https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&feedformat=atom&user=Darren+WeberNCBO Wiki - User contributions [en]2026-06-05T09:05:21ZUser contributionsMediaWiki 1.35.9https://www.bioontology.org//mediawiki/index.php?title=Resource_Index&diff=12604Resource Index2013-04-09T02:16:32Z<p>Darren Weber: </p>
<hr />
<div>''Indexing biomedical resources with ontology concepts ''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. <br />
<br />
Using the annotation workflow of the [[Annotator_Web_service|Annotator Web Service]] NCBO has built an biomedical resources index in which biomedical data is indexed by ontology concepts. The index allows a user to search for biomedical data based on ontology concepts. The NCBO Resource Index is directly queriable in the [http://bioportal.bioontology.org BioPortal] ontology repository: when a user browses a given concept, he has access (link) to the list of resource elements that have been annotated with this concept. A user can also search for resources directly using the 'All resources' tab.<br />
<br />
In the NCBO Resource Index, we have processed the textual metadata of elements from several biomedical resources such as: [http://www.ebi.ac.uk/arrayexpress/ ArrayExpress], [http://clinicaltrials.gov/ Clinical Trials.gov], [http://goldminer.arrs.org GoldMiner], [http://www.ncbi.nlm.nih.gov/geo/ Gene Expression Omnibus (GEO)] and others. The annotations in the index keeps track of the structures of elements that have been annotated i.e., from which part of the element (e.g., title, description) an annotation has been produced. This information is used to score annotations. <br />
<br />
[[Image:NCBO_Resource_Index_workflow.png|thumb|NCBO Resource Index workflow]]<br />
<br />
[[Image:OBR_index_creation_resources.png|thumb|NCBO Resource Index creation]]<br />
<br />
Please try the [http://bioportal.bioontology.org/resources NCBO Resource Index] in BioPortal.<br />
<br />
=== Contacts ===<br />
<br />
*For questions or feature requests, contact [mailto:support@bioontology.org?subject=NCBO%20Resources%20Index%20support Support] <br />
<br />
=== Documentation ===<br />
<br />
* [[Resource Index REST Web Service User Guide]]<br />
<br />
* [http://rest.bioontology.org/resource_index/resources/list/ Currently available resource list.]<br />
<br />
* Add your own resource by developing a [http://stanford.edu/~whetzel/downloads/RATDevelopment.pdf Resource Access Tool] <br />
<br />
* Resource index design and underlying data model (see the bottom image on the right) [[Image:OBR_result_model.png|thumb| NCBO Resource Index data model]]<br />
<br />
* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.<br />
<br />
* [[Populating_OBS_database]] - Notes on the population of the NCBO Resource Index DB used in the annotation workflow - Developers only.<br />
<br />
* [https://bmir-gforge.stanford.edu/gf/project/obs/ Corresponding Gforge project] - Developers only.<br />
<br />
=== References === <br />
<br />
* Clement Jonquet, Mark A. Musen and Nigam H. Shah, '''A System for Ontology-Based Annotation of Biomedical Data''', ''In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08,'' Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. [http://dils2008.lri.fr/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-DILS08_Jonquet_Musen_Shah_published.pdf pdf - 431Kb]<br />
<br />
* Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, '''Ontology-driven Indexing of Public Datasets for Translational Bioinformatics''', ''BMC Bioinformatics'', Vol. 10, February 2009. [http://www.biomedcentral.com/bmcbioinformatics/ journal's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-BMCBioInformatics08-Shah-Jonquet-Ontolgy-based_Indexing.pdf pdf - 651 Kb]<br />
<br />
<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* February 2009 - New prototype release (v1.2). API: http://obs.bioontology.org/obr/OBR_v1.2_rest.html<br />
<br />
* March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore, please do not use.<br />
<br />
* December 2008 - API specification for the new prototype (v1.2) - not maintained anymore, please do not use.<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The annotation workflow used to create the NCBO Resource Index uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the NCBO Resource Index client in BioPortal (http://bioportal.bioontology.org/all_resources) is designed & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=Ontology_Notes&diff=12595Ontology Notes2013-03-22T22:06:28Z<p>Darren Weber: /* Creating a 'New Term Proposal' proposal */ resolve inconsistency in parameter names between 'signature' and 'arguments'. The 'new*' parameters don't work.</p>
<hr />
<div>BioPortal uses Notes to describe a variety of user-specified comments and metadata for an ontology, including new term proposals, requests for changes, comments and questions. <br />
<br />
The prefix for all production service URLs in the table below is http://rest.bioontology.org/bioportal<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO REST Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
== Types of notes in BioPortal ==<br />
The following are the types of notes in BioPortal. Please, email us at [mailto:support@bioontology.org support@bioontology.org] if you have suggestions for other note types (or specific parameters for the notes).<br />
<br />
* Basic comments (as they are in BioPortal currently)<br />
* Proposals <br />
** New term proposal<br />
*** PrefName<br />
*** Synonym<br />
*** Definition<br />
*** Superclass<br />
*** Comment<br />
** New relationship proposal<br />
*** Relationship type: is-a, part-of<br />
*** Relationship target<br />
** New attribute value proposal<br />
*** Attribute: documentation, definition, etc.<br />
*** New value<br />
*** Flag: replaces the current value (which one, in case of multiple values) or in addition to the current value(s)<br />
*** (future implementation) Special kind of new attribute value proposal: Assigning UMLS semantic type <br />
**** Semantic type<br />
**** Semantic typeID<br />
<br />
* (future implementation) Structured annotations with user-defined structure<br />
* (future implementation) Usage-guideline notes<br />
<br />
== Web services to access and generate notes ==<br />
If you have specific requirements that the list of services below does not satisfy, please contact us at [mailto:support@bioontology.org support@bioontology.org]<br />
<br />
=== Get notes for an ontology by version id ===<br />
<br />
* '''Signature''': ./notes/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/notes/44450?apikey=YourAPIKey<br />
* '''Description''': returns all notes for a specific version of the ontology <br />
* '''Optional arguments:'''<br />
** conceptid={conceptid} - returns notes associated with the given term.<br />
** instanceid={instanceid} - returns notes associated with the given instance (individual).<br />
** noteid={noteid} - returns notes associated with the given note id.<br />
** threaded=[true|false] - returns notes in a threaded format where responses are nested in their parent notes. Default is false.<br />
** Planned (not yet implemented):<br />
*** notetype={notetype} - returns only the notes of the specific type.<br />
*** includearchived=[true|false] - include archived notes. Default is false.<br />
<br />
=== Get notes for an ontology by virtual id ===<br />
<br />
* '''Signature''': ./virtual/notes/{ontology virtual id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/notes/1104?apikey=YourAPIKey<br />
* '''Description''': returns all notes for the virtual ontology, i.e., all notes associated with any version of this ontology <br />
* '''Optional arguments:'''<br />
** conceptid={conceptid} - returns notes associated with the given term.<br />
** instanceid={instanceid} - returns notes associated with the given instance (individual).<br />
** noteid={noteid} - returns notes associated with the given note id.<br />
** threaded=[true|false] - returns notes in a threaded format where responses are nested in their parent notes. Default is false.<br />
** Planned (not yet implemented):<br />
*** notetype={notetype} - returns only the notes of the specific type.<br />
*** includearchived=[true|false] - include archived notes. Default is false.<br />
<br />
=== Sample of the XML returned for a note ===<br />
<br />
==== Possible Values ====<br />
Some elements have a range of possible returned values.<br />
* appliesTo/type: Ontology|Class|Individual|Property|Note<br />
* noteBean/type: Comment|ProposalForCreateEntity|ProposalForChangeHierarchy|ProposalForPropertyValueChange<br />
** Notes with types other than Comment will have an element in noteBean/values that matches the noteBean/type. This contains information specific to these Notes types.<br />
<br />
==== A single 'Comment' note ====<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/virtual/notes/1104</accessedResource><br />
<accessDate>2010-04-26 13:02:57.418 PDT</accessDate><br />
<data><br />
<list><br />
<noteBean><br />
<id>Note_0a78922c-3d1e-4689-8af8-48d10d4cdaa8</id><br />
<ontologyId>1104</ontologyId><br />
<type>Comment</type><br />
<author>38143</author><br />
<created>1272070868364</created><br />
<updated>1272070868250</updated><br />
<subject>Including clinical trial data as clinical data</subject><br />
<body>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.</body><br />
<createdInOntologyVersion>2</createdInOntologyVersion><br />
<appliesToList><br />
<appliesTo><br />
<fullId>http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Clinical_Data</fullId><br />
<type>Class</type><br />
</appliesTo><br />
</appliesToList><br />
</noteBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
==== A single 'New Term Proposal' note ====<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/virtual/notes/1104/</accessedResource><br />
<accessDate>2010-04-26 18:13:24.407 PDT</accessDate><br />
<data><br />
<list><br />
<noteBean><br />
<id>Note_f8bb4dc0-10b3-48b9-ab69-79aed042c0ff</id><br />
<ontologyId>1104</ontologyId><br />
<type>ProposalForCreateEntity</type><br />
<author>1234</author><br />
<created>1272319359680</created><br />
<updated>1272319377224</updated><br />
<subject>Test Proposal Reply</subject><br />
<body>Testing new term submission</body><br />
<appliesToList><br />
<appliesTo><br />
<ontologyId>1104</ontologyId><br />
<type>Ontology</type><br />
</appliesTo><br />
</appliesToList><br />
<values><br />
<ProposalForCreateEntity><br />
<reasonForChange>Bad data</reasonForChange><br />
<contactInfo>palexander@stanford.edu</contactInfo><br />
<id>TERM_1100</id><br />
<preferredName>New Term</preferredName><br />
<definition>Test new definition</definition><br />
<synonyms><br />
<string>best term</string><br />
<string>amazing term</string><br />
<string>great term</string><br />
</synonyms><br />
<parent><br />
<string>http://www.owl-ontologies.com/2009/9/24/Ontology1253802770.owl#Summary</string><br />
</parent><br />
</ProposalForCreateEntity><br />
</values><br />
</noteBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
==== A single 'Change Relationship/Hierarchy Proposal' note ====<br />
<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/virtual/notes/1104</accessedResource><br />
<accessDate>2010-04-26 18:21:52.474 PDT</accessDate><br />
<data><br />
<noteBean><br />
<id>Note_b4e749c8-5ca7-414f-a123-acd16ba656fe</id><br />
<ontologyId>1104</ontologyId><br />
<type>ProposalForChangeHierarchy</type><br />
<author>1234</author><br />
<created>1272331290991</created><br />
<updated>1272331295114</updated><br />
<subject>Change Relationship</subject><br />
<body>Testing change hierarchy</body><br />
<appliesToList><br />
<appliesTo><br />
<fullId>http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Clinical_Data</fullId><br />
<type>Class</type><br />
</appliesTo><br />
</appliesToList><br />
<values><br />
<ProposalForChangeHierarchy><br />
<reasonForChange>Incorrect data</reasonForChange><br />
<contactInfo>palexander@stanford.edu/contactInfo><br />
<relationshipTarget><br />
<string>http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Software</string><br />
</relationshipTarget><br />
<oldRelationshipTarget><br />
<string>isa</string><br />
</oldRelationshipTarget><br />
</ProposalForChangeHierarchy><br />
</values><br />
</noteBean><br />
</data><br />
</success><br />
</pre><br />
<br />
==== A single 'Property Value Change Proposal' note ====<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/virtual/notes/1104</accessedResource><br />
<accessDate>2010-04-26 18:25:30.465 PDT</accessDate><br />
<data><br />
<noteBean><br />
<id>Note_8cfde654-2c2c-42e3-8187-0f6c05c6deff</id><br />
<ontologyId>1104</ontologyId><br />
<type>ProposalForPropertyValueChange</type><br />
<author>1234</author><br />
<created>1272331520036</created><br />
<updated>1272331522822</updated><br />
<subject>Tet Property Value Change</subject><br />
<body>Testing a proposal to change a property value</body><br />
<appliesToList><br />
<appliesTo><br />
<fullId>http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Clinical_Data</fullId><br />
<type>Class</type><br />
</appliesTo><br />
</appliesToList><br />
<values><br />
<ProposalForPropertyValueChange><br />
<reasonForChange>The value was entered incorrectly initially</reasonForChange><br />
<contactInfo>palexander@stanford.edu</contactInfo><br />
<newValue>200</newValue><br />
<oldValue>100</oldValue><br />
<propertyId>Cell_Count</propertyId><br />
</ProposalForPropertyValueChange><br />
</values><br />
</noteBean><br />
</data><br />
</success><br />
</pre><br />
<br />
==== A nested thread of 'Comment' notes ====<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/virtual/notes/1104</accessedResource><br />
<accessDate>2010-04-26 13:21:28.104 PDT</accessDate><br />
<data><br />
<list><br />
<noteBean><br />
<id>Note_0a78922c-3d1e-4689-8af8-48d10d4cdaa8</id><br />
<ontologyId>1104</ontologyId><br />
<type>Comment</type><br />
<author>38143</author><br />
<created>1272070868364</created><br />
<updated>1272070868250</updated><br />
<subject>Including clinical trial data as clinical data</subject><br />
<body>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.</body><br />
<createdInOntologyVersion>2</createdInOntologyVersion><br />
<appliesToList><br />
<appliesTo><br />
<fullId>http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Clinical_Data</fullId><br />
<type>Class</type><br />
</appliesTo><br />
</appliesToList><br />
<associated><br />
<noteBean><br />
<id>Note_02e4b8cd-f582-411c-8561-035a0f7d1dd9</id><br />
<ontologyId>1104</ontologyId><br />
<type>Comment</type><br />
<author>38144</author><br />
<created>1272070984380</created><br />
<updated>1272070984243</updated><br />
<subject>RE:Including clinical trial data as clinical data</subject><br />
<body>Not sure I follow the argument here.&amp;nbsp; Clinical trial data is covered under PHI so no distinction there.&amp;nbsp; Data generated in the course of delivering routine standard of care may be needed in the course of a clinical trial.&amp;nbsp; Does this make clinical trial data an overlapping superset of clinical data?</body><br />
<createdInOntologyVersion>2</createdInOntologyVersion><br />
<appliesToList><br />
<appliesTo><br />
<noteId>Note_0a78922c-3d1e-4689-8af8-48d10d4cdaa8</noteId><br />
<type>Note</type><br />
</appliesTo><br />
</appliesToList><br />
<associated><br />
<noteBean><br />
<id>Note_6bdc5fae-bd95-492c-ab47-0aaae7a2193a</id><br />
<ontologyId>1104</ontologyId><br />
<type>Comment</type><br />
<author>38143</author><br />
<created>1272070985097</created><br />
<updated>1272070985195</updated><br />
<subject>RE:RE:Including clinical trial data as clinical data</subject><br />
<body>I was only reacting to the definition of BRO:Clinical_Data in the current version: &quot;Any type of data obtained in the course of caring for humans outside of measurements obtained in clinical trials&quot;. I think I&apos;m agreeing with you that clinical trial data should be overlapping clinical data (whether its a superset I&apos;m not sure). So I&apos;m not clear why the definition that is in the current version is there. Somehow this might be related to the fact that BRO:Data_Object is subclassed partly by function (eg clinical data) and partly by data type (eg image). I would think images could also be a type of clinical data.</body><br />
<createdInOntologyVersion>2</createdInOntologyVersion><br />
<appliesToList><br />
<appliesTo><br />
<noteId>Note_02e4b8cd-f582-411c-8561-035a0f7d1dd9</noteId><br />
<type>Note</type><br />
</appliesTo><br />
</appliesToList><br />
</noteBean><br />
<noteBean><br />
<id>Note_1b490c3a-dd19-458a-9446-5184e42d03ab</id><br />
<ontologyId>1104</ontologyId><br />
<type>Comment</type><br />
<author>38145</author><br />
<created>1272070986051</created><br />
<updated>1272070986093</updated><br />
<subject>RE: Including clinical trial data as clinical data</subject><br />
<body>Hi David and all,&lt;br&gt;&lt;br&gt;Clinical Trial Data should probably be dealt with separately from Clinical Data&lt;br&gt;collected in the course of administering clinical care.&amp;nbsp; The use of Clinical&lt;br&gt;Trial data will be governed by the Consent that the patient signs as part of the&lt;br&gt;IRB Protocol that is set up to allow its collection, while the use Clinical Care&lt;br&gt;Data will be governed by the HIPAA notification that the patient receives, as&lt;br&gt;well as any IRB Protocols set up for the research involved.&lt;br&gt;</body><br />
<createdInOntologyVersion>2</createdInOntologyVersion><br />
<appliesToList><br />
<appliesTo><br />
<noteId>Note_02e4b8cd-f582-411c-8561-035a0f7d1dd9</noteId><br />
<type>Note</type><br />
</appliesTo><br />
</appliesToList><br />
</noteBean><br />
</associated><br />
</noteBean><br />
</associated><br />
</noteBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Creating Notes in BioPortal =<br />
BioPortal uses ontology notes to describe a variety of user-specified comments and metadata on ontology, including new-term proposals, proposals for changes, comments and questions about classes, and so on.<br />
<br />
== BioPortal and REST Principles ==<br />
BioPortal utilizes REST principles to create, read, update, and delete resources. The following service documentation uses the HTTP POST method to create notes in the BioPortal system. For more information, please see [http://www.w3.org/Protocols/rfc2616/rfc2616-sec9.html W3C's documentation on HTTP methods].<br />
<br />
== Types of notes in BioPortal ==<br />
The following are the types of notes in BioPortal. Please, email us at [mailto:support@bioontology.org support@bioontology.org] if you have suggestions for other note types (or specific parameters for the notes).<br />
<br />
* Basic comments (as they are in BioPortal currently)<br />
* Proposals <br />
** New term proposal<br />
** New relationship proposal<br />
** New attribute value proposal<br />
<br />
=== Creating a 'Comment' note ===<br />
<br />
* '''Signature (HTTP POST)''': ./virtual/notes/{ontology virtual id}?type=Comment&appliesto={appliestoid}&appliestotype={appliestotype}&subject={subject}&content={content}&author={author}&email={email_address}<br />
* '''Alt Signature (HTTP POST)''': ./notes/{ontology version id}?type=Comment&appliesto={appliestoid}&appliestotype={appliestotype}&subject={subject}&content={content}&author={author}&email={email_address}<br />
* '''Description''': creates a new note of the type 'Comment'<br />
* '''Arguments''':<br />
** type=Comment - the type of note to create.<br />
** appliesto={appliestoid} - The id of the thing to associate the note with. This can be a class (term), individual, property, or another note. For classes, individuals, and properties, the specified id must exist in the target ontology. URIs must be URL-encoded.<br />
** appliestotype={Ontology|Class|Individual|Property|Note} - The type of the thing that the note is associated with.<br />
** subject={subject} - The subject for the comment.<br />
** content={content} - The content of the comment.<br />
** author={authorid} - The author's BioPortal user id.<br />
** status={status} - Status for this notes. The Changes and Annotation Ontology provides a default set of statuses for proposals (Submitted, Rejected, Under Discussion, Under Review, Approved, Rejected, Implemented, Published) but the service also accepts arbitrary strings.<br />
<br />
=== Creating a 'New Term Proposal' proposal ===<br />
<br />
* '''Signature (HTTP POST)''': ./virtual/notes/{ontology virtual id}?type=ProposalForCreateEntity&appliesto={appliestoid}&appliestotype=Ontology&subject={subject}&reasonforchange={reasonforchange}&author={author}&termdefinition={definition}&termparent={termparent}&termpreferredname={preferredname}&email={email_address}<br />
* '''Alt Signature (HTTP POST)''': ./notes/{ontology version id}?type=ProposalForCreateEntity&appliesto={appliestoid}&appliestotype=Ontology&subject={subject}&reasonforchange={reasonforchange}&author={author}&termdefinition={definition}&termparent={termparent}&termpreferredname={preferredname}&email={email_address}<br />
* '''Description''': creates a new note of the type 'New Term Proposal'<br />
* '''Arguments''' (* required):<br />
** * type=ProposalForCreateEntity - the type of note to create.<br />
** * appliesto={appliestoid} - The id of the thing to associate the note with. This can be a class (term), individual, property, or another note. For classes, individuals, and properties, the specified id must exist in the target ontology. URIs must be URL-encoded.<br />
** * appliestotype={Ontology|Class} - The type of the thing that the note is associated with.<br />
** * author={authorid} - The author's BioPortal user id.<br />
** * reasonforchange={reason for change} - An explanation for why the proposal is being made.<br />
** * termpreferredname={preferredname} - Preferred name for the new term.<br />
** * termdefinition={definition} - Definition for the new term.<br />
** * termparent={termparent} - ID for the parent of the new term. Must be a valid IRI or 'root' to include the term at the root of the ontology.<br />
** subject={subject} - The subject for the comment.<br />
** content={content} - The content of the comment.<br />
** contactinfo={contact information} - Contact information for the entity making the request.<br />
** termsynonyms={synonym1,synonym2,synonym3} - Synonyms for the new term. Can be a single entry or comma-separated list.<br />
** status={status} - Status for this notes. The Changes and Annotation Ontology provides a default set of statuses for proposals (Submitted, Rejected, Under Discussion, Under Review, Approved, Rejected, Implemented, Published) but the service also accepts arbitrary strings.<br />
* '''Removed Arugments''' (no longer used):<br />
