHitList>
			</contents>
		</page>
	</data>
</success>

Term services

(formerly referred to as Concept services)

Get term

  • Signature: ./concepts/{ontology version id}/{concept id}?email={email_address}
  • Alt Signature: ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}
  • Optional arguments:
    • light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children
    • norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.
  • Examples:

http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource?email=example@example.org
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&light=0&email=example@example.org
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&norelations=1&email=example@example.org

  • Sample Output:
<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>/bioportal/concepts/40644/</accessedResource>
	<accessDate>2009-12-16 10:06:10.727 PST</accessDate>
	<data>
		<classBean>
			<id>Melanoma</id>
			<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanoma</fullId>
			<label>Melanoma</label>
			<type>Class</type>
			<synonyms>
				<string>Malignant Melanoma</string>
				<string>Melanoma</string>
				<string>melanoma</string>
			</synonyms>
			<definitions>
				<string>A malignant, usually aggressive tumor composed of atypical,
					neoplastic melanocytes.</string>
			</definitions>
			<relations>
				<entry>
					<string>UMLS_CUI</string>
					<list>
						<string>C0025202</string>
					</list>
				</entry>
				<entry>
					<string>owl:equivalentClass</string>
					<list>
						<string>'Common Neoplasm' and 'Melanocytic Neoplasm' and
							(Disease_Has_Abnormal_Cell only 'Melanoma Cell')</string>
					</list>
				</entry>
				<entry>
					<string>ALT_DEFINITION</string>
					<list>
						<string>
							<def-source>NCI-GLOSS</def-source>
							<def-definition>A form of skin cancer that arises in
								melanocytes, the cells that produce pigment.</def-definition>
						</string>
					</list>
				</entry>
				<entry>
					<string>ICD-O-3_Code</string>
					<list>
						<string>8720/3</string>
					</list>
				</entry>
				<entry>
					<string>Semantic_Type</string>
					<list>
						<string>Neoplastic Process</string>
					</list>
				</entry>
				<entry>
					<string>SubClass</string>
					<list>
						<classBean>
							<id>Non-Cutaneous_Melanoma</id>
							<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Non-Cutaneous_Melanoma</fullId>
							<label>Non-Cutaneous Melanoma</label>
							<type>Class</type>
							<synonyms>
								<string>Extracutaneous Melanoma</string>
								<string>Non-Cutaneous Melanoma</string>
							</synonyms>
							<definitions>
								<string>Melanoma is a malignant tumor of melanocytes,
									cells that are derived from the neural crest.</string>
							</definitions>
							<relations>
								<entry>
									<string>code</string>
									<list>
										<string>C8711</string>
									</list>
								</entry>
							</relations>
						</classBean>
					</list>
				</entry>
			</relations>
		</classBean>
	</data>
</success>

Get all root terms for an ontology version id

Get term for latest ontology version id

NOTE: This signature will change in BioPortal release 2.2


Get all terms using the specific ontology version id

Get all terms using the virtual ontology id

Hierarchy Services

NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies

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

  • Signature: ./concepts/[parents|children]/{ontlogyVersionId}/{conceptId}[?email={email_address}&{optional args}]
<?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

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

<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/concepts/rootpath/40644/Melanoma
	</accessedResource>
	<accessDate>2009-04-21 11:06:23.439 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>40644</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>40644</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

Get siblings of a given concept in a specific ontology version

<?xml version="1.0" encoding="UTF-8" ?>
<success>
	<accessedResource>
		/bioportal/concepts/siblings/40644/Melanoma
	</accessedResource>
	<accessDate>2009-04-21 11:15:13.427 PDT</accessDate>
	<data>
		<list>
			<classBean>
				<ontologyVersionId>40644</ontologyVersionId>
				<id>Common_Germ_Cell_Neoplasm</id>
				<relations>
					<entry>
						<string>Level</string>
						<int>1</int>
					</entry>
				</relations>
			</classBean>
			<classBean>
				<ontologyVersionId>40644</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>&email={email_address}&[&{optional args}]
  • Example: http://rest.bioontology.org/bioportal/virtual/siblings/1009/DOID:1909?level=1&email=example@example.org
  • 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.

RDF Dump Service

This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file

Annotator Service

The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others.

The Annotator can be tested via a Web interface available through BioPortal. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.

Resource Index Service

The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.