** newtermid={termid} - Proposed or generated id for the new term.<br />
*** This has been removed to allow for automatic generation of temporary URI ids for use with terms. This will allow you to refer to a term immediately after creating a new term proposal.<br />
<br />
=== Creating a 'Change Relationship/Hierarchy' proposal ===<br />
<br />
* '''Signature (HTTP POST)''': ./virtual/notes/{ontology virtual id}?type=ProposalForChangeHierarchy&appliesto={appliestoid}&appliestotype={appliestotype}&subject={subject}&content={content}&author={author}&newtermdefinition={definition}&newtermid={termid}&newtermparent={parent}&newtermpreferredname={preferredname}&newtermsynonyms={listofsynonyms}&email={email_address}<br />
* '''Alt Signature (HTTP POST)''': ./notes/{ontology version id}?type=ProposalForChangeHierarchy&appliesto={appliestoid}&appliestotype={appliestotype}&subject={subject}&content={content}&author={author}&newtermdefinition={definition}&newtermid={termid}&newtermparent={parent}&newtermpreferredname={preferredname}&newtermsynonyms={listofsynonyms}&email={email_address}<br />
* '''Description''': creates a new note of the type 'Comment'<br />
* '''Arguments''':<br />
** type=ProposalForChangeHierarchy - the type of note to create.<br />
** appliesto={appliestoid} - The id of the thing to associate the note with. This can be a class (term), individual, property, or another note. For classes, individuals, and properties, the specified id must exist in the target ontology. URIs must be URL-encoded.<br />
** appliestotype=Class - The type of the thing that the note is associated with.<br />
** subject={subject} - The subject for the comment.<br />
** content={content} - The content of the comment.<br />
** author={authorid} - The author's BioPortal user id.<br />
** reasonforchange={reason for change} - An explanation for why the proposal is being made.<br />
** contactinfo={contact information} - Contact information for the entity making the request.<br />
** relationshiptype={relationshiptype} - The type of relationship that should be created (is_a, part_of, has_part, etc)<br />
** relationshiptarget={relationshiptarget} - The term to create the relationship with.<br />
** oldrelationshiptarget={oldrelationshiptarget} - The term that the relationship is being changed from (if different than relationshiptarget).<br />
** status={status} - Status for this notes. The Changes and Annotation Ontology provides a default set of statuses for proposals (Submitted, Rejected, Under Discussion, Under Review, Approved, Rejected, Implemented, Published) but the service also accepts arbitrary strings.<br />
<br />
=== Creating a 'Change Property Value' proposal ===<br />
<br />
* '''Signature (HTTP POST)''': ./virtual/notes/{ontology virtual id}?type=ProposalForPropertyValueChange&appliesto={appliestoid}&appliestotype={appliestotype}&subject={subject}&content={content}&author={author}&newpropertyvalue={newvalue}&oldpropertyvalue={oldvalue}&propertyid={propertyid}&email={email_address}<br />
* '''Alt Signature (HTTP POST)''': ./notes/{ontology version id}?type=ProposalForPropertyValueChange&appliesto={appliestoid}&appliestotype={appliestotype}&subject={subject}&content={content}&author={author}&newpropertyvalue={newvalue}&oldpropertyvalue={oldvalue}&propertyid={propertyid}&email={email_address}<br />
* '''Description''': creates a new note of the type 'Change Property Value'<br />
* '''Arguments''':<br />
** type=ProposalForPropertyValueChange - the type of note to create.<br />
** appliesto={appliestoid} - The id of the thing to associate the note with. This can be a class (term), individual, property, or another note. For classes, individuals, and properties, the specified id must exist in the target ontology. URIs must be URL-encoded.<br />
** appliestotype=Property - The type of the thing that the note is associated with.<br />
** subject={subject} - The subject for the comment.<br />
** content={content} - The content of the comment.<br />
** author={authorid} - The author's BioPortal user id.<br />
** reasonforchange={reason for change} - An explanation for why the proposal is being made.<br />
** contactinfo={contact information} - Contact information for the entity making the request.<br />
** newpropertyvalue={newpropertyvalue} - The new value for the property.<br />
** oldpropertyvalue={oldpropertyvalue} - The old value for the property.<br />
** propertyid={propertyid}= The ID of the property to change.<br />
** status={status} - Status for this notes. The Changes and Annotation Ontology provides a default set of statuses for proposals (Submitted, Rejected, Under Discussion, Under Review, Approved, Rejected, Implemented, Published) but the service also accepts arbitrary strings.<br />
<br />
== Updating an Existing Note ==<br />
<br />
* '''Signature (HTTP PUT)''': ./virtual/notes/{ontology virtual id}?noteid={note_id}<br />
* '''Alt Signature (HTTP PUT)''': ./notes/{ontology version id}?noteid={note_id}<br />
* '''Description''': updates an existing note using the given note id.<br />
* '''Arguments:''' (* = required)<br />
** * noteid={note_id} - Id of the note to update.<br />
** archive=true - Archives the note with the given note id.<br />
** archivethread=true - Archives all of the notes that are listed as associated to the given note id plus all of their children.<br />
** unarchive=true - Unarchives the note with the given note id.<br />
** unarchivethread=true - Unarchives all of the notes that are listed as associated to the given note id plus all of their children.<br />
** type=Comment|ProposalForCreateEntity|ProposalForChangeHierarchy|ProposalForPropertyValueChange - the type of note.<br />
** appliesto={appliestoid} - The id of the thing to associate the note with. This can be a class (term), individual, property, or another note. For classes, individuals, and properties, the specified id must exist in the target ontology. URIs must be URL-encoded.<br />
** appliestotype=Property - The type of the thing that the note is associated with.<br />
** subject={subject} - The subject for the note.<br />
** content={content} - The content of the note.<br />
** author={authorid} - The author's BioPortal user id.<br />
** status={status} - Status for this notes. The Changes and Annotation Ontology provides a default set of statuses for proposals (Submitted, Rejected, Under Discussion, Under Review, Approved, Rejected, Implemented, Published) but the service also accepts arbitrary strings.<br />
<br />
== Web services to submit Terms ==<br />
* See http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12591BioPortal REST services2013-03-13T18:58:28Z<p>Darren Weber: /* Overview - Using NCBO Technology in Your Project */ Refer to CTS2 wrapper.</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use. See also work on wrapping Bioportal REST services as a [[CTS2_BioPortal_wrapper]].<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
Ontology files that were successfully parsed have a value of 3 for the <statusId> attribute in the XML response.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== Get Metrics for an ontology version ==<br />
* '''Signature''': ./ontologies/metrics/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40133?apikey=YourAPIKey<br />
* More documentation: http://www.bioontology.org/wiki/index.php/Ontology_Metrics<br />
<br />
== Get all the namespace prefixes for an ontology version ==<br />
* '''Signature''': ./ontologies/namespaces/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/namespaces/44450?apikey=YourAPIKey<br />
<br />
== List all ontology categories == <br />
* '''Signature''': ./categories?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories?apikey=YourAPIKey<br />
<br />
== List all ontology groups ==<br />
* '''Signature''': ./groups?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups?apikey=YourAPIKey<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
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.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** 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.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
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).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}/{concept id}&apikey={YourAPIKey}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}?conceptid={uri-encoded concept id}<br />
** To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** 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<br />
** 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.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
Examples using Alt Signature<br />
* http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
Examples using Alt Virtual Signature<br />
* http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
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. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
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.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id},{concept id},...,{concept id}&apikey=YourAPIKey<br />
** '''NOTE''': To ensure that the Web service works within your application, url-encode the concept id as some ontologies may contain terms where the concept id is a URI.<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/?conceptid=NEMO_0000024&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/47799/?conceptid=NEMO_1398000&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=CTS2_BioPortal_wrapper&diff=12590CTS2 BioPortal wrapper2013-03-13T18:55:40Z<p>Darren Weber: Change reference to widget page to the generic page on using Bioportal.</p>
<hr />
<div>== Introduction ==<br />
<br />
This page contains a summary of the current state of the CTS2 / BioPortal wrapper. It covers the goals of the project, the approach and methodology that was used and finishes with a summary of the current state of the project, a discussion of some of the issues that were encountered and a list of what remains to be resolved.<br />
<br />
== Project Goals ==<br />
The [http://bioportal.bioontology.org/ NCBO BioPortal] was created "to access and share ontologies that are actively used in biomedical communities." To meet this goal, BioPortal has developed the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services BioPortal REST API], which can be used to access BioPortal using http. One of the primary applications of this API are web browsers that can use Ajax widgets to browse and access ontology content for a variety of uses (see [[Using_NCBO_Technology_In_Your_Project]]).<br />
<br />
The Common Terminology Services 2 (CTS2) specification was created in response to a set of requirements published by Health Level Seven (HL7) and an RFP that was issued by the Object Management Group. This Platform Independent Model (PIM) was designed to be fully compatible with Fielding's notion of the RESTful Architectural Style and one of the key Platform Specific Models (PSM's) is based on http/REST. The model, documentation, schema and WADL can be found on the home page of this wiki.<br />
<br />
The NCBO community believes that it will be advantageous to be able to access the BioPortal content through both the existing BioPortal REST API and, where appropriate, the nascent CTS2 REST API. The BioPortal API was used as an one of the inputs to the CTS2 specification. The CTS2 specification was heavily influenced by the LexGrid terminology model and the LexEVS service specification and LexEVS is one of the back end components of the BioPortal implementation. There were, however, decisions made in the CTS2 specification that weren't fully compatible with the existing BioPortal model. <br />
<br />
The purpose of this project was to create a mapping between the existing BioPortal API and the corresponding components of the CTS2 REST specification to determine where potential issues and incompatibilities may lie and to use the results of this evaluation to determine (a) the best approach would be to creating a complete, robust CTS2 REST wrapper (b) uncover errors and omissions in the CTS2 specification and (c) to come up with recommendations about how the BioPortal REST API might be enhanced or improved.<br />
<br />
== Approach ==<br />
We began by gathering a list of the key BioPortal resources - Ontology, AbstractConcept, Class, Property and Instance along with various lists. Lacking a formal XML Schema for these resources, we used a combination of sample content from the REST service and the java bean classes for each of the resources to assemble lists of the properties for each of these resources, their types and, where it could be determined their cardinality. We went through these lists, gathering sample input from the REST API - both in form of lists of elements and individual elements. <br />
<br />
There were a number of conceptual issues that were uncovered in this process, including:<br />
* CTS2 has a notions of ''Code System'' and ''Code System Version''. While BioPortal has similar concepts - "virtual ontology" and "ontology" in the ontology interface and "ontology" and "ontology version" in the search interface, the "virtual ontology" has no attributes besides its identifier. <br />
* BioPortal treats both full ontologies and subsets derived from full ontologies as instances of "ontology". Lists and queries apply to both types of resource - [[bpr:ontologies|a list of the latest version of ontologies]] returns both the ontologies themselves as well as all subsets. Similarly, term queries return both the ontology in which the term is defined and any subsets that include that term. CTS2 treats Code Systems (ontologies) and Value Sets (subsets) as separate resources. Lists and queries go against one or the other resource but not both.<br />
* BioPortal assumes that all terms are instances of exactly one of "class", "property" or "instance". CTS2 allows ''entity'' (the equivalent of "term") to exist without making this distinction. In addition, while the CTS2 REST model does not clearly show how this could be done, the intent of the CTS2 model is to allow an entity to simultaneously be a Class and Instance, Class and Property, etc.<br />
<br />
We then created a [[CTS2_BioPortal_Rest_mapping|map]] from each of the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services BioPortal REST signatures] and the equivalent [http://informatics.mayo.edu/cts2/index.php/Rest_Signatures CTS2 REST signature(s)], wherever possible.<br />
<br />
These documents were then used to construct a CTS2 REST Server that used the BioPortal REST services as the back end implementation. In addition, we took a number of the interesting BioPortal Ajax widgets and modified them to use the CTS2 REST api instead. A synopsis of the REST services that were implemented can be found [[BioPortal_wrapper_summary|here]] and a list of the translated Ajax Widgets can be found [http://informatics.mayo.edu/cts2/index.php/BioPortal_Ajax here ].<br />
<br />
== Results ==<br />
As expected, a number of issues were encountered in this process including:<br />
* This is the link to the subset of the CTS2 rest service was implemented is in the [[CTS2_BioPortal_wrapper_summary| CTS2 BioPortal wrapper]]<br />
* Resource/Resource Version mismatch - discussed earlier<br />
* MetaOntology and MetaOntology mapping - BioPortal has several enumerations (Category, Group, Status) that aren't first class ontologies and, even if they were, might be better served were they drawn from OMV or a similar resource<br />
* URI's - BioPortal has its own URI's but many of these ontologies have one or more "official" URI's drawn from outside sources.<br />
* REST hyperlinks - one of the key aspects of the REST architectural style is to provide the ability to navigate the web of resources without having to know how to construct URI's. As an example, an entity reference in CTS2 (e.g. http://informatics.mayo.edu:19280/exist/cts2/codesystem/SCT/version/SCT_2010_01_31/entity/900000000000002006) carries in it a link to both the code system and the code system version in which it is described. Similarly, the descriptionType, language and any other attribute that references an ontology component has the potential for containing a hyperlink. Constructing some of these hyperlinks from the BioPortal REST service can be non-trivial. <br />
<br />
The proposed next steps would be to review the mapping and determine whether to:<br />
(a) Complete the remaining tasks using the current wrapper paradigm<br />
(b) Re-implement the interfaces against the lower level BioPortal interfaces and databases<br />
(c) Produce a hybrid for the time being and focus on an RDF based implementation.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=CTS2_BioPortal_wrapper&diff=12589CTS2 BioPortal wrapper2013-03-13T18:48:42Z<p>Darren Weber: Add wiki link to NCBO Widget documentation</p>
<hr />
<div>== Introduction ==<br />
<br />
This page contains a summary of the current state of the CTS2 / BioPortal wrapper. It covers the goals of the project, the approach and methodology that was used and finishes with a summary of the current state of the project, a discussion of some of the issues that were encountered and a list of what remains to be resolved.<br />
<br />
== Project Goals ==<br />
The [http://bioportal.bioontology.org/ NCBO BioPortal] was created "to access and share ontologies that are actively used in biomedical communities." To meet this goal, BioPortal has developed the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services BioPortal REST API], which can be used to access BioPortal using http. One of the primary applications of this API are web browsers that can use Ajax widgets to browse and access ontology content for a variety of uses (see [[NCBO_Widgets]]).<br />
<br />
The Common Terminology Services 2 (CTS2) specification was created in response to a set of requirements published by Health Level Seven (HL7) and an RFP that was issued by the Object Management Group. This Platform Independent Model (PIM) was designed to be fully compatible with Fielding's notion of the RESTful Architectural Style and one of the key Platform Specific Models (PSM's) is based on http/REST. The model, documentation, schema and WADL can be found on the home page of this wiki.<br />
<br />
The NCBO community believes that it will be advantageous to be able to access the BioPortal content through both the existing BioPortal REST API and, where appropriate, the nascent CTS2 REST API. The BioPortal API was used as an one of the inputs to the CTS2 specification. The CTS2 specification was heavily influenced by the LexGrid terminology model and the LexEVS service specification and LexEVS is one of the back end components of the BioPortal implementation. There were, however, decisions made in the CTS2 specification that weren't fully compatible with the existing BioPortal model. <br />
<br />
The purpose of this project was to create a mapping between the existing BioPortal API and the corresponding components of the CTS2 REST specification to determine where potential issues and incompatibilities may lie and to use the results of this evaluation to determine (a) the best approach would be to creating a complete, robust CTS2 REST wrapper (b) uncover errors and omissions in the CTS2 specification and (c) to come up with recommendations about how the BioPortal REST API might be enhanced or improved.<br />
<br />
== Approach ==<br />
We began by gathering a list of the key BioPortal resources - Ontology, AbstractConcept, Class, Property and Instance along with various lists. Lacking a formal XML Schema for these resources, we used a combination of sample content from the REST service and the java bean classes for each of the resources to assemble lists of the properties for each of these resources, their types and, where it could be determined their cardinality. We went through these lists, gathering sample input from the REST API - both in form of lists of elements and individual elements. <br />
<br />
There were a number of conceptual issues that were uncovered in this process, including:<br />
* CTS2 has a notions of ''Code System'' and ''Code System Version''. While BioPortal has similar concepts - "virtual ontology" and "ontology" in the ontology interface and "ontology" and "ontology version" in the search interface, the "virtual ontology" has no attributes besides its identifier. <br />
* BioPortal treats both full ontologies and subsets derived from full ontologies as instances of "ontology". Lists and queries apply to both types of resource - [[bpr:ontologies|a list of the latest version of ontologies]] returns both the ontologies themselves as well as all subsets. Similarly, term queries return both the ontology in which the term is defined and any subsets that include that term. CTS2 treats Code Systems (ontologies) and Value Sets (subsets) as separate resources. Lists and queries go against one or the other resource but not both.<br />
* BioPortal assumes that all terms are instances of exactly one of "class", "property" or "instance". CTS2 allows ''entity'' (the equivalent of "term") to exist without making this distinction. In addition, while the CTS2 REST model does not clearly show how this could be done, the intent of the CTS2 model is to allow an entity to simultaneously be a Class and Instance, Class and Property, etc.<br />
<br />
We then created a [[CTS2_BioPortal_Rest_mapping|map]] from each of the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services BioPortal REST signatures] and the equivalent [http://informatics.mayo.edu/cts2/index.php/Rest_Signatures CTS2 REST signature(s)], wherever possible.<br />
<br />
These documents were then used to construct a CTS2 REST Server that used the BioPortal REST services as the back end implementation. In addition, we took a number of the interesting BioPortal Ajax widgets and modified them to use the CTS2 REST api instead. A synopsis of the REST services that were implemented can be found [[BioPortal_wrapper_summary|here]] and a list of the translated Ajax Widgets can be found [http://informatics.mayo.edu/cts2/index.php/BioPortal_Ajax here ].<br />
<br />
== Results ==<br />
As expected, a number of issues were encountered in this process including:<br />
* This is the link to the subset of the CTS2 rest service was implemented is in the [[CTS2_BioPortal_wrapper_summary| CTS2 BioPortal wrapper]]<br />
* Resource/Resource Version mismatch - discussed earlier<br />
* MetaOntology and MetaOntology mapping - BioPortal has several enumerations (Category, Group, Status) that aren't first class ontologies and, even if they were, might be better served were they drawn from OMV or a similar resource<br />
* URI's - BioPortal has its own URI's but many of these ontologies have one or more "official" URI's drawn from outside sources.<br />
* REST hyperlinks - one of the key aspects of the REST architectural style is to provide the ability to navigate the web of resources without having to know how to construct URI's. As an example, an entity reference in CTS2 (e.g. http://informatics.mayo.edu:19280/exist/cts2/codesystem/SCT/version/SCT_2010_01_31/entity/900000000000002006) carries in it a link to both the code system and the code system version in which it is described. Similarly, the descriptionType, language and any other attribute that references an ontology component has the potential for containing a hyperlink. Constructing some of these hyperlinks from the BioPortal REST service can be non-trivial. <br />
<br />
The proposed next steps would be to review the mapping and determine whether to:<br />
(a) Complete the remaining tasks using the current wrapper paradigm<br />
(b) Re-implement the interfaces against the lower level BioPortal interfaces and databases<br />
(c) Produce a hybrid for the time being and focus on an RDF based implementation.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12460BioPortal REST services2012-09-17T22:53:06Z<p>Darren Weber: /* Get Metrics for an ontology version */ fix the signature syntax.</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== Get Metrics for an ontology version ==<br />
* '''Signature''': ./ontologies/metrics/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40133?apikey=YourAPIKey<br />
* More documentation: http://www.bioontology.org/wiki/index.php/Ontology_Metrics<br />
<br />
== Get all the namespace prefixes for an ontology version ==<br />
* '''Signature''': ./ontologies/namespaces/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/namespaces/44450?apikey=YourAPIKey<br />
<br />
== List all ontology categories == <br />
* '''Signature''': ./categories?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories?apikey=YourAPIKey<br />
<br />
== List all ontology groups ==<br />
* '''Signature''': ./groups?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups?apikey=YourAPIKey<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
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.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** 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.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
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).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** 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<br />
** 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.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
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. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
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.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id},{concept id},...,{concept id}&apikey=YourAPIKey<br />
** '''NOTE''': To ensure that the Web service works within your application, url-encode the concept id as some ontologies may contain terms where the concept id is a URI.<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/?conceptid=NEMO_0000024&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/47799/?conceptid=NEMO_1398000&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12447BioPortal REST services2012-09-06T22:35:24Z<p>Darren Weber: /* Services to access ontologies and ontology versions */ Add documentation for the 'namespaces' of an ontology version.</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== Get Metrics for an ontology version ==<br />
* '''Signature''': ./ontologies/metrics?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40133?apikey=YourAPIKey<br />
* More documentation: http://www.bioontology.org/wiki/index.php/Ontology_Metrics<br />
<br />
== Get all the namespace prefixes for an ontology version ==<br />
* '''Signature''': ./ontologies/namespaces/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/namespaces/44450?apikey=YourAPIKey<br />
<br />
== List all ontology categories == <br />
* '''Signature''': ./categories?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories?apikey=YourAPIKey<br />
<br />
== List all ontology groups ==<br />
* '''Signature''': ./groups?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups?apikey=YourAPIKey<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
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.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** 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.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
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).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** 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<br />
** 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.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
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. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
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.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id},{concept id},...,{concept id}&apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/?conceptid=NEMO_0000024&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/47799/?conceptid=NEMO_1398000&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12440BioPortal REST services2012-09-05T19:24:24Z<p>Darren Weber: /* RDF Term Service */ revised ontology version term so it works</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
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.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** 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.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
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).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** 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<br />
** 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.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
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. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
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.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id},{concept id},...,{concept id}&apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/?conceptid=NEMO_0000024&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/47799/?conceptid=NEMO_1398000&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12439BioPortal REST services2012-09-05T19:18:23Z<p>Darren Weber: /* RDF Term Service */</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
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.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** 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.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
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).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** 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<br />
** 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.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
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. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
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.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id},{concept id},...,{concept id}&apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/?conceptid=NEMO_0000024&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/42743/?conceptid=NEMO_0000023&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12438BioPortal REST services2012-09-05T19:16:25Z<p>Darren Weber: /* RDF Term Service */ add explicit 'conceptid=' parameter</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
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.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** 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.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
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).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** 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<br />
** 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.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
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. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
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.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/conceptid={concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/conceptid={concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/conceptid={concept id},{concept id},...,{concept id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/conceptid=NEMO_0000024?apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/42743/conceptid=NEMO_0000023?apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12422BioPortal REST services2012-08-02T21:51:39Z<p>Darren Weber: /* Get an instance and its property/value pairs */</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
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.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** 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.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
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).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** 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<br />
** 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.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
== Get siblings of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&apikey={YourAPIKey}&[&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
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. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
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.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_0000024?apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_0000023?apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12421BioPortal REST services2012-08-02T21:48:00Z<p>Darren Weber: /* Get all direct instances for a given term */ conceptid is not an optional parameter</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
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.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** 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.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
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).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** 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<br />
** 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.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&apikey={YourAPIKey}]<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
== Get siblings of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&apikey={YourAPIKey}&[&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
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. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
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.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_0000024?apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_0000023?apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Widgets&diff=12410NCBO Widgets2012-07-18T20:03:50Z<p>Darren Weber: /* Term-selection field on a form */ Adding documentation for object type attributes in auto-complete widgets</p>
<hr />
<div>NCBO widgets are the HTML or Javascript code that you can put on your Web site or Web form to use BioPortal functionality there. Using NCBO Widgets is just one of [[Using_NCBO_Technology_In_Your_Project|the ways in which you can use the NCBO technology directly on your Web site or in your application]].<br />
<br />
= Types of NCBO Widgets and use cases = <br />
* '''[[#Term-selection field on a form|Term-selection field on a form]]''': You can add a text field to your Web form that will let users enter a term from a controlled vocabulary (e.g., terms from a single ontology)<br />
** ''Example use case'': Suppose you are running a tissue microarray database and users upload sample descriptions to your database using a web form. There is usually a field for the user to enter the diagnosis for the tissue sample that she is entering. Usually, this field is a text-box or a drop down menu populated with a list of controlled terms. The free text-box is prone to errors, the drop-down gets too unwieldy with large terminologies. Using the NCBO term-selection widget to have users easily select a term from an ontology or controlled vocabulary (such as the NCI Thesaurus) to fill in the field. For example, when the user starts typing "cutaneous me", the term "cutaneous melanoma" pops up.<br />
** ''What does the term-selection field get you'': <br />
*** Look-ahead so that you don't need to type the whole term<br />
*** Controlled vocabulary provides consistency of the way different users use the term (If you want to put "Malignant melanoma", it will always be the same term from NCIT, regardless of how a user started typing it<br />
*** When a new version of your controlled vocabulary becomes available in BioPortal, the widget will automatically use that new version.<br />
*'''[[#Ontology search widget|Ontology search widget]]''': You can add to your Web site a search box that searches a specific BioPortal ontology. When the user selects the term of interest (with the help of the look-ahead feature), he can jump to the BioPortal page for the corresponding concept in BioPortal.<br />
*'''[[#Feed widget|Feed widget]]''': you can put a widget on your site that will have a live feed of all the changes to your ontology of interest, such as uploads of a new version, comments from other users, new mappings for concepts in your ontology.<br />
*'''[[#Ontology visualization widget|Ontology visualization widget]]''': You can put a widget on your Web site that visualizes your entire ontology of interest, or some part of it, as on the [http://bioportal.bioontology.org/visualize/39478#t_tab1: "Visualize" tab in BioPortal].<br />
*<font color="red">**NEW**</font> '''[[#OntologyTree Widget|OntologyTree Widget]]''': You can put a widget on your Web site that displays the ontology tree, or some part of it, as on the [http://bioportal.bioontology.org/visualize/39478#t_tab1: "Visualize" tab in BioPortal].<br />
<br />
= How to use NCBO Widgets=<br />
<br />
The easiest way to add any NCBO widget to your HTML page or Web form is by following these steps:<br />
* Find your ontology of interest in the [http://bioportal.bioontology.org/ontologies list of BioPortal ontologies] (e.g., NCI Thesaurus)<br />
* Click on the ontology name to get to the page with '''Details''' for that ontology (e.g., the [http://bioportal.bioontology.org/ontologies/39478 Details for NCI Thesaurus])<br />
* On the Ontology Details page, go to '''Ontology Widgets''' tab<br />
* Select the widget you want<br />
* Click the button below the widgets to get instructions for the specific widget<br />
<br />
== Term-selection field on a form ==<br />
<br />
To add a field to your form that lets the user fetch a term from your ontology of interest, do the following:<br />
<ul><br />
<li>Download the [http://bioportal.bioontology.org/javascripts/widgets/form_complete.js <b>form_complete.js file</b>] and put it on your server<br />
</li><br />
<li>In the header for the page where you want the form field, include the <b>form_complete.js</b> file<br />
</li><br />
<li>On your form, for the fields where you want to use the term-selection widget, specify the field's class in the following format: <code>bp_form_complete-{ontology_id_list}-{value}</code><br />
<ul><br />
<li>For example, <code>bp_form_complete-1032-uri</code> will use NCI Thesaurus (ontology id is 1032) and will put the term URI in the field after the user selects the term from the pull-down list.<br />
<ul><br />
<li><br />
<b>Note:</b> In addition to single ontology ids, you can use a list:<br><br />
<code>bp_form_complete-1032,1089-uri</code><br />
</li><br />
<li><br />
<b>OR</b> use 'all' to search across all BioPortal ontologies:<br><br />
<code>bp_form_complete-all-uri</code><br />
</li><br />
</ul><br />
</li><br />
<li>You can use the following parameters to select which value will be placed into the user-visible input field:<br />
<ul><br />
<li><br />
<code>uri</code> : put the complete URI of the term (e.g., "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Neoplasm");<br />
</li><br />
<li><br />
<code>shortid</code> : put the short id of the term, as used in BioPortal (e.g., "Common_Neoplasm");<br />
</li><br />
<li><br />
<code>name</code> : put the preferred name of the term (e.g., "Common Neoplasm");<br />
</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
==== Hidden form elements auto-generated ====<br />
In addition to the input element you defined, there are four hidden form elements that are created and then set when a user selects a term from the list. For example, if you create a field with this code:<br />
<pre><br />
&lt;input type="text" name="a" class="bp_form_complete-all-uri" size="100"/&gt;<br />
</pre><br />
The 'name' attribute is used to create the four following fields (note how the 'a' from the name attribute is appended to the id attribute):<br />
<pre><br />
&lt;input type="hidden" id="a_bioportal_preferred_name"&gt;<br />
&lt;input type="hidden" id="a_bioportal_concept_id"&gt;<br />
&lt;input type="hidden" id="a_bioportal_ontology_id"&gt;<br />
&lt;input type="hidden" id="a_bioportal_full_id"&gt;<br />
</pre><br />
<br />
==== Optional attributes ====<br />
<ul><br />
<li><br />
<strong>Include term definitions.</strong><br />
Use <code>data-bp_include_definitions="true"</code>.<br />
This will display definitions with the list of terms that are returned. For example, use this code to display search results for 'heart' terms, with<br />
definitions, in the NCI Thesaurus.<br />
<br/><br />
<code><input type="text" name="m" data-bp_include_definitions="true" class="bp_form_complete-1032-name"/></code><br />
</li><br />
<li><br />
<strong>Limit lookup to terms below a root term.</strong><br />
Use <code>data-bp_search_branch="{conceptid}"</code><br />
(replace {conceptid} with the term id for the term to use as the <br />
branch root). For example, use this code to limit the search for 'heart' to terms <br />
within the 'Anatomic_Structure_System_or_Substance'<br />
branch of the NCI Thesaurus.<br />
<br/><br />
<code><input type="text" name="n" data-bp_search_branch="Anatomic_Structure_System_or_Substance" class="bp_form_complete-1032-name"/></code><br />
</li><br />
<br />
<li><strong>Object types</strong><br />
<ul><br />
<br />
<li><br />
<strong>Search 'class' and 'property' objects.</strong><br />
Use <code>data-bp_objecttypes="class,property".</code><br />
For example, use this code to search for 'function' among both 'class' and<br />
'property' objects from the "Adverse Event Reporting Ontology".<br />
<br/><br />
<code><input type="text" name="o" data-bp_objecttypes="class,property" class="bp_form_complete-1580-uri"/></code><br />
</li><br />
<li><br />
<strong>Search only 'property' objects.</strong><br />
Use <code>data-bp_objecttypes="property".</code><br />
For example, use this code to search for 'function' among only <br />
'property' objects from the "Adverse Event Reporting Ontology".<br />
<br/><br />
<code><input type="text" name="p" data-bp_objecttypes="property" class="bp_form_complete-1580-uri"/></code><br />
</li><br />
<li><br />
<strong>Search 'class' and 'individual' objects.</strong><br />
Use <code>data-bp_objecttypes="class,individual".</code><br />
For example, use this code to search for 'seizure' among 'class' and<br />
'individual' objects from the "Adverse Event Reporting Ontology".<br />
<br/><br />
<code><input type="text" name="q" data-bp_objecttypes="class,individual" class="bp_form_complete-1580-uri"/></code><br />
</li><br />
<li><br />
<strong>Only search 'individual' objects.</strong><br />
Use <code>data-bp_objecttypes="individual".</code><br />
For example, use this code to this search for 'seizure' only among <br />
'individual' objects from the "Adverse Event Reporting Ontology".<br />
<br/><br />
<code><input type="text" name="r" data-bp_objecttypes="individual" class="bp_form_complete-1580-uri"/></code><br />
</li><br />
</ul><br />
</ul><br />
<br />
</ul><br />
<br />
== Ontology search widget ==<br />
<br />
To add a search widget to your HTML page that searches a specific ontology, do the following:<br />
<ul><br />
<li>Download the [http://bioportal.bioontology.org/javascripts/widgets/quick_jump.js <b>quick_jump.js file</b>] and put it on your server<br />
</li><br />
<li>Copy the code below and paste it to your HTML page. <br />
<pre><br />
<div id="bp_quick_jump"></div><br />
<script type="text/javascript"><br />
var BP_ontology_id = "1016";<br />
</script><br />
<script src="quick_jump.js" type="text/javascript" charset="utf-8"><br />
</script><br />
</pre><br />
</li><br />
<li><br />
<b>Note:</b> If you would like to use Quick Jump across multiple ontologies:<br />
<ul><br />
<li>You can enter a comma-separated list of ontology ids:<br><br />
var BP_ontology_id = "1032,1089";<br />
</li><br />
<li>You cans set the variable to 'all' to search all ontologies in BioPortal:<br><br />
var BP_ontology_id = "all";<br />
</li><br />
</ul><br />
</li><br />
<li>In the code that you just pasted, make sure to change the path to the quick_jump.js file to point to the location where you put the file (relative to your HTML file)<br />
<ul><br />
<li>For example, if you put the quick_jump.js file in the same directory as your HTML file, this is the code you would use:<br />
<pre><br />
<script type="text/javascript"><br />
var BP_ontology_id = "1032";<br />
</script><br />
<script src="quick_jump.js" type="text/javascript" charset="utf-8"></script><br />
</pre><br />
</li><br />
</ul><br />
</li><br />
<li><br />
To limit the term lookup to a particular branch of an ontology, include the following Javascript in your page (replace conceptid with the id for the term which you would like to use as the root of your branch): <br />
<code>var BP_search_branch = "{conceptid}";</code><br />
</li><br />
<li><br />
To display definitions with the list of terms that are returned, include the following Javascript in your page: <br />
<code>var BP_include_definitions = true;</code><br />
</li><br />
</ul><br />
<br />
== Feed widget ==<br />
<br />
To add a Feed widget to your HTML page, simple copy the code from the Ontology Widget page for your ontology of interest. Here is a sample:<br />
<br />
<pre><br />