Prototypes

Notes Service

<records type="array">
  <record>
    <comment>
    I note that clinical data is specifically defined not to include clinical trial data. So is anyone already thinking about where at a high level subtrees might be added to deal with clinical trial data and clinical trial management systems? Or is it premature to do that? This is for the CTSAs.
    </comment>
    <created-at>2008-08-07 11:21:00</created-at>
    <ontology-id>1104</ontology-id>
    <updated-at>2008-08-07 11:21:00</updated-at>
    <mapping-id nil="true"/>
    <subject>Including clinical trial data as clinical data</subject>
    <id>75</id>
    <user-id>38143</user-id>
    <parent-id nil="true"/>
    <ontology-version-id>38407</ontology-version-id>
    <concept-id>BRO:Clinical_Data</concept-id>
    <note-type>Question</note-type>
  </record>
  <record>
    <comment> Not sure I follow the argument here.  Clinical trial data is covered under PHI so no distinction there.  Data generated in the course of delivering routine standard of care may be needed in the course of a clinical trial.  Does this make clinical trial data an overlapping superset of clinical data?
    </comment>
    <created-at>2008-08-07 11:24:04</created-at>
    <ontology-id>1104</ontology-id>
    <updated-at>2008-08-07 11:24:04</updated-at>
    <mapping-id nil="true"/>
    <subject>RE:Including clinical trial data as clinical data</subject>
    <id>76</id>
    <user-id>38144</user-id>
    <parent-id>75</parent-id>
    <ontology-version-id>38407</ontology-version-id>
    <concept-id>BRO:Clinical_Data</concept-id>
    <note-type>Comment</note-type>
  </record>
</records>

Mapping Service

  • Signature: ./mappings/service/{ontology_id}/{concept_id}
  • Example: http://bioportal.bioontology.org/mappings/service/1083/
  • Required arguments:
    • ontology_id
  • Optional arguments:
    • concept_id=if concept_id is included, the service will return all mappings to and from the given concept
  • Description: returns BioPortal Mappings as XML. This is a prototype web service, for updates subscribe to bioportal-announce
  • Sample Output:
<hash>
  <mapping-from type="array">
    <mapping-from>
      <comment nil="true"></comment>
      <map-type>Human</map-type>
      <created-at>2008-05-09 08:25:23</created-at>
      <updated-at>2008-08-05 17:26:06</updated-at>

      <source-name>Carbon</source-name>
      <source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
      <destination-id>CHEBI:27594</destination-id>
      <id>98216</id>
      <user-id>38139</user-id>
      <relationship-type nil="true"></relationship-type>

      <destination-ont-name>Chemical entities of biological interest</destination-ont-name>
      <destination-name>Carbon</destination-name>
      <map-source nil="true"></map-source>
      <destination-ont>1007</destination-ont>
      <source-id>Carbon</source-id>
      <destination-version-id>38377</destination-version-id>

      <source-version-id>29531</source-version-id>
      <source-ont>1083</source-ont>
    </mapping-from>   
    <mapping-from>
      <comment nil="true"></comment>
      <map-type>Human</map-type>
      <created-at>2008-05-09 08:27:05</created-at>

      <updated-at>2008-08-05 17:26:06</updated-at>
      <source-name>Gold</source-name>
      <source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
      <destination-id>CHEBI:29287</destination-id>
      <id>98218</id>
      <user-id>38139</user-id>

      <relationship-type nil="true"></relationship-type>
      <destination-ont-name>Chemical entities of biological interest</destination-ont-name>
      <destination-name>Gold</destination-name>
      <map-source nil="true"></map-source>
      <destination-ont>1007</destination-ont>
      <source-id>Gold</source-id>
      <destination-version-id>38377</destination-version-id>

      <source-version-id>29531</source-version-id>
      <source-ont>1083</source-ont>
    </mapping-from>
  </mapping-from>
  <mapping-to type="array">
    <mapping-to>
      <comment nil="true"></comment>
      <map-type>Human</map-type>

      <created-at>2008-05-09 08:35:27</created-at>
      <updated-at>2008-08-05 17:26:06</updated-at>
      <source-name>Carbohydrate</source-name>
      <source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
      <destination-id>Carbohydrate</destination-id>
      <id>98219</id>

      <user-id>38139</user-id>
      <relationship-type nil="true"></relationship-type>
      <destination-ont-name>NanoParticle Ontology (NPO)</destination-ont-name>
      <destination-name>Carbohydrate</destination-name>
      <map-source nil="true"></map-source>
      <destination-ont>1083</destination-ont>
      <source-id>Carbohydrate</source-id>

      <destination-version-id>29531</destination-version-id>
      <source-version-id>29531</source-version-id>
      <source-ont>1083</source-ont>
    </mapping-to>
  </mapping-to>
</hash>


XML Schema Definitions for the REST services

XML Schema for concept and hierarchy services is available (courtesy Eamonn Maguire).

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