<script type="text/javascript"><br />
var BP_ontology_id = "1032"<br />
</script><br />
<script src="http://bioportal.bioontology.org/javascripts/widgets/feed_widget.js" type="text/javascript" charset="utf-8"></script><br />
</pre><br />
<br />
== Ontology visualization widget ==<br />
To add a widget visualizing your ontology to your HTML page, simple copy the code from the Ontology Widget page for your ontology of interest. Here is a sample:<br />
<br />
<pre><br />
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"<br />
id="FlexoViz" width="100%" height="100%"<br />
codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab"><br />
<param name="movie" value="http://keg.cs.uvic.ca/ncbo/flexviz/FlexoViz.swf" /><br />
<param name="quality" value="high" /><br />
<param name="bgcolor" value="#ffffff" /><br />
<param name="allowScriptAccess" value="always" /><br />
<embed src="http://keg.cs.uvic.ca/ncbo/flexviz/FlexoViz.swf" bgcolor="#ffffff"<br />
width="100%" height="100%" name="FlexoViz" align="middle"<br />
play="true"<br />
loop="false"<br />
quality="high"<br />
allowScriptAccess="always"<br />
type="application/x-shockwave-flash"<br />
flashVars="widget=true&ontology=39478&server=http://rest.bioontology.org/bioportal/"<br />
pluginspage="http://www.adobe.com/go/getflashplayer"><br />
</embed><br />
</object> <br />
</pre><br />
<br />
If you want the visualization to be focused on a particular term in the ontology, you can add the term id to the parameters above. For example, to have the widget focus on Melanoma in NCI Thesaurus, replace the following line in the snippet above:<br />
<pre><br />
flashVars="widget=true&ontology=39478&server=http://rest.bioontology.org/bioportal/"<br />
</pre><br />
<br />
with <br />
<pre><br />
flashVars="widget=true&ontology=39478&nodeid=Melanoma&server=http://rest.bioontology.org/bioportal/"<br />
</pre><br />
<br />
(''note "&nodeid=Melanoma"'')<br />
<br />
== OntologyTree Widget ==<br />
<br />
'''Description'''<br><br />
The OntologyTree widget is an embeddable Flex application that allows a user to interact with a tree browser for ontologies. The widget can be configured to display a list of all the ontologies in BioPortal, allowing the user to select which one to view, or can be setup to view a particular ontology. Additionally, there are several Javascript helper functions for the widget, allowing it to be utilized as a fully functional component in other applications.<br />
<br />
'''Location'''<br><br />
http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf<br />
<br />
'''Parameters'''<br />
* '''ontology''' = The id of the ontology to use, by default it assumes this value is the ontology version id<br />
* '''virtual''' [true|false] - If true then the above ontology parameter is assumed to be a virtual ontology id<br />
* '''canchangeontology''' [true|false] = If false then users can't change the current ontology<br />
* '''canchangeroot''' [true|false] = If true the the user can specify a root concept (using the context menu)<br />
* '''rootconceptid''' = The id of the root concept to show in the tree, leave out to show the ontology roots<br />
* '''server''' = The rest server to use. Defaults to "http://rest.bioontology.org/bioportal/".<br />
* '''redirecturl''' = The url to redirect to for terms and ontologies (in BioPortal). Defaults to "http://bioportal.bioontology.org/".<br />
* '''alerterrors''' [true|false] = If true then errors will be displayed in an annoying popup box.<br />
* '''title''' = The title for the browser window<br />
<br />
'''Embed Example'''<br><br />
Using Javascript (preferred):<br />
<pre><br />
<script src="http://keg.cs.uvic.ca/ncbo/ontologytree/AC_OETags.js" language="javascript"></script><br />
<!--<br />
// -----------------------------------------------------------------------------<br />
// Globals<br />
// Major version of Flash required<br />
var requiredMajorVersion = 9;<br />
// Minor version of Flash required<br />
var requiredMinorVersion = 0;<br />
// Minor version of Flash required<br />
var requiredRevision = 124;<br />
// -----------------------------------------------------------------------------<br />
// --><br />
<br />
// Version check for the Flash Player that has the ability to start Player Product Install (6.0r65)<br />
var hasProductInstall = DetectFlashVer(6, 0, 65);<br />
<br />
// Version check based upon the values defined in globals<br />
var hasRequestedVersion = DetectFlashVer(requiredMajorVersion, requiredMinorVersion, requiredRevision);<br />
<br />
if (hasProductInstall && !hasRequestedVersion) {<br />
// DO NOT MODIFY THE FOLLOWING FOUR LINES<br />
// Location visited after installation is complete if installation is required<br />
var MMPlayerType = (isIE == true) ? "ActiveX": "PlugIn";<br />
var MMredirectURL = window.location;<br />
document.title = document.title.slice(0, 47) + " - Flash Player Installation";<br />
var MMdoctitle = document.title;<br />
<br />
AC_FL_RunContent(<br />
"src", "playerProductInstall",<br />
"FlashVars", "MMredirectURL=" + MMredirectURL + '&MMplayerType=' + MMPlayerType + '&MMdoctitle=' + MMdoctitle + "",<br />
"width", "300",<br />
"height", "100%",<br />
"align", "middle",<br />
"id", "OntologyTree",<br />
"quality", "high",<br />
"bgcolor", "#ffffff",<br />
"name", "OntologyTree",<br />
"allowScriptAccess", "always",<br />
"type", "application/x-shockwave-flash",<br />
"pluginspage", "http://www.adobe.com/go/getflashplayer"<br />
);<br />
} else if (hasRequestedVersion) {<br />
// if we've detected an acceptable version<br />
// embed the Flash Content SWF when all tests are passed<br />
AC_FL_RunContent(<br />
"src", "http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf",<br />
"width", "300",<br />
"height", "100%",<br />
"align", "middle",<br />
"id", "OntologyTree",<br />
"quality", "high",<br />
"bgcolor", "#ffffff",<br />
"name", "OntologyTree",<br />
"allowScriptAccess", "always",<br />
"flashVars", "ontology=&virtual=false&alerterrors=false&canchangeontology=true&rootconceptid=",<br />
"type", "application/x-shockwave-flash",<br />
"pluginspage", "http://www.adobe.com/go/getflashplayer"<br />
);<br />
} else {<br />
// flash is too old or we can't detect the plugin<br />
var alternateContent = 'Alternate HTML content should be placed here. '<br />
+ 'This content requires the Adobe Flash Player. '<br />
+ '<a href=http://www.adobe.com/go/getflash/>Get Flash</a>';<br />
document.write(alternateContent);<br />
// insert non-flash content<br />
}<br />
</pre><br />
<br />
Using HTML:<br />
<pre><br />
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"<br />
id="OntologyTree" width="300" height="100%"<br />
codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab"><br />
<param name="movie" value="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" /><br />
<param name="quality" value="high" /><br />
<param name="bgcolor" value="#ffffff" /><br />
<param name="allowScriptAccess" value="always" /><br />
<param name="flashVars" value="ontology=&alerterrors=false&canchangeontology=true" /><br />
<embed src="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" quality="high" bgcolor="#ffffff"<br />
width="300" height="100%" name="OntologyTree" align="middle"<br />
play="true"<br />
loop="false"<br />
allowScriptAccess="always"<br />
type="application/x-shockwave-flash"<br />
flashVars="ontology=&alerterrors=false&canchangeontology=true"<br />
pluginspage="http://www.adobe.com/go/getflashplayer"><br />
</embed><br />
</object><br />
</pre><br />
<br />
Using GWT:<br />
* See http://code.google.com/p/gwt2swf/ for information on how to embed SWF in GWT.<br />
<br />
<br />
'''Javascript API Calls'''<br><br />
You will need to copy/paste this code to a Javascript file or embed directly in the HTML for usage in your page.<br><br />
<pre><br />
/* <br />
* The following JavaScript functions allow you to interact with the Flash BioPortal Ontology Tree. <br />
* You can load an ontology by id, and get the current ontology id or name.<br />
* Once an ontology is loaded then you can get the currently selected concept by id or name,<br />
* and you can also select a concept by id or name. <br />
* You can also listen for one of these events by implementing the following functions (see the stubs below):<br />
* appComplete, treeSelectionChanged, treeNodeDoubleClicked, or errorLoadingOntology<br />
*<br />
* These are the parameters that you can pass into the application using the "flashVars" parameter:<br />
* (see the examples below):<br />
* - ontology: the id of the ontology (version or virtual)<br />
* - virtual: if false (default) then the ontology id above is the version id<br />
* if true then the above ontology id is assumed to be the virtual id <br />
* - alerterrors: (true/false) determines whether the application will display errors (default is false)<br />
* - server: defines the URL of the rest server (null by default)<br />
* - title: changes the default title for the page <br />
* - canchangeontology: if true then the ontology can be changed<br />
* - rootconceptid: sets the optional root node of the tree<br />
* - canchangeroot: if false then the root of the tree cannot be changed by the user (using context menu items)<br />
*/<br />
<br />
// get a handle for the flash application<br />
function getApp() {<br />
if (navigator.appName.indexOf ("Microsoft") != -1) {<br />
app = window["OntologyTree"];<br />
} else {<br />
app = document["OntologyTree"];<br />
}<br />
if (app == null) {<br />
app = document.getElementById("OntologyTree");<br />
}<br />
if (app == null) {<br />
alert("Could not get Flash object, JavaScript/Flex communication failed.");<br />
}<br />
return app;<br />
}<br />
<br />
// these are the available functions that you can call ONCE the <br />
// flash SWF has finished loading<br />
<br />
/** Loads a new ontology by id. */<br />
function loadOntology(ontologyID) {<br />
var app = getApp();<br />
if (app && app.loadOntology) {<br />
app.loadOntology(ontologyID);<br />
}<br />
}<br />
<br />
/** Gets the id of the current ontology, will be null if no ontology is loaded. */<br />
function getOntologyID() {<br />
var ontologyID = null;<br />
var app = getApp();<br />
if (app && app.getOntologyID) {<br />
ontologyID = app.getOntologyID();<br />
}<br />
return ontologyID;<br />
}<br />
<br />
/** Gets the name of the current ontology, will be null if no ontology is loaded. */<br />
function getOntologyName() {<br />
var ontologyName = null;<br />
var app = getApp();<br />
if (app && app.getOntologyName) {<br />
ontologyName = app.getOntologyName();<br />
}<br />
return ontologyName;<br />
}<br />
<br />
/** Gets the id of the currently selected concept, will be null if nothing is selected. */<br />
function getSelectedConceptID() {<br />
var conceptID = null;<br />
var app = getApp();<br />
if (app && app.getSelectedConceptID) {<br />
conceptID = app.getSelectedConceptID();<br />
}<br />
return conceptID;<br />
}<br />
<br />
/** <br />
* Gets the full id (not all ontologies support this) of the currently selected concept. <br />
* Will be null if nothing is selected, will be the same as the conceptID if no fullID exists. <br />
*/<br />
function getSelectedConceptFullID() {<br />
var conceptID = null;<br />
var app = getApp();<br />
if (app && app.getSelectedConceptFullID) {<br />
conceptID = app.getSelectedConceptFullID();<br />
}<br />
return conceptID;<br />
}<br />
<br />
/** Gets the name of the currently selected concept, will be null if nothing is selected. */<br />
function getSelectedConceptName() {<br />
var conceptName = null;<br />
var app = getApp();<br />
if (app && app.getSelectedConceptName) {<br />
conceptName = app.getSelectedConceptName();<br />
}<br />
return conceptName;<br />
}<br />
<br />
/** Loads and selects a concept (by id) in the current ontology. */<br />
function loadConceptByID(conceptID) {<br />
var app = getApp();<br />
if (app && app.loadConceptByID) {<br />
app.loadConceptByID(conceptID);<br />
}<br />
}<br />
<br />
/** Attempts to load and select a concept (by name) in the current ontology. */<br />
function loadConceptByName(conceptName) {<br />
var app = getApp();<br />
if (app && app.loadConceptByName) {<br />
app.loadConceptByName(conceptName);<br />
}<br />
}<br />
<br />
/** This function gets call by flash when the swf has finished loading. */<br />
function appComplete(swfID) {<br />
// alert("flash app finished loading: " + swfID);<br />
}<br />
<br />
/** Implement this function to listen for tree selection changes */<br />
function treeSelectionChanged(nodeID, nodeName, swfID) {<br />
// alert("tree selection: " + nodeID + " - " + nodeName + " - " + swfID);<br />
}<br />
<br />
/** Implement this function to listen for tree double click events */<br />
function treeNodeDoubleClicked(nodeID, nodeName, swfID) {<br />
alert("tree node double clicked: " + nodeID + " - " + nodeName + " - " + swfID);<br />
}<br />
<br />
/** Implement this function to listen for error messages when loading an ontology */<br />
function errorLoadingOntology(errorMsg, swfID) {<br />
// alert("Error: " + errorMsg);<br />
}<br />
</pre><br />
<br />
= Referencing your ontology of interest in the widgets = <br />
<br />
Most of the time you would want your widget to use the latest version of your ontology of interest that is available in BioPortal. Thus, you would want to use the ontology id and not the version is in your widget. To find the ontology id, go to the "Ontology Details" page for your ontology of interest in BioPortal (e.g., the page for [http://bioportal.bioontology.org/ontologies/39478 NCI Thesaurus]). You will find the ontology id on the Metadata tab there (e.g., the ontology id for NCI Thesaurus is 1032).</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12376BioPortal REST services2012-07-06T23:00:31Z<p>Darren Weber: /* Search BioPortal */ document field values for object type.</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
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.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** 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.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
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).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** 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<br />
** 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.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&apikey={YourAPIKey}]<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
== Get siblings of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&apikey={YourAPIKey}&[&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
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. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
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.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_0000024?apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_0000023?apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12375BioPortal REST services2012-07-06T22:44:30Z<p>Darren Weber: /* Search BioPortal */ Document the <recordType></recordType> values.</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
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.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** 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.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
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).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Search Record Types'''<br />
The following values can appear in the '<recordType></recordType>' entries:<br />
- PREFERRED_NAME = "apreferredname"<br />
- CONCEPT_ID = "bconceptid"<br />
- SYNONYM = "csynonym"<br />
- PROPERTY = "dproperty"<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** 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<br />
** 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.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&apikey={YourAPIKey}]<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
== Get siblings of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&apikey={YourAPIKey}&[&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
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. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
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.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_0000024?apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_0000023?apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12374BioPortal REST services2012-07-06T17:32:42Z<p>Darren Weber: /* Search BioPortal */ Use a gene search for the example (restricted to NCI Thesaurus and exact matches)</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
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.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** 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.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
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).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** 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<br />
** 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.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&apikey={YourAPIKey}]<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
== Get siblings of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&apikey={YourAPIKey}&[&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
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. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
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.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_0000024?apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_0000023?apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12373BioPortal REST services2012-07-06T17:27:57Z<p>Darren Weber: /* Search BioPortal */ updating example with new API syntax and corresponding sample output</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
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.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** 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.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
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).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=software&ontologyids=1104&isexactmatch=1&apikey=YourAPIKey<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:26:31.370 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>1</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>44450</ontologyVersionId><br />
<ontologyId>1104</ontologyId><br />
<ontologyDisplayLabel>Biomedical Resource Ontology</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Software</conceptId><br />
<conceptIdShort>BRO:Software</conceptIdShort><br />
<preferredName>Software</preferredName><br />
<contents>Software</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>44450</ontologyVersionId><br />
<ontologyId>1104</ontologyId><br />
<ontologyDisplayLabel>Biomedical Resource Ontology</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>2</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
<br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** 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<br />
** 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.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&apikey={YourAPIKey}]<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
== Get siblings of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&apikey={YourAPIKey}&[&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
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. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
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.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_0000024?apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_0000023?apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Widgets&diff=12372NCBO Widgets2012-07-06T00:50:50Z<p>Darren Weber: </p>
<hr />
<div>NCBO widgets are the HTML or Javascript code that you can put on your Web site or Web form to use BioPortal functionality there. Using NCBO Widgets is just one of [[Using_NCBO_Technology_In_Your_Project|the ways in which you can use the NCBO technology directly on your Web site or in your application]].<br />
<br />
= Types of NCBO Widgets and use cases = <br />
* '''[[#Term-selection field on a form|Term-selection field on a form]]''': You can add a text field to your Web form that will let users enter a term from a controlled vocabulary (e.g., terms from a single ontology)<br />
** ''Example use case'': Suppose you are running a tissue microarray database and users upload sample descriptions to your database using a web form. There is usually a field for the user to enter the diagnosis for the tissue sample that she is entering. Usually, this field is a text-box or a drop down menu populated with a list of controlled terms. The free text-box is prone to errors, the drop-down gets too unwieldy with large terminologies. Using the NCBO term-selection widget to have users easily select a term from an ontology or controlled vocabulary (such as the NCI Thesaurus) to fill in the field. For example, when the user starts typing "cutaneous me", the term "cutaneous melanoma" pops up.<br />
** ''What does the term-selection field get you'': <br />
*** Look-ahead so that you don't need to type the whole term<br />
*** Controlled vocabulary provides consistency of the way different users use the term (If you want to put "Malignant melanoma", it will always be the same term from NCIT, regardless of how a user started typing it<br />
*** When a new version of your controlled vocabulary becomes available in BioPortal, the widget will automatically use that new version.<br />
*'''[[#Ontology search widget|Ontology search widget]]''': You can add to your Web site a search box that searches a specific BioPortal ontology. When the user selects the term of interest (with the help of the look-ahead feature), he can jump to the BioPortal page for the corresponding concept in BioPortal.<br />
*'''[[#Feed widget|Feed widget]]''': you can put a widget on your site that will have a live feed of all the changes to your ontology of interest, such as uploads of a new version, comments from other users, new mappings for concepts in your ontology.<br />
*'''[[#Ontology visualization widget|Ontology visualization widget]]''': You can put a widget on your Web site that visualizes your entire ontology of interest, or some part of it, as on the [http://bioportal.bioontology.org/visualize/39478#t_tab1: "Visualize" tab in BioPortal].<br />
*<font color="red">**NEW**</font> '''[[#OntologyTree Widget|OntologyTree Widget]]''': You can put a widget on your Web site that displays the ontology tree, or some part of it, as on the [http://bioportal.bioontology.org/visualize/39478#t_tab1: "Visualize" tab in BioPortal].<br />
<br />
= How to use NCBO Widgets=<br />
<br />
The easiest way to add any NCBO widget to your HTML page or Web form is by following these steps:<br />
* Find your ontology of interest in the [http://bioportal.bioontology.org/ontologies list of BioPortal ontologies] (e.g., NCI Thesaurus)<br />
* Click on the ontology name to get to the page with '''Details''' for that ontology (e.g., the [http://bioportal.bioontology.org/ontologies/39478 Details for NCI Thesaurus])<br />
* On the Ontology Details page, go to '''Ontology Widgets''' tab<br />
* Select the widget you want<br />
* Click the button below the widgets to get instructions for the specific widget<br />
<br />
== Term-selection field on a form ==<br />
<br />
To add a field to your form that lets the user fetch a term from your ontology of interest, do the following:<br />
<ul><br />
<li>Download the [http://bioportal.bioontology.org/javascripts/widgets/form_complete.js <b>form_complete.js file</b>] and put it on your server<br />
</li><br />
<li>In the header for the page where you want the form field, include the <b>form_complete.js</b> file<br />
</li><br />
<li>On your form, for the fields where you want to use the term-selection widget, specify the field's class in the following format: <code>bp_form_complete-{ontology_id_list}-{value}</code><br />
<ul><br />
<li>For example, <code>bp_form_complete-1032-uri</code> will use NCI Thesaurus (ontology id is 1032) and will put the term URI in the field after the user selects the term from the pull-down list.<br />
<ul><br />
<li><br />
<b>Note:</b> In addition to single ontology ids, you can use a list:<br><br />
<code>bp_form_complete-1032,1089-uri</code><br />
</li><br />
<li><br />
<b>OR</b> use 'all' to search across all BioPortal ontologies:<br><br />
<code>bp_form_complete-all-uri</code><br />
</li><br />
</ul><br />
</li><br />
<li>You can use the following parameters to select which value will be placed into the user-visible input field:<br />
<ul><br />
<li><br />
<code>uri</code> : put the complete URI of the term (e.g., "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Neoplasm");<br />
</li><br />
<li><br />
<code>shortid</code> : put the short id of the term, as used in BioPortal (e.g., "Common_Neoplasm");<br />
</li><br />
<li><br />
<code>name</code> : put the preferred name of the term (e.g., "Common Neoplasm");<br />
</li><br />
</ul><br />
</li><br />
<li>In addition to the input element you defined, there are four hidden form elements that are created and then set when a user selects a term from the list. For example, if you create a field with this code:<br />
<pre><br />
&lt;input type="text" name="a" class="bp_form_complete-all-uri" size="100"/&gt;<br />
</pre><br />
The 'name' attribute is used to create the four following fields (note how the 'a' from the name attribute is appended to the id attribute):<br />
<ul><br />
<li><br />
<pre><br />
&lt;input type="hidden" id="a_bioportal_preferred_name"&gt;<br />
</pre><br />
</li><br />
<li><br />
<pre><br />
&lt;input type="hidden" id="a_bioportal_concept_id"&gt;<br />
</pre><br />
</li><br />
<li><br />
<pre><br />
&lt;input type="hidden" id="a_bioportal_ontology_id"&gt;<br />
</pre><br />
</li><br />
<li><br />
<pre><br />
&lt;input type="hidden" id="a_bioportal_full_id"&gt;<br />
</pre><br />
</li><br />
</ul><br />
</li><br />
<li><br />
To limit the term lookup to a particular branch of an ontology, include the following as an attribute on the field's element (replace conceptid with the id for the term which you would like to use as the root of your branch): <code>data-bp_search_branch="{conceptid}"</code><br />
</li><br />
<li><br />
To display definitions with the list of terms that are returned, include the following as an attribute on the field's element: <code>data-bp_include_definitions="true"</code><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Ontology search widget ==<br />
<br />
To add a search widget to your HTML page that searches a specific ontology, do the following:<br />
<ul><br />
<li>Download the [http://bioportal.bioontology.org/javascripts/widgets/quick_jump.js <b>quick_jump.js file</b>] and put it on your server<br />
</li><br />
<li>Copy the code below and paste it to your HTML page. <br />
<pre><br />
<div id="bp_quick_jump"></div><br />
<script type="text/javascript"><br />
var BP_ontology_id = "1016";<br />
</script><br />
<script src="quick_jump.js" type="text/javascript" charset="utf-8"><br />
</script><br />
</pre><br />
</li><br />
<li><br />
<b>Note:</b> If you would like to use Quick Jump across multiple ontologies:<br />
<ul><br />
<li>You can enter a comma-separated list of ontology ids:<br><br />
var BP_ontology_id = "1032,1089";<br />
</li><br />
<li>You cans set the variable to 'all' to search all ontologies in BioPortal:<br><br />
var BP_ontology_id = "all";<br />
</li><br />
</ul><br />
</li><br />
<li>In the code that you just pasted, make sure to change the path to the quick_jump.js file to point to the location where you put the file (relative to your HTML file)<br />
<ul><br />
<li>For example, if you put the quick_jump.js file in the same directory as your HTML file, this is the code you would use:<br />
<pre><br />
<script type="text/javascript"><br />
var BP_ontology_id = "1032";<br />
</script><br />
<script src="quick_jump.js" type="text/javascript" charset="utf-8"></script><br />
</pre><br />
</li><br />
</ul><br />
</li><br />
<li><br />
To limit the term lookup to a particular branch of an ontology, include the following Javascript in your page (replace conceptid with the id for the term which you would like to use as the root of your branch): <br />
<code>var BP_search_branch = "{conceptid}";</code><br />
</li><br />
<li><br />
To display definitions with the list of terms that are returned, include the following Javascript in your page: <br />
<code>var BP_include_definitions = true;</code><br />
</li><br />
</ul><br />
<br />
== Feed widget ==<br />
<br />
To add a Feed widget to your HTML page, simple copy the code from the Ontology Widget page for your ontology of interest. Here is a sample:<br />
<br />
<pre><br />
<script type="text/javascript"><br />
var BP_ontology_id = "1032"<br />
</script><br />
<script src="http://bioportal.bioontology.org/javascripts/widgets/feed_widget.js" type="text/javascript" charset="utf-8"></script><br />
</pre><br />
<br />
== Ontology visualization widget ==<br />
To add a widget visualizing your ontology to your HTML page, simple copy the code from the Ontology Widget page for your ontology of interest. Here is a sample:<br />
<br />
<pre><br />
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"<br />
id="FlexoViz" width="100%" height="100%"<br />
codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab"><br />
<param name="movie" value="http://keg.cs.uvic.ca/ncbo/flexviz/FlexoViz.swf" /><br />
<param name="quality" value="high" /><br />
<param name="bgcolor" value="#ffffff" /><br />
<param name="allowScriptAccess" value="always" /><br />
<embed src="http://keg.cs.uvic.ca/ncbo/flexviz/FlexoViz.swf" bgcolor="#ffffff"<br />
width="100%" height="100%" name="FlexoViz" align="middle"<br />
play="true"<br />
loop="false"<br />
quality="high"<br />
allowScriptAccess="always"<br />
type="application/x-shockwave-flash"<br />
flashVars="widget=true&ontology=39478&server=http://rest.bioontology.org/bioportal/"<br />
pluginspage="http://www.adobe.com/go/getflashplayer"><br />
</embed><br />
</object> <br />
</pre><br />
<br />
If you want the visualization to be focused on a particular term in the ontology, you can add the term id to the parameters above. For example, to have the widget focus on Melanoma in NCI Thesaurus, replace the following line in the snippet above:<br />
<pre><br />
flashVars="widget=true&ontology=39478&server=http://rest.bioontology.org/bioportal/"<br />
</pre><br />
<br />
with <br />
<pre><br />
flashVars="widget=true&ontology=39478&nodeid=Melanoma&server=http://rest.bioontology.org/bioportal/"<br />
</pre><br />
<br />
(''note "&nodeid=Melanoma"'')<br />
<br />
== OntologyTree Widget ==<br />
<br />
'''Description'''<br><br />
The OntologyTree widget is an embeddable Flex application that allows a user to interact with a tree browser for ontologies. The widget can be configured to display a list of all the ontologies in BioPortal, allowing the user to select which one to view, or can be setup to view a particular ontology. Additionally, there are several Javascript helper functions for the widget, allowing it to be utilized as a fully functional component in other applications.<br />
<br />
'''Location'''<br><br />
http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf<br />
<br />
'''Parameters'''<br />
* '''ontology''' = The id of the ontology to use, by default it assumes this value is the ontology version id<br />
* '''virtual''' [true|false] - If true then the above ontology parameter is assumed to be a virtual ontology id<br />
* '''canchangeontology''' [true|false] = If false then users can't change the current ontology<br />
* '''canchangeroot''' [true|false] = If true the the user can specify a root concept (using the context menu)<br />
* '''rootconceptid''' = The id of the root concept to show in the tree, leave out to show the ontology roots<br />
* '''server''' = The rest server to use. Defaults to "http://rest.bioontology.org/bioportal/".<br />
* '''redirecturl''' = The url to redirect to for terms and ontologies (in BioPortal). Defaults to "http://bioportal.bioontology.org/".<br />
* '''alerterrors''' [true|false] = If true then errors will be displayed in an annoying popup box.<br />
* '''title''' = The title for the browser window<br />
<br />
'''Embed Example'''<br><br />
Using Javascript (preferred):<br />
<pre><br />
<script src="http://keg.cs.uvic.ca/ncbo/ontologytree/AC_OETags.js" language="javascript"></script><br />
<!--<br />
// -----------------------------------------------------------------------------<br />
// Globals<br />
// Major version of Flash required<br />
var requiredMajorVersion = 9;<br />
// Minor version of Flash required<br />
var requiredMinorVersion = 0;<br />
// Minor version of Flash required<br />
var requiredRevision = 124;<br />
// -----------------------------------------------------------------------------<br />
// --><br />
<br />
// Version check for the Flash Player that has the ability to start Player Product Install (6.0r65)<br />
var hasProductInstall = DetectFlashVer(6, 0, 65);<br />
<br />
// Version check based upon the values defined in globals<br />
var hasRequestedVersion = DetectFlashVer(requiredMajorVersion, requiredMinorVersion, requiredRevision);<br />
<br />
if (hasProductInstall && !hasRequestedVersion) {<br />
// DO NOT MODIFY THE FOLLOWING FOUR LINES<br />
// Location visited after installation is complete if installation is required<br />
var MMPlayerType = (isIE == true) ? "ActiveX": "PlugIn";<br />
var MMredirectURL = window.location;<br />
document.title = document.title.slice(0, 47) + " - Flash Player Installation";<br />
var MMdoctitle = document.title;<br />
<br />
AC_FL_RunContent(<br />
"src", "playerProductInstall",<br />
"FlashVars", "MMredirectURL=" + MMredirectURL + '&MMplayerType=' + MMPlayerType + '&MMdoctitle=' + MMdoctitle + "",<br />
"width", "300",<br />
"height", "100%",<br />
"align", "middle",<br />
"id", "OntologyTree",<br />
"quality", "high",<br />
"bgcolor", "#ffffff",<br />
"name", "OntologyTree",<br />
"allowScriptAccess", "always",<br />
"type", "application/x-shockwave-flash",<br />
"pluginspage", "http://www.adobe.com/go/getflashplayer"<br />
);<br />
} else if (hasRequestedVersion) {<br />
// if we've detected an acceptable version<br />
// embed the Flash Content SWF when all tests are passed<br />
AC_FL_RunContent(<br />
"src", "http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf",<br />
"width", "300",<br />
"height", "100%",<br />
"align", "middle",<br />
"id", "OntologyTree",<br />
"quality", "high",<br />
"bgcolor", "#ffffff",<br />
"name", "OntologyTree",<br />
"allowScriptAccess", "always",<br />
"flashVars", "ontology=&virtual=false&alerterrors=false&canchangeontology=true&rootconceptid=",<br />
"type", "application/x-shockwave-flash",<br />
"pluginspage", "http://www.adobe.com/go/getflashplayer"<br />
);<br />
} else {<br />
// flash is too old or we can't detect the plugin<br />
var alternateContent = 'Alternate HTML content should be placed here. '<br />
+ 'This content requires the Adobe Flash Player. '<br />
+ '<a href=http://www.adobe.com/go/getflash/>Get Flash</a>';<br />
document.write(alternateContent);<br />
// insert non-flash content<br />
}<br />
</pre><br />
<br />
Using HTML:<br />
<pre><br />
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"<br />
id="OntologyTree" width="300" height="100%"<br />
codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab"><br />
<param name="movie" value="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" /><br />
<param name="quality" value="high" /><br />
<param name="bgcolor" value="#ffffff" /><br />
<param name="allowScriptAccess" value="always" /><br />
<param name="flashVars" value="ontology=&alerterrors=false&canchangeontology=true" /><br />
<embed src="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" quality="high" bgcolor="#ffffff"<br />
width="300" height="100%" name="OntologyTree" align="middle"<br />
play="true"<br />
loop="false"<br />
allowScriptAccess="always"<br />
type="application/x-shockwave-flash"<br />
flashVars="ontology=&alerterrors=false&canchangeontology=true"<br />
pluginspage="http://www.adobe.com/go/getflashplayer"><br />
</embed><br />
</object><br />
</pre><br />
<br />
Using GWT:<br />
* See http://code.google.com/p/gwt2swf/ for information on how to embed SWF in GWT.<br />
<br />
<br />
'''Javascript API Calls'''<br><br />
You will need to copy/paste this code to a Javascript file or embed directly in the HTML for usage in your page.<br><br />
<pre><br />
/* <br />
* The following JavaScript functions allow you to interact with the Flash BioPortal Ontology Tree. <br />
* You can load an ontology by id, and get the current ontology id or name.<br />
* Once an ontology is loaded then you can get the currently selected concept by id or name,<br />
* and you can also select a concept by id or name. <br />
* You can also listen for one of these events by implementing the following functions (see the stubs below):<br />
* appComplete, treeSelectionChanged, treeNodeDoubleClicked, or errorLoadingOntology<br />
*<br />
* These are the parameters that you can pass into the application using the "flashVars" parameter:<br />
* (see the examples below):<br />
* - ontology: the id of the ontology (version or virtual)<br />
* - virtual: if false (default) then the ontology id above is the version id<br />
* if true then the above ontology id is assumed to be the virtual id <br />
* - alerterrors: (true/false) determines whether the application will display errors (default is false)<br />
* - server: defines the URL of the rest server (null by default)<br />
* - title: changes the default title for the page <br />
* - canchangeontology: if true then the ontology can be changed<br />
* - rootconceptid: sets the optional root node of the tree<br />
* - canchangeroot: if false then the root of the tree cannot be changed by the user (using context menu items)<br />
*/<br />
<br />
// get a handle for the flash application<br />
function getApp() {<br />
if (navigator.appName.indexOf ("Microsoft") != -1) {<br />
app = window["OntologyTree"];<br />
} else {<br />
app = document["OntologyTree"];<br />
}<br />
if (app == null) {<br />
app = document.getElementById("OntologyTree");<br />
}<br />
if (app == null) {<br />
alert("Could not get Flash object, JavaScript/Flex communication failed.");<br />
}<br />
return app;<br />
}<br />
<br />
// these are the available functions that you can call ONCE the <br />
// flash SWF has finished loading<br />
<br />
/** Loads a new ontology by id. */<br />
function loadOntology(ontologyID) {<br />
var app = getApp();<br />
if (app && app.loadOntology) {<br />
app.loadOntology(ontologyID);<br />
}<br />
}<br />
<br />
/** Gets the id of the current ontology, will be null if no ontology is loaded. */<br />
function getOntologyID() {<br />
var ontologyID = null;<br />
var app = getApp();<br />
if (app && app.getOntologyID) {<br />
ontologyID = app.getOntologyID();<br />
}<br />
return ontologyID;<br />
}<br />
<br />
/** Gets the name of the current ontology, will be null if no ontology is loaded. */<br />
function getOntologyName() {<br />
var ontologyName = null;<br />
var app = getApp();<br />
if (app && app.getOntologyName) {<br />
ontologyName = app.getOntologyName();<br />
}<br />
return ontologyName;<br />
}<br />
<br />
/** Gets the id of the currently selected concept, will be null if nothing is selected. */<br />
function getSelectedConceptID() {<br />
var conceptID = null;<br />
var app = getApp();<br />
if (app && app.getSelectedConceptID) {<br />
conceptID = app.getSelectedConceptID();<br />
}<br />
return conceptID;<br />
}<br />
<br />
/** <br />
* Gets the full id (not all ontologies support this) of the currently selected concept. <br />
* Will be null if nothing is selected, will be the same as the conceptID if no fullID exists. <br />
*/<br />
function getSelectedConceptFullID() {<br />
var conceptID = null;<br />
var app = getApp();<br />
if (app && app.getSelectedConceptFullID) {<br />
conceptID = app.getSelectedConceptFullID();<br />
}<br />
return conceptID;<br />
}<br />
<br />
/** Gets the name of the currently selected concept, will be null if nothing is selected. */<br />
function getSelectedConceptName() {<br />
var conceptName = null;<br />
var app = getApp();<br />
if (app && app.getSelectedConceptName) {<br />
conceptName = app.getSelectedConceptName();<br />
}<br />
return conceptName;<br />
}<br />
<br />
/** Loads and selects a concept (by id) in the current ontology. */<br />
function loadConceptByID(conceptID) {<br />
var app = getApp();<br />
if (app && app.loadConceptByID) {<br />
app.loadConceptByID(conceptID);<br />
}<br />
}<br />
<br />
/** Attempts to load and select a concept (by name) in the current ontology. */<br />
function loadConceptByName(conceptName) {<br />
var app = getApp();<br />
if (app && app.loadConceptByName) {<br />
app.loadConceptByName(conceptName);<br />
}<br />
}<br />
<br />
/** This function gets call by flash when the swf has finished loading. */<br />
function appComplete(swfID) {<br />
// alert("flash app finished loading: " + swfID);<br />
}<br />
<br />
/** Implement this function to listen for tree selection changes */<br />
function treeSelectionChanged(nodeID, nodeName, swfID) {<br />
// alert("tree selection: " + nodeID + " - " + nodeName + " - " + swfID);<br />
}<br />
<br />
/** Implement this function to listen for tree double click events */<br />
function treeNodeDoubleClicked(nodeID, nodeName, swfID) {<br />
alert("tree node double clicked: " + nodeID + " - " + nodeName + " - " + swfID);<br />
}<br />
<br />
/** Implement this function to listen for error messages when loading an ontology */<br />
function errorLoadingOntology(errorMsg, swfID) {<br />
// alert("Error: " + errorMsg);<br />
}<br />
</pre><br />
<br />
= Referencing your ontology of interest in the widgets = <br />
<br />
Most of the time you would want your widget to use the latest version of your ontology of interest that is available in BioPortal. Thus, you would want to use the ontology id and not the version is in your widget. To find the ontology id, go to the "Ontology Details" page for your ontology of interest in BioPortal (e.g., the page for [http://bioportal.bioontology.org/ontologies/39478 NCI Thesaurus]). You will find the ontology id on the Metadata tab there (e.g., the ontology id for NCI Thesaurus is 1032).</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Widgets&diff=12371NCBO Widgets2012-07-06T00:48:58Z<p>Darren Weber: Updating URI for NCI Thesaurus term "Common Neoplasm"</p>
<hr />
<div>NCBO widgets are the HTML or Javascript code that you can put on your Web site or Web form to use BioPortal functionality there. Using NCBO Widgets is just one of [[Using_NCBO_Technology_In_Your_Project|the ways in which you can use the NCBO technology directly on your Web site or in your application]].<br />
<br />
= Types of NCBO Widgets and use cases = <br />
* '''[[#Term-selection field on a form|Term-selection field on a form]]''': You can add a text field to your Web form that will let users enter a term from a controlled vocabulary (e.g., terms from a single ontology)<br />
** ''Example use case'': Suppose you are running a tissue microarray database and users upload sample descriptions to your database using a web form. There is usually a field for the user to enter the diagnosis for the tissue sample that she is entering. Usually, this field is a text-box or a drop down menu populated with a list of controlled terms. The free text-box is prone to errors, the drop-down gets too unwieldy with large terminologies. Using the NCBO term-selection widget to have users easily select a term from an ontology or controlled vocabulary (such as the NCI Thesaurus) to fill in the field. For example, when the user starts typing "cutaneous me", the term "cutaneous melanoma" pops up.<br />
** ''What does the term-selection field get you'': <br />
*** Look-ahead so that you don't need to type the whole term<br />
*** Controlled vocabulary provides consistency of the way different users use the term (If you want to put "Malignant melanoma", it will always be the same term from NCIT, regardless of how a user started typing it<br />
*** When a new version of your controlled vocabulary becomes available in BioPortal, the widget will automatically use that new version.<br />
*'''[[#Ontology search widget|Ontology search widget]]''': You can add to your Web site a search box that searches a specific BioPortal ontology. When the user selects the term of interest (with the help of the look-ahead feature), he can jump to the BioPortal page for the corresponding concept in BioPortal.<br />
*'''[[#Feed widget|Feed widget]]''': you can put a widget on your site that will have a live feed of all the changes to your ontology of interest, such as uploads of a new version, comments from other users, new mappings for concepts in your ontology.<br />
*'''[[#Ontology visualization widget|Ontology visualization widget]]''': You can put a widget on your Web site that visualizes your entire ontology of interest, or some part of it, as on the [http://bioportal.bioontology.org/visualize/39478#t_tab1: "Visualize" tab in BioPortal].<br />
*<font color="red">**NEW**</font> '''[[#OntologyTree Widget|OntologyTree Widget]]''': You can put a widget on your Web site that displays the ontology tree, or some part of it, as on the [http://bioportal.bioontology.org/visualize/39478#t_tab1: "Visualize" tab in BioPortal].<br />
<br />
= How to use NCBO Widgets=<br />
<br />
The easiest way to add any NCBO widget to your HTML page or Web form is by following these steps:<br />
* Find your ontology of interest in the [http://bioportal.bioontology.org/ontologies list of BioPortal ontologies] (e.g., NCI Thesaurus)<br />
* Click on the ontology name to get to the page with '''Details''' for that ontology (e.g., the [http://bioportal.bioontology.org/ontologies/39478 Details for NCI Thesaurus])<br />
* On the Ontology Details page, go to '''Ontology Widgets''' tab<br />
* Select the widget you want<br />
* Click the button below the widgets to get instructions for the specific widget<br />
<br />
== Term-selection field on a form ==<br />
<br />
To add a field to your form that lets the user fetch a term from your ontology of interest, do the following:<br />
<ul><br />
<li>Download the [http://bioportal.bioontology.org/javascripts/widgets/form_complete.js <b>form_complete.js file</b>] and put it on your server<br />
</li><br />
<li>In the header for the page where you want the form field, include the <b>form_complete.js</b> file<br />
</li><br />
<li>On your form, for the fields where you want to use the term-selection widget, specify the field's class in the following format: <code>bp_form_complete-{ontology_id_list}-{value}</code><br />
<ul><br />
<li>For example, <code>bp_form_complete-1032-uri</code> will use NCI Thesaurus (ontology id is 1032) and will put the term URI in the field after the user selects the term from the pull-down list.<br />
<ul><br />
<li><br />
<b>Note:</b> In addition to single ontology ids, you can use a list:<br><br />
<code>bp_form_complete-1032,1089-uri</code><br />
</li><br />
<li><br />
<b>OR</b> use 'all' to search across all BioPortal ontologies:<br><br />
<code>bp_form_complete-all-uri</code><br />
</li><br />
</ul><br />
</li><br />
<li>You can use the following parameters to select which value will be placed into the user-visible input field:<br />
<ul><br />
<li><br />
<code>uri</code> put the complete URI of the term (e.g., "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Neoplasm");<br />
</li><br />
<li><br />
<code>shortid</code> put the short id of the term, as used in BioPortal (e.g., "Common_Neoplasm");<br />
</li><br />
<li><br />
<code>name</code> put the preferred name of the term (e.g., "Common Neoplasm");<br />
</li><br />
</ul><br />
</li><br />
<li>In addition to the input element you defined, there are four hidden form elements that are created and then set when a user selects a term from the list. For example, if you create a field with this code:<br />
<pre><br />
&lt;input type="text" name="a" class="bp_form_complete-all-uri" size="100"/&gt;<br />
</pre><br />
The 'name' attribute is used to create the four following fields (note how the 'a' from the name attribute is appended to the id attribute):<br />
<ul><br />
<li><br />
<pre><br />
&lt;input type="hidden" id="a_bioportal_preferred_name"&gt;<br />
</pre><br />
</li><br />
<li><br />
<pre><br />
&lt;input type="hidden" id="a_bioportal_concept_id"&gt;<br />
</pre><br />
</li><br />
<li><br />
<pre><br />
&lt;input type="hidden" id="a_bioportal_ontology_id"&gt;<br />
</pre><br />
</li><br />
<li><br />
<pre><br />
&lt;input type="hidden" id="a_bioportal_full_id"&gt;<br />
</pre><br />
</li><br />
</ul><br />
</li><br />
<li><br />
To limit the term lookup to a particular branch of an ontology, include the following as an attribute on the field's element (replace conceptid with the id for the term which you would like to use as the root of your branch): <code>data-bp_search_branch="{conceptid}"</code><br />
</li><br />
<li><br />
To display definitions with the list of terms that are returned, include the following as an attribute on the field's element: <code>data-bp_include_definitions="true"</code><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Ontology search widget ==<br />
<br />
To add a search widget to your HTML page that searches a specific ontology, do the following:<br />
<ul><br />
<li>Download the [http://bioportal.bioontology.org/javascripts/widgets/quick_jump.js <b>quick_jump.js file</b>] and put it on your server<br />
</li><br />
<li>Copy the code below and paste it to your HTML page. <br />
<pre><br />
<div id="bp_quick_jump"></div><br />
<script type="text/javascript"><br />
var BP_ontology_id = "1016";<br />
</script><br />
<script src="quick_jump.js" type="text/javascript" charset="utf-8"><br />
</script><br />
</pre><br />
</li><br />
<li><br />
<b>Note:</b> If you would like to use Quick Jump across multiple ontologies:<br />
<ul><br />
<li>You can enter a comma-separated list of ontology ids:<br><br />
var BP_ontology_id = "1032,1089";<br />
</li><br />
<li>You cans set the variable to 'all' to search all ontologies in BioPortal:<br><br />
var BP_ontology_id = "all";<br />
</li><br />
</ul><br />
</li><br />
<li>In the code that you just pasted, make sure to change the path to the quick_jump.js file to point to the location where you put the file (relative to your HTML file)<br />
<ul><br />
<li>For example, if you put the quick_jump.js file in the same directory as your HTML file, this is the code you would use:<br />
<pre><br />
<script type="text/javascript"><br />
var BP_ontology_id = "1032";<br />
</script><br />
<script src="quick_jump.js" type="text/javascript" charset="utf-8"></script><br />
</pre><br />
</li><br />
</ul><br />
</li><br />
<li><br />
To limit the term lookup to a particular branch of an ontology, include the following Javascript in your page (replace conceptid with the id for the term which you would like to use as the root of your branch): <br />
<code>var BP_search_branch = "{conceptid}";</code><br />
</li><br />
<li><br />
To display definitions with the list of terms that are returned, include the following Javascript in your page: <br />
<code>var BP_include_definitions = true;</code><br />
</li><br />
</ul><br />
<br />
== Feed widget ==<br />
<br />
To add a Feed widget to your HTML page, simple copy the code from the Ontology Widget page for your ontology of interest. Here is a sample:<br />
<br />
<pre><br />
<script type="text/javascript"><br />
var BP_ontology_id = "1032"<br />
</script><br />
<script src="http://bioportal.bioontology.org/javascripts/widgets/feed_widget.js" type="text/javascript" charset="utf-8"></script><br />
</pre><br />
<br />
== Ontology visualization widget ==<br />
To add a widget visualizing your ontology to your HTML page, simple copy the code from the Ontology Widget page for your ontology of interest. Here is a sample:<br />
<br />
<pre><br />
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"<br />
id="FlexoViz" width="100%" height="100%"<br />
codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab"><br />
<param name="movie" value="http://keg.cs.uvic.ca/ncbo/flexviz/FlexoViz.swf" /><br />
<param name="quality" value="high" /><br />
<param name="bgcolor" value="#ffffff" /><br />
<param name="allowScriptAccess" value="always" /><br />
<embed src="http://keg.cs.uvic.ca/ncbo/flexviz/FlexoViz.swf" bgcolor="#ffffff"<br />
width="100%" height="100%" name="FlexoViz" align="middle"<br />
play="true"<br />
loop="false"<br />
quality="high"<br />
allowScriptAccess="always"<br />
type="application/x-shockwave-flash"<br />
flashVars="widget=true&ontology=39478&server=http://rest.bioontology.org/bioportal/"<br />
pluginspage="http://www.adobe.com/go/getflashplayer"><br />
</embed><br />
</object> <br />
</pre><br />
<br />
If you want the visualization to be focused on a particular term in the ontology, you can add the term id to the parameters above. For example, to have the widget focus on Melanoma in NCI Thesaurus, replace the following line in the snippet above:<br />
<pre><br />
flashVars="widget=true&ontology=39478&server=http://rest.bioontology.org/bioportal/"<br />
</pre><br />
<br />
with <br />
<pre><br />
flashVars="widget=true&ontology=39478&nodeid=Melanoma&server=http://rest.bioontology.org/bioportal/"<br />
</pre><br />
<br />
(''note "&nodeid=Melanoma"'')<br />
<br />
== OntologyTree Widget ==<br />
<br />
'''Description'''<br><br />
The OntologyTree widget is an embeddable Flex application that allows a user to interact with a tree browser for ontologies. The widget can be configured to display a list of all the ontologies in BioPortal, allowing the user to select which one to view, or can be setup to view a particular ontology. Additionally, there are several Javascript helper functions for the widget, allowing it to be utilized as a fully functional component in other applications.<br />
<br />
'''Location'''<br><br />
http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf<br />
<br />
'''Parameters'''<br />
* '''ontology''' = The id of the ontology to use, by default it assumes this value is the ontology version id<br />
* '''virtual''' [true|false] - If true then the above ontology parameter is assumed to be a virtual ontology id<br />
* '''canchangeontology''' [true|false] = If false then users can't change the current ontology<br />
* '''canchangeroot''' [true|false] = If true the the user can specify a root concept (using the context menu)<br />
* '''rootconceptid''' = The id of the root concept to show in the tree, leave out to show the ontology roots<br />
* '''server''' = The rest server to use. Defaults to "http://rest.bioontology.org/bioportal/".<br />
* '''redirecturl''' = The url to redirect to for terms and ontologies (in BioPortal). Defaults to "http://bioportal.bioontology.org/".<br />
* '''alerterrors''' [true|false] = If true then errors will be displayed in an annoying popup box.<br />
* '''title''' = The title for the browser window<br />
<br />
'''Embed Example'''<br><br />
Using Javascript (preferred):<br />
<pre><br />
<script src="http://keg.cs.uvic.ca/ncbo/ontologytree/AC_OETags.js" language="javascript"></script><br />
<!--<br />
// -----------------------------------------------------------------------------<br />
// Globals<br />
// Major version of Flash required<br />
var requiredMajorVersion = 9;<br />
// Minor version of Flash required<br />
var requiredMinorVersion = 0;<br />
// Minor version of Flash required<br />
var requiredRevision = 124;<br />
// -----------------------------------------------------------------------------<br />
// --><br />
<br />
// Version check for the Flash Player that has the ability to start Player Product Install (6.0r65)<br />
var hasProductInstall = DetectFlashVer(6, 0, 65);<br />
<br />
// Version check based upon the values defined in globals<br />
var hasRequestedVersion = DetectFlashVer(requiredMajorVersion, requiredMinorVersion, requiredRevision);<br />
<br />
if (hasProductInstall && !hasRequestedVersion) {<br />
// DO NOT MODIFY THE FOLLOWING FOUR LINES<br />
// Location visited after installation is complete if installation is required<br />
var MMPlayerType = (isIE == true) ? "ActiveX": "PlugIn";<br />
var MMredirectURL = window.location;<br />
document.title = document.title.slice(0, 47) + " - Flash Player Installation";<br />
var MMdoctitle = document.title;<br />
<br />
AC_FL_RunContent(<br />
"src", "playerProductInstall",<br />
"FlashVars", "MMredirectURL=" + MMredirectURL + '&MMplayerType=' + MMPlayerType + '&MMdoctitle=' + MMdoctitle + "",<br />
"width", "300",<br />
"height", "100%",<br />
"align", "middle",<br />
"id", "OntologyTree",<br />
"quality", "high",<br />
"bgcolor", "#ffffff",<br />
"name", "OntologyTree",<br />
"allowScriptAccess", "always",<br />
"type", "application/x-shockwave-flash",<br />
"pluginspage", "http://www.adobe.com/go/getflashplayer"<br />
);<br />
} else if (hasRequestedVersion) {<br />
// if we've detected an acceptable version<br />
// embed the Flash Content SWF when all tests are passed<br />
AC_FL_RunContent(<br />
"src", "http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf",<br />
"width", "300",<br />
"height", "100%",<br />
"align", "middle",<br />
"id", "OntologyTree",<br />
"quality", "high",<br />
"bgcolor", "#ffffff",<br />
"name", "OntologyTree",<br />
"allowScriptAccess", "always",<br />
"flashVars", "ontology=&virtual=false&alerterrors=false&canchangeontology=true&rootconceptid=",<br />
"type", "application/x-shockwave-flash",<br />
"pluginspage", "http://www.adobe.com/go/getflashplayer"<br />
);<br />
} else {<br />
// flash is too old or we can't detect the plugin<br />
var alternateContent = 'Alternate HTML content should be placed here. '<br />
+ 'This content requires the Adobe Flash Player. '<br />
+ '<a href=http://www.adobe.com/go/getflash/>Get Flash</a>';<br />
document.write(alternateContent);<br />
// insert non-flash content<br />
}<br />
</pre><br />
<br />
Using HTML:<br />
<pre><br />
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"<br />
id="OntologyTree" width="300" height="100%"<br />
codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab"><br />
<param name="movie" value="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" /><br />
<param name="quality" value="high" /><br />
<param name="bgcolor" value="#ffffff" /><br />
<param name="allowScriptAccess" value="always" /><br />
<param name="flashVars" value="ontology=&alerterrors=false&canchangeontology=true" /><br />
<embed src="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" quality="high" bgcolor="#ffffff"<br />
width="300" height="100%" name="OntologyTree" align="middle"<br />
play="true"<br />
loop="false"<br />
allowScriptAccess="always"<br />
type="application/x-shockwave-flash"<br />
flashVars="ontology=&alerterrors=false&canchangeontology=true"<br />
pluginspage="http://www.adobe.com/go/getflashplayer"><br />
</embed><br />
</object><br />
</pre><br />
<br />
Using GWT:<br />
* See http://code.google.com/p/gwt2swf/ for information on how to embed SWF in GWT.<br />
<br />
<br />
'''Javascript API Calls'''<br><br />
You will need to copy/paste this code to a Javascript file or embed directly in the HTML for usage in your page.<br><br />
<pre><br />
/* <br />
* The following JavaScript functions allow you to interact with the Flash BioPortal Ontology Tree. <br />
* You can load an ontology by id, and get the current ontology id or name.<br />
* Once an ontology is loaded then you can get the currently selected concept by id or name,<br />
* and you can also select a concept by id or name. <br />
* You can also listen for one of these events by implementing the following functions (see the stubs below):<br />
* appComplete, treeSelectionChanged, treeNodeDoubleClicked, or errorLoadingOntology<br />
*<br />
* These are the parameters that you can pass into the application using the "flashVars" parameter:<br />
* (see the examples below):<br />
* - ontology: the id of the ontology (version or virtual)<br />
* - virtual: if false (default) then the ontology id above is the version id<br />
* if true then the above ontology id is assumed to be the virtual id <br />
* - alerterrors: (true/false) determines whether the application will display errors (default is false)<br />
* - server: defines the URL of the rest server (null by default)<br />
* - title: changes the default title for the page <br />
* - canchangeontology: if true then the ontology can be changed<br />
* - rootconceptid: sets the optional root node of the tree<br />
* - canchangeroot: if false then the root of the tree cannot be changed by the user (using context menu items)<br />
*/<br />
<br />
// get a handle for the flash application<br />
function getApp() {<br />
if (navigator.appName.indexOf ("Microsoft") != -1) {<br />
app = window["OntologyTree"];<br />
} else {<br />
app = document["OntologyTree"];<br />
}<br />
if (app == null) {<br />
app = document.getElementById("OntologyTree");<br />
}<br />
if (app == null) {<br />
alert("Could not get Flash object, JavaScript/Flex communication failed.");<br />
}<br />
return app;<br />
}<br />
<br />
// these are the available functions that you can call ONCE the <br />
// flash SWF has finished loading<br />
<br />
/** Loads a new ontology by id. */<br />
function loadOntology(ontologyID) {<br />
var app = getApp();<br />
if (app && app.loadOntology) {<br />
app.loadOntology(ontologyID);<br />
}<br />
}<br />
<br />
/** Gets the id of the current ontology, will be null if no ontology is loaded. */<br />
function getOntologyID() {<br />
var ontologyID = null;<br />
var app = getApp();<br />
if (app && app.getOntologyID) {<br />
ontologyID = app.getOntologyID();<br />
}<br />
return ontologyID;<br />
}<br />
<br />
/** Gets the name of the current ontology, will be null if no ontology is loaded. */<br />
function getOntologyName() {<br />
var ontologyName = null;<br />
var app = getApp();<br />
if (app && app.getOntologyName) {<br />
ontologyName = app.getOntologyName();<br />
}<br />
return ontologyName;<br />
}<br />
<br />
/** Gets the id of the currently selected concept, will be null if nothing is selected. */<br />
function getSelectedConceptID() {<br />
var conceptID = null;<br />
var app = getApp();<br />
if (app && app.getSelectedConceptID) {<br />
conceptID = app.getSelectedConceptID();<br />
}<br />
return conceptID;<br />
}<br />
<br />
/** <br />
* Gets the full id (not all ontologies support this) of the currently selected concept. <br />
* Will be null if nothing is selected, will be the same as the conceptID if no fullID exists. <br />
*/<br />
function getSelectedConceptFullID() {<br />
var conceptID = null;<br />
var app = getApp();<br />
if (app && app.getSelectedConceptFullID) {<br />
conceptID = app.getSelectedConceptFullID();<br />
}<br />
return conceptID;<br />
}<br />
<br />
/** Gets the name of the currently selected concept, will be null if nothing is selected. */<br />
function getSelectedConceptName() {<br />
var conceptName = null;<br />
var app = getApp();<br />
if (app && app.getSelectedConceptName) {<br />
conceptName = app.getSelectedConceptName();<br />
}<br />
return conceptName;<br />
}<br />
<br />
/** Loads and selects a concept (by id) in the current ontology. */<br />
function loadConceptByID(conceptID) {<br />
var app = getApp();<br />
if (app && app.loadConceptByID) {<br />
app.loadConceptByID(conceptID);<br />
}<br />
}<br />
<br />
/** Attempts to load and select a concept (by name) in the current ontology. */<br />
function loadConceptByName(conceptName) {<br />
var app = getApp();<br />
if (app && app.loadConceptByName) {<br />
app.loadConceptByName(conceptName);<br />
}<br />
}<br />
<br />
/** This function gets call by flash when the swf has finished loading. */<br />
function appComplete(swfID) {<br />
// alert("flash app finished loading: " + swfID);<br />
}<br />
<br />
/** Implement this function to listen for tree selection changes */<br />
function treeSelectionChanged(nodeID, nodeName, swfID) {<br />
// alert("tree selection: " + nodeID + " - " + nodeName + " - " + swfID);<br />
}<br />
<br />
/** Implement this function to listen for tree double click events */<br />
function treeNodeDoubleClicked(nodeID, nodeName, swfID) {<br />
alert("tree node double clicked: " + nodeID + " - " + nodeName + " - " + swfID);<br />
}<br />
<br />
/** Implement this function to listen for error messages when loading an ontology */<br />
function errorLoadingOntology(errorMsg, swfID) {<br />
// alert("Error: " + errorMsg);<br />
}<br />
</pre><br />
<br />
= Referencing your ontology of interest in the widgets = <br />
<br />
Most of the time you would want your widget to use the latest version of your ontology of interest that is available in BioPortal. Thus, you would want to use the ontology id and not the version is in your widget. To find the ontology id, go to the "Ontology Details" page for your ontology of interest in BioPortal (e.g., the page for [http://bioportal.bioontology.org/ontologies/39478 NCI Thesaurus]). You will find the ontology id on the Metadata tab there (e.g., the ontology id for NCI Thesaurus is 1032).</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Mappings&diff=12228BioPortal Mappings2012-05-31T14:40:08Z<p>Darren Weber: /* Mapping Sources */ Adding links to web sites for NCBO, UMLS, and OBO foundry.</p>
<hr />
<div>= BioPortal Mapping Notes =<br />
<br />
This page documents mapping sources and common relationships in the [http://bioportal.bioontology.org NCBO BioPortal], with examples of different mappings that already exist in BioPortal. We welcome comments on the mapping processes and relations; please send email to [mailto:support@bioontology.org support@bioontology.org].<br />
<br />
== Related Mapping Documents ==<br />
<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service REST Service for Mappings]<br />
* [http://bioportal.bioontology.org/mappings BioPortal Mappings]<br />
<br />
= Mapping Sources =<br />
<br />
* [http://www.bioontology.org/ The National Center for Biomedical Ontology (NCBO)] <br />
** '''NCBO lexical mapping (loom)''': Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym. The lexical match involves removing white-space and punctuation from labels. Any labels with no more than 3 characters are excluded.<br />
** '''NCBO (Identical URI)''': Mapping for terms with the same URI from different ontologies.<br />
<br />
* [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS)]<br />
** '''NLM UMLS (CUI)''': Mappings between terms from different ontologies that were created automatically, linking terms with the same UMLS concept unique identifier (CUI). The CUIs are assigned to terms in the UMLS by editors at the NLM.<br />
** '''NLM UMLS (MRMAP)''': Mappings between terms from the UMLS MRMAP.RRF data.<br />
<br />
* [http://obofoundry.org/ The Open Biological and Biomedical Ontologies (OBO)]<br />
** '''OBO xref''': Mappings between ontology terms related by an OBO xref property.<br />
** See also, [http://obofoundry.org/index.cgi?show=mappings OBO mappings]<br />
<br />
= Mapping Relationships =<br />
<br />
There are mappings of the following types in BioPortal:<br />
<br />
* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]<br />
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual<br />
<br />
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]<br />
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource. <br />
<br />
* '''related match''': [http://www.w3.org/2004/02/skos/core#relatedMatch skos:relatedMatch]<br />
** '''Definition''': (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:relatedMatch</tt> is used to state an associative mapping link between two concepts; <tt>skos:relatedMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>. <br />
** '''Symmetry''': <tt>skos:relatedMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:relatedMatch <conceptB> .<br />
<conceptB> skos:relatedMatch <conceptA> .<br />
<br />
* '''close match''': [http://www.w3.org/2004/02/skos#closeMatch skos:closeMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property. The <tt>skos:closeMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:closeMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:closeMatch <conceptB> .<br />
<conceptB> skos:closeMatch <conceptA> .<br />
<br />
* '''exact match''': [http://www.w3.org/2004/02/skos#exactMatch skos:exactMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. The <tt>skos:exactMatch</tt> it is a sub-property of <tt>skos:closeMatch</tt> and, in addition, it is an instance of <tt>owl:TransitiveProperty</tt>. Also, <tt>skos:exactMatch</tt> is disjoint with each of the properties <tt>skos:relatedMatch</tt>, <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt>.<br />
** '''Symmetry''': <tt>skos:exactMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:exactMatch <conceptB> .<br />
<conceptB> skos:exactMatch <conceptA> .<br />
<br />
* '''broad match''': [http://www.w3.org/2004/02/skos/core#broadMatch skos:broadMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:broadMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:broadMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:narrowMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:broadMatch <conceptB> .<br />
<conceptB> skos:narrowMatch <conceptA> .<br />
<br />
* '''narrow match''': [http://www.w3.org/2004/02/skos/core#narrowMatch skos:narrowMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:narrowMatch</tt> and <tt>skos:broadMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:narrowMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:narrowMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:broadMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:narrowMatch <conceptB> .<br />
<conceptB> skos:broadMatch <conceptA> .<br />
<br />
* '''homologous to''' (for anatomical terms): ''not defined yet''<br />
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).<br />
<br />
= Survey of BioPortal Mappings =<br />
The table below presents the statistics and examples of BioPortal mappings as of July 2010.<br />
<br />
{| border="1" cellpadding="2"<br />
| align="center" style="background:#f0f0f0;"|'''relationship'''<br />
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''<br />
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''<br />
| align="center" style="background:#f0f0f0;"|'''Source'''<br />
| align="center" style="background:#f0f0f0;"|'''Total mappings'''<br />
| width="1025" align="center" style="background:#f0f0f0;"|'''Notes'''<br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||LEXEVS_UMLS_MAPPER||2,028,186||Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings<br />
<br />
<tt>select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||LOOM||1,449,303||Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "lexical similarity";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||||2,562||Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings<br />
<br />
<tt>select * from mappings where map_source = "exact match or synonym match";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Manual||||628||Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology<br />
<br />
<tt>select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";</tt><br />
|-<br />
| owl:sameAs||shared id||Manual||||271,000||Mappings between the terms that share the same ID<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "direct reference";</tt><br />
|-<br />
| rdfs:seeAlso||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms<br />
<br />
<tt>select * from mappings where map_source = "OBO xref";</tt><br />
|-<br />
| skos:exactMatch||Dbxref||Manual||||7,028||Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs<br />
<br />
<tt>select * from mappings where map_source = "DbXref";</tt><br />
|-<br />
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO<br />
<br />
<tt>select * from mappings where map_source = "Upload"; </tt><br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";</tt><br />
|-<br />
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface<br />
<br />
<tt>select * from mappings where map_source = "BioPortal UI"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT <br />
<br />
<tt>select * from mappings where map_source = "NCICB"</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT<br />
<br />
<tt>select * from mappings where map_source = "NLM"</tt><br />
|}</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Mappings&diff=12227BioPortal Mappings2012-05-31T14:27:55Z<p>Darren Weber: </p>
<hr />
<div>= BioPortal Mapping Notes =<br />
<br />
This page documents mapping sources and common relationships in the [http://bioportal.bioontology.org NCBO BioPortal], with examples of different mappings that already exist in BioPortal. We welcome comments on the mapping processes and relations; please send email to [mailto:support@bioontology.org support@bioontology.org].<br />
<br />
== Related Mapping Documents ==<br />
<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service REST Service for Mappings]<br />
* [http://bioportal.bioontology.org/mappings BioPortal Mappings]<br />
<br />
= Mapping Sources =<br />
<br />
* '''NCBO lexical mapping (loom)''': Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym. The lexical match involves removing white-space and punctuation from labels. Any labels with no more than 3 characters are excluded.<br />
* '''NCBO (Identical URI)''': Mapping for terms with the same URI from different ontologies.<br />
* '''NLM UMLS (CUI)''': Mappings between terms from different ontologies that were created automatically, linking terms with the same UMLS concept unique identifier (CUI). The CUIs are assigned to terms in the UMLS by editors at the NLM.<br />
* '''NLM UMLS (MRMAP)''': Mappings between terms from the UMLS MRMAP.RRF data.<br />
* '''OBO xref''': Mappings between ontology terms related by an OBO xref.<br />
<br />
= Mapping Relationships =<br />
<br />
There are mappings of the following types in BioPortal:<br />
<br />
* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]<br />
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual<br />
<br />
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]<br />
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource. <br />
<br />
* '''related match''': [http://www.w3.org/2004/02/skos/core#relatedMatch skos:relatedMatch]<br />
** '''Definition''': (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:relatedMatch</tt> is used to state an associative mapping link between two concepts; <tt>skos:relatedMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>. <br />
** '''Symmetry''': <tt>skos:relatedMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:relatedMatch <conceptB> .<br />
<conceptB> skos:relatedMatch <conceptA> .<br />
<br />
* '''close match''': [http://www.w3.org/2004/02/skos#closeMatch skos:closeMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property. The <tt>skos:closeMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:closeMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:closeMatch <conceptB> .<br />
<conceptB> skos:closeMatch <conceptA> .<br />
<br />
* '''exact match''': [http://www.w3.org/2004/02/skos#exactMatch skos:exactMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. The <tt>skos:exactMatch</tt> it is a sub-property of <tt>skos:closeMatch</tt> and, in addition, it is an instance of <tt>owl:TransitiveProperty</tt>. Also, <tt>skos:exactMatch</tt> is disjoint with each of the properties <tt>skos:relatedMatch</tt>, <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt>.<br />
** '''Symmetry''': <tt>skos:exactMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:exactMatch <conceptB> .<br />
<conceptB> skos:exactMatch <conceptA> .<br />
<br />
* '''broad match''': [http://www.w3.org/2004/02/skos/core#broadMatch skos:broadMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:broadMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:broadMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:narrowMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:broadMatch <conceptB> .<br />
<conceptB> skos:narrowMatch <conceptA> .<br />
<br />
* '''narrow match''': [http://www.w3.org/2004/02/skos/core#narrowMatch skos:narrowMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:narrowMatch</tt> and <tt>skos:broadMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:narrowMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:narrowMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:broadMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:narrowMatch <conceptB> .<br />
<conceptB> skos:broadMatch <conceptA> .<br />
<br />
* '''homologous to''' (for anatomical terms): ''not defined yet''<br />
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).<br />
<br />
= Survey of BioPortal Mappings =<br />
The table below presents the statistics and examples of BioPortal mappings as of July 2010.<br />
<br />
{| border="1" cellpadding="2"<br />
| align="center" style="background:#f0f0f0;"|'''relationship'''<br />
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''<br />
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''<br />
| align="center" style="background:#f0f0f0;"|'''Source'''<br />
| align="center" style="background:#f0f0f0;"|'''Total mappings'''<br />
| width="1025" align="center" style="background:#f0f0f0;"|'''Notes'''<br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||LEXEVS_UMLS_MAPPER||2,028,186||Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings<br />
<br />
<tt>select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||LOOM||1,449,303||Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "lexical similarity";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||||2,562||Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings<br />
<br />
<tt>select * from mappings where map_source = "exact match or synonym match";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Manual||||628||Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology<br />
<br />
<tt>select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";</tt><br />
|-<br />
| owl:sameAs||shared id||Manual||||271,000||Mappings between the terms that share the same ID<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "direct reference";</tt><br />
|-<br />
| rdfs:seeAlso||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms<br />
<br />
<tt>select * from mappings where map_source = "OBO xref";</tt><br />
|-<br />
| skos:exactMatch||Dbxref||Manual||||7,028||Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs<br />
<br />
<tt>select * from mappings where map_source = "DbXref";</tt><br />
|-<br />
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO<br />
<br />
<tt>select * from mappings where map_source = "Upload"; </tt><br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";</tt><br />
|-<br />
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface<br />
<br />
<tt>select * from mappings where map_source = "BioPortal UI"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT <br />
<br />
<tt>select * from mappings where map_source = "NCICB"</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT<br />
<br />
<tt>select * from mappings where map_source = "NLM"</tt><br />
|}</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Mappings&diff=12226BioPortal Mappings2012-05-31T14:26:54Z<p>Darren Weber: </p>
<hr />
<div>= BioPortal Mapping Notes =<br />
<br />
This page documents mapping processes and common mapping types in the [http://bioportal.bioontology.org NCBO BioPortal], with examples of different mappings that already exist in BioPortal. We welcome comments on the mapping processes and relations; please send email to [mailto:support@bioontology.org support@bioontology.org].<br />
<br />
== Related Mapping Documents ==<br />
<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service REST Service for Mappings]<br />
* [http://bioportal.bioontology.org/mappings BioPortal Mappings]<br />
<br />
= Mapping Processes =<br />
<br />
* '''NCBO lexical mapping (loom)''': Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym. The lexical match involves removing white-space and punctuation from labels. Any labels with no more than 3 characters are excluded.<br />
* '''NCBO (Identical URI)''': Mapping for terms with the same URI from different ontologies.<br />
* '''NLM UMLS (CUI)''': Mappings between terms from different ontologies that were created automatically, linking terms with the same UMLS concept unique identifier (CUI). The CUIs are assigned to terms in the UMLS by editors at the NLM.<br />
* '''NLM UMLS (MRMAP)''': Mappings between terms from the UMLS MRMAP.RRF data.<br />
* '''OBO xref''': Mappings between ontology terms related by an OBO xref.<br />
<br />
= Mapping Relationships =<br />
<br />
There are mappings of the following types in BioPortal:<br />
<br />
* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]<br />
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual<br />
<br />
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]<br />
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource. <br />
<br />
* '''related match''': [http://www.w3.org/2004/02/skos/core#relatedMatch skos:relatedMatch]<br />
** '''Definition''': (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:relatedMatch</tt> is used to state an associative mapping link between two concepts; <tt>skos:relatedMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>. <br />
** '''Symmetry''': <tt>skos:relatedMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:relatedMatch <conceptB> .<br />
<conceptB> skos:relatedMatch <conceptA> .<br />
<br />
* '''close match''': [http://www.w3.org/2004/02/skos#closeMatch skos:closeMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property. The <tt>skos:closeMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:closeMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:closeMatch <conceptB> .<br />
<conceptB> skos:closeMatch <conceptA> .<br />
<br />
* '''exact match''': [http://www.w3.org/2004/02/skos#exactMatch skos:exactMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. The <tt>skos:exactMatch</tt> it is a sub-property of <tt>skos:closeMatch</tt> and, in addition, it is an instance of <tt>owl:TransitiveProperty</tt>. Also, <tt>skos:exactMatch</tt> is disjoint with each of the properties <tt>skos:relatedMatch</tt>, <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt>.<br />
** '''Symmetry''': <tt>skos:exactMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:exactMatch <conceptB> .<br />
<conceptB> skos:exactMatch <conceptA> .<br />
<br />
* '''broad match''': [http://www.w3.org/2004/02/skos/core#broadMatch skos:broadMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:broadMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:broadMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:narrowMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:broadMatch <conceptB> .<br />
<conceptB> skos:narrowMatch <conceptA> .<br />
<br />
* '''narrow match''': [http://www.w3.org/2004/02/skos/core#narrowMatch skos:narrowMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:narrowMatch</tt> and <tt>skos:broadMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:narrowMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:narrowMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:broadMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:narrowMatch <conceptB> .<br />
<conceptB> skos:broadMatch <conceptA> .<br />
<br />
* '''homologous to''' (for anatomical terms): ''not defined yet''<br />
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).<br />
<br />
= Survey of BioPortal Mappings =<br />
The table below presents the statistics and examples of BioPortal mappings as of July 2010.<br />
<br />
{| border="1" cellpadding="2"<br />
| align="center" style="background:#f0f0f0;"|'''relationship'''<br />
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''<br />
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''<br />
| align="center" style="background:#f0f0f0;"|'''Source'''<br />
| align="center" style="background:#f0f0f0;"|'''Total mappings'''<br />
| width="1025" align="center" style="background:#f0f0f0;"|'''Notes'''<br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||LEXEVS_UMLS_MAPPER||2,028,186||Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings<br />
<br />
<tt>select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||LOOM||1,449,303||Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "lexical similarity";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||||2,562||Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings<br />
<br />
<tt>select * from mappings where map_source = "exact match or synonym match";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Manual||||628||Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology<br />
<br />
<tt>select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";</tt><br />
|-<br />
| owl:sameAs||shared id||Manual||||271,000||Mappings between the terms that share the same ID<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "direct reference";</tt><br />
|-<br />
| rdfs:seeAlso||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms<br />
<br />
<tt>select * from mappings where map_source = "OBO xref";</tt><br />
|-<br />
| skos:exactMatch||Dbxref||Manual||||7,028||Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs<br />
<br />
<tt>select * from mappings where map_source = "DbXref";</tt><br />
|-<br />
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO<br />
<br />
<tt>select * from mappings where map_source = "Upload"; </tt><br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";</tt><br />
|-<br />
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface<br />
<br />
<tt>select * from mappings where map_source = "BioPortal UI"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT <br />
<br />
<tt>select * from mappings where map_source = "NCICB"</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT<br />
<br />
<tt>select * from mappings where map_source = "NLM"</tt><br />
|}</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Mappings&diff=12222BioPortal Mappings2012-05-30T01:39:07Z<p>Darren Weber: </p>
<hr />
<div>= BioPortal Mapping Notes =<br />
<br />
This page documents mapping processes and common mapping types in the [http://bioportal.bioontology.org NCBO BioPortal], with examples of different mappings that already exist in BioPortal. We welcome comments on the mapping processes and relations; please send email to [mailto:support@bioontology.org support@bioontology.org].<br />
<br />
== Related Mapping Documents ==<br />
<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service REST Service for Mappings]<br />
* [http://bioportal.bioontology.org/mappings BioPortal Mappings]<br />
<br />
= Mapping Processes =<br />
<br />
* '''NCBO lexical mapping (loom)''': Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym. The lexical match involves removing white-space and punctuation from labels. Any labels with no more than 3 characters are excluded.<br />
* '''NCBO (Identical URI)''': Mapping for terms with the same URI from different ontologies.<br />
* '''NLM UMLS (CUI)''': Mappings between terms from different ontologies that were created automatically, linking terms with the same UMLS concept unique identifier (CUI). The CUIs are assigned to terms in the UMLS by editors at the NLM.<br />
* '''NLM UMLS (MRMAP)''': Mappings between terms from the UMLS MRMAP.RRF data.<br />
* '''OBO xref''': Mappings between ontology terms related by an OBO xref.<br />
<br />
= BioPortal Mapping Types =<br />
<br />
There are mappings of the following types in BioPortal:<br />
<br />
* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]<br />
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual<br />
<br />
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]<br />
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource. <br />
<br />
* '''related match''': [http://www.w3.org/2004/02/skos/core#relatedMatch skos:relatedMatch]<br />
** '''Definition''': (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:relatedMatch</tt> is used to state an associative mapping link between two concepts; <tt>skos:relatedMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>. <br />
** '''Symmetry''': <tt>skos:relatedMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:relatedMatch <conceptB> .<br />
<conceptB> skos:relatedMatch <conceptA> .<br />
<br />
* '''close match''': [http://www.w3.org/2004/02/skos#closeMatch skos:closeMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property. The <tt>skos:closeMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:closeMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:closeMatch <conceptB> .<br />
<conceptB> skos:closeMatch <conceptA> .<br />
<br />
* '''exact match''': [http://www.w3.org/2004/02/skos#exactMatch skos:exactMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. The <tt>skos:exactMatch</tt> it is a sub-property of <tt>skos:closeMatch</tt> and, in addition, it is an instance of <tt>owl:TransitiveProperty</tt>. Also, <tt>skos:exactMatch</tt> is disjoint with each of the properties <tt>skos:relatedMatch</tt>, <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt>.<br />
** '''Symmetry''': <tt>skos:exactMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:exactMatch <conceptB> .<br />
<conceptB> skos:exactMatch <conceptA> .<br />
<br />
* '''broad match''': [http://www.w3.org/2004/02/skos/core#broadMatch skos:broadMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:broadMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:broadMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:narrowMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:broadMatch <conceptB> .<br />
<conceptB> skos:narrowMatch <conceptA> .<br />
<br />
* '''narrow match''': [http://www.w3.org/2004/02/skos/core#narrowMatch skos:narrowMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:narrowMatch</tt> and <tt>skos:broadMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:narrowMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:narrowMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:broadMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:narrowMatch <conceptB> .<br />
<conceptB> skos:broadMatch <conceptA> .<br />
<br />
* '''homologous to''' (for anatomical terms): ''not defined yet''<br />
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).<br />
<br />
= Survey of BioPortal Mappings =<br />
The table below presents the statistics and examples of BioPortal mappings as of July 2010.<br />
<br />
{| border="1" cellpadding="2"<br />
| align="center" style="background:#f0f0f0;"|'''relationship'''<br />
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''<br />
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''<br />
| align="center" style="background:#f0f0f0;"|'''Source'''<br />
| align="center" style="background:#f0f0f0;"|'''Total mappings'''<br />
| width="1025" align="center" style="background:#f0f0f0;"|'''Notes'''<br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||LEXEVS_UMLS_MAPPER||2,028,186||Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings<br />
<br />
<tt>select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||LOOM||1,449,303||Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "lexical similarity";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||||2,562||Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings<br />
<br />
<tt>select * from mappings where map_source = "exact match or synonym match";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Manual||||628||Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology<br />
<br />
<tt>select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";</tt><br />
|-<br />
| owl:sameAs||shared id||Manual||||271,000||Mappings between the terms that share the same ID<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "direct reference";</tt><br />
|-<br />
| rdfs:seeAlso||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms<br />
<br />
<tt>select * from mappings where map_source = "OBO xref";</tt><br />
|-<br />
| skos:exactMatch||Dbxref||Manual||||7,028||Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs<br />
<br />
<tt>select * from mappings where map_source = "DbXref";</tt><br />
|-<br />
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO<br />
<br />
<tt>select * from mappings where map_source = "Upload"; </tt><br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";</tt><br />
|-<br />
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface<br />
<br />
<tt>select * from mappings where map_source = "BioPortal UI"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT <br />
<br />
<tt>select * from mappings where map_source = "NCICB"</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT<br />
<br />
<tt>select * from mappings where map_source = "NLM"</tt><br />
|}</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Mappings&diff=12221BioPortal Mappings2012-05-30T01:38:26Z<p>Darren Weber: </p>
<hr />
<div>= BioPortal Mapping Notes =<br />
<br />
This page documents mapping processes and common mapping types in the [http://bioportal.bioontology.org NCBO BioPortal], with examples of different mappings that already exist in BioPortal. We welcome comments on the mapping processes and relations; please send email to [mailto:support@bioontology.org support@bioontology.org].<br />
<br />
== Related Mapping Documents ==<br />
<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service REST Service for Mappings]<br />
* [http://bioportal.bioontology.org/mappings BioPortal Mappings]<br />
<br />
<br />
= Mapping Processes =<br />
<br />
* '''NCBO lexical mapping (loom)''': Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym. The lexical match involves removing white-space and punctuation from labels. Any labels with no more than 3 characters are excluded.<br />
<br />
* '''NCBO (Identical URI)''': Mapping for terms with the same URI from different ontologies.<br />
<br />
* '''NLM UMLS (CUI)''': Mappings between terms from different ontologies that were created automatically, linking terms with the same UMLS concept unique identifier (CUI). The CUIs are assigned to terms in the UMLS by editors at the NLM.<br />
<br />
* '''NLM UMLS (MRMAP)''': Mappings between terms from the UMLS MRMAP.RRF data.<br />
<br />
* '''OBO xref''': Mappings between ontology terms related by an OBO xref.<br />
<br />
<br />
<br />
<br />
= BioPortal Mapping Types =<br />
<br />
There are mappings of the following types in BioPortal:<br />
<br />
* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]<br />
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual<br />
<br />
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]<br />
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource. <br />
<br />
* '''related match''': [http://www.w3.org/2004/02/skos/core#relatedMatch skos:relatedMatch]<br />
** '''Definition''': (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:relatedMatch</tt> is used to state an associative mapping link between two concepts; <tt>skos:relatedMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>. <br />
** '''Symmetry''': <tt>skos:relatedMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:relatedMatch <conceptB> .<br />
<conceptB> skos:relatedMatch <conceptA> .<br />
<br />
* '''close match''': [http://www.w3.org/2004/02/skos#closeMatch skos:closeMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property. The <tt>skos:closeMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:closeMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:closeMatch <conceptB> .<br />
<conceptB> skos:closeMatch <conceptA> .<br />
<br />
* '''exact match''': [http://www.w3.org/2004/02/skos#exactMatch skos:exactMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. The <tt>skos:exactMatch</tt> it is a sub-property of <tt>skos:closeMatch</tt> and, in addition, it is an instance of <tt>owl:TransitiveProperty</tt>. Also, <tt>skos:exactMatch</tt> is disjoint with each of the properties <tt>skos:relatedMatch</tt>, <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt>.<br />
** '''Symmetry''': <tt>skos:exactMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:exactMatch <conceptB> .<br />
<conceptB> skos:exactMatch <conceptA> .<br />
<br />
* '''broad match''': [http://www.w3.org/2004/02/skos/core#broadMatch skos:broadMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:broadMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:broadMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:narrowMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:broadMatch <conceptB> .<br />
<conceptB> skos:narrowMatch <conceptA> .<br />
<br />
* '''narrow match''': [http://www.w3.org/2004/02/skos/core#narrowMatch skos:narrowMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:narrowMatch</tt> and <tt>skos:broadMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:narrowMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:narrowMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:broadMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:narrowMatch <conceptB> .<br />
<conceptB> skos:broadMatch <conceptA> .<br />
<br />
* '''homologous to''' (for anatomical terms): ''not defined yet''<br />
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).<br />
<br />
= Survey of BioPortal Mappings =<br />
The table below presents the statistics and examples of BioPortal mappings as of July 2010.<br />
<br />
{| border="1" cellpadding="2"<br />
| align="center" style="background:#f0f0f0;"|'''relationship'''<br />
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''<br />
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''<br />
| align="center" style="background:#f0f0f0;"|'''Source'''<br />
| align="center" style="background:#f0f0f0;"|'''Total mappings'''<br />
| width="1025" align="center" style="background:#f0f0f0;"|'''Notes'''<br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||LEXEVS_UMLS_MAPPER||2,028,186||Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings<br />
<br />
<tt>select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||LOOM||1,449,303||Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "lexical similarity";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||||2,562||Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings<br />
<br />
<tt>select * from mappings where map_source = "exact match or synonym match";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Manual||||628||Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology<br />
<br />
<tt>select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";</tt><br />
|-<br />
| owl:sameAs||shared id||Manual||||271,000||Mappings between the terms that share the same ID<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "direct reference";</tt><br />
|-<br />
| rdfs:seeAlso||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms<br />
<br />
<tt>select * from mappings where map_source = "OBO xref";</tt><br />
|-<br />
| skos:exactMatch||Dbxref||Manual||||7,028||Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs<br />
<br />
<tt>select * from mappings where map_source = "DbXref";</tt><br />
|-<br />
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO<br />
<br />
<tt>select * from mappings where map_source = "Upload"; </tt><br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";</tt><br />
|-<br />
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface<br />
<br />
<tt>select * from mappings where map_source = "BioPortal UI"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT <br />
<br />
<tt>select * from mappings where map_source = "NCICB"</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT<br />
<br />
<tt>select * from mappings where map_source = "NLM"</tt><br />
|}</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Mappings&diff=12219BioPortal Mappings2012-05-29T22:01:56Z<p>Darren Weber: Retitle document, so it can incorporate notes on mapping processes.</p>
<hr />
<div>= BioPortal Mapping Notes =<br />
<br />
This page documents mapping processes and common mapping types in the [http://bioportal.bioontology.org NCBO BioPortal], with examples of different mappings that already exist in BioPortal. We welcome comments on the mapping processes and relations; please send email to [mailto:support@bioontology.org support@bioontology.org].<br />
<br />
== Related Mapping Documents ==<br />
<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service REST Service for Mappings]<br />
* [http://bioportal.bioontology.org/mappings BioPortal Mappings]<br />
<br />
<br />
= Mapping Processes =<br />
<br />
= BioPortal Mapping Types =<br />
<br />
There are mappings of the following types in BioPortal:<br />
<br />
* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]<br />
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual<br />
<br />
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]<br />
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource. <br />
<br />
* '''related match''': [http://www.w3.org/2004/02/skos/core#relatedMatch skos:relatedMatch]<br />
** '''Definition''': (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:relatedMatch</tt> is used to state an associative mapping link between two concepts; <tt>skos:relatedMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>. <br />
** '''Symmetry''': <tt>skos:relatedMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:relatedMatch <conceptB> .<br />
<conceptB> skos:relatedMatch <conceptA> .<br />
<br />
* '''close match''': [http://www.w3.org/2004/02/skos#closeMatch skos:closeMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property. The <tt>skos:closeMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:closeMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:closeMatch <conceptB> .<br />
<conceptB> skos:closeMatch <conceptA> .<br />
<br />
* '''exact match''': [http://www.w3.org/2004/02/skos#exactMatch skos:exactMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. The <tt>skos:exactMatch</tt> it is a sub-property of <tt>skos:closeMatch</tt> and, in addition, it is an instance of <tt>owl:TransitiveProperty</tt>. Also, <tt>skos:exactMatch</tt> is disjoint with each of the properties <tt>skos:relatedMatch</tt>, <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt>.<br />
** '''Symmetry''': <tt>skos:exactMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:exactMatch <conceptB> .<br />
<conceptB> skos:exactMatch <conceptA> .<br />
<br />
* '''broad match''': [http://www.w3.org/2004/02/skos/core#broadMatch skos:broadMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:broadMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:broadMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:narrowMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:broadMatch <conceptB> .<br />
<conceptB> skos:narrowMatch <conceptA> .<br />
<br />
* '''narrow match''': [http://www.w3.org/2004/02/skos/core#narrowMatch skos:narrowMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:narrowMatch</tt> and <tt>skos:broadMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:narrowMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:narrowMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:broadMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:narrowMatch <conceptB> .<br />
<conceptB> skos:broadMatch <conceptA> .<br />
<br />
* '''homologous to''' (for anatomical terms): ''not defined yet''<br />
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).<br />
<br />
= Survey of BioPortal Mappings =<br />
The table below presents the statistics and examples of BioPortal mappings as of July 2010.<br />
<br />
{| border="1" cellpadding="2"<br />
| align="center" style="background:#f0f0f0;"|'''relationship'''<br />
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''<br />
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''<br />
| align="center" style="background:#f0f0f0;"|'''Source'''<br />
| align="center" style="background:#f0f0f0;"|'''Total mappings'''<br />
| width="1025" align="center" style="background:#f0f0f0;"|'''Notes'''<br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||LEXEVS_UMLS_MAPPER||2,028,186||Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings<br />
<br />
<tt>select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||LOOM||1,449,303||Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "lexical similarity";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||||2,562||Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings<br />
<br />
<tt>select * from mappings where map_source = "exact match or synonym match";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Manual||||628||Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology<br />
<br />
<tt>select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";</tt><br />
|-<br />
| owl:sameAs||shared id||Manual||||271,000||Mappings between the terms that share the same ID<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "direct reference";</tt><br />
|-<br />
| rdfs:seeAlso||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms<br />
<br />
<tt>select * from mappings where map_source = "OBO xref";</tt><br />
|-<br />
| skos:exactMatch||Dbxref||Manual||||7,028||Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs<br />
<br />
<tt>select * from mappings where map_source = "DbXref";</tt><br />
|-<br />
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO<br />
<br />
<tt>select * from mappings where map_source = "Upload"; </tt><br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";</tt><br />
|-<br />
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface<br />
<br />
<tt>select * from mappings where map_source = "BioPortal UI"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT <br />
<br />
<tt>select * from mappings where map_source = "NCICB"</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT<br />
<br />
<tt>select * from mappings where map_source = "NLM"</tt><br />
|}</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Mappings&diff=12218BioPortal Mappings2012-05-29T21:59:13Z<p>Darren Weber: </p>
<hr />
<div>This page defines common mapping types in the [http://bioportal.bioontology.org NCBO BioPortal] and provides examples of different mappings that already exist in BioPortal. We welcome comments on this set of mapping relations. Please send email to [mailto:support@bioontology.org support@bioontology.org].<br />
<br />
= Related Mapping Documents =<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service REST Service for Mappings]<br />
* [http://bioportal.bioontology.org/mappings BioPortal Mappings]<br />
<br />
<br />
= BioPortal Mapping Types =<br />
<br />
There are mappings of the following types in BioPortal:<br />
<br />
* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]<br />
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual<br />
<br />
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]<br />
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource. <br />
<br />
* '''related match''': [http://www.w3.org/2004/02/skos/core#relatedMatch skos:relatedMatch]<br />
** '''Definition''': (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:relatedMatch</tt> is used to state an associative mapping link between two concepts; <tt>skos:relatedMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>. <br />
** '''Symmetry''': <tt>skos:relatedMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:relatedMatch <conceptB> .<br />
<conceptB> skos:relatedMatch <conceptA> .<br />
<br />
* '''close match''': [http://www.w3.org/2004/02/skos#closeMatch skos:closeMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property. The <tt>skos:closeMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:closeMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:closeMatch <conceptB> .<br />
<conceptB> skos:closeMatch <conceptA> .<br />
<br />
* '''exact match''': [http://www.w3.org/2004/02/skos#exactMatch skos:exactMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. The <tt>skos:exactMatch</tt> it is a sub-property of <tt>skos:closeMatch</tt> and, in addition, it is an instance of <tt>owl:TransitiveProperty</tt>. Also, <tt>skos:exactMatch</tt> is disjoint with each of the properties <tt>skos:relatedMatch</tt>, <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt>.<br />
** '''Symmetry''': <tt>skos:exactMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:exactMatch <conceptB> .<br />
<conceptB> skos:exactMatch <conceptA> .<br />
<br />
* '''broad match''': [http://www.w3.org/2004/02/skos/core#broadMatch skos:broadMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:broadMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:broadMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:narrowMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:broadMatch <conceptB> .<br />
<conceptB> skos:narrowMatch <conceptA> .<br />
<br />
* '''narrow match''': [http://www.w3.org/2004/02/skos/core#narrowMatch skos:narrowMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:narrowMatch</tt> and <tt>skos:broadMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:narrowMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:narrowMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:broadMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:narrowMatch <conceptB> .<br />
<conceptB> skos:broadMatch <conceptA> .<br />
<br />
* '''homologous to''' (for anatomical terms): ''not defined yet''<br />
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).<br />
<br />
= Survey of BioPortal Mappings =<br />
The table below presents the statistics and examples of BioPortal mappings as of July 2010.<br />
<br />
{| border="1" cellpadding="2"<br />
| align="center" style="background:#f0f0f0;"|'''relationship'''<br />
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''<br />
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''<br />
| align="center" style="background:#f0f0f0;"|'''Source'''<br />
| align="center" style="background:#f0f0f0;"|'''Total mappings'''<br />
| width="1025" align="center" style="background:#f0f0f0;"|'''Notes'''<br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||LEXEVS_UMLS_MAPPER||2,028,186||Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings<br />
<br />
<tt>select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||LOOM||1,449,303||Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "lexical similarity";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||||2,562||Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings<br />
<br />
<tt>select * from mappings where map_source = "exact match or synonym match";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Manual||||628||Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology<br />
<br />
<tt>select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";</tt><br />
|-<br />
| owl:sameAs||shared id||Manual||||271,000||Mappings between the terms that share the same ID<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "direct reference";</tt><br />
|-<br />
| rdfs:seeAlso||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms<br />
<br />
<tt>select * from mappings where map_source = "OBO xref";</tt><br />
|-<br />
| skos:exactMatch||Dbxref||Manual||||7,028||Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs<br />
<br />
<tt>select * from mappings where map_source = "DbXref";</tt><br />
|-<br />
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO<br />
<br />
<tt>select * from mappings where map_source = "Upload"; </tt><br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";</tt><br />
|-<br />
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface<br />
<br />
<tt>select * from mappings where map_source = "BioPortal UI"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT <br />
<br />
<tt>select * from mappings where map_source = "NCICB"</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT<br />
<br />
<tt>select * from mappings where map_source = "NLM"</tt><br />
|}</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Mappings&diff=12215BioPortal Mappings2012-05-29T21:53:05Z<p>Darren Weber: Add related links for mappings.</p>
<hr />
<div>This page defines common mapping types in the [http://bioportal.bioontology.org NCBO BioPortal] and provides examples of different mappings that already exist in BioPortal. We welcome comments on this set of mapping relations. Please send email to [mailto:support@bioontology.org support@bioontology.org].<br />
<br />
Related mapping documents:<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service REST service for mappings]<br />
* [http://bioportal.bioontology.org/mappings Bioportal mappings]<br />
<br />
<br />
= BioPortal Mapping Types =<br />
<br />
There are mappings of the following types in BioPortal:<br />
<br />
* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]<br />
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual<br />
<br />
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]<br />
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource. <br />
<br />
* '''related match''': [http://www.w3.org/2004/02/skos/core#relatedMatch skos:relatedMatch]<br />
** '''Definition''': (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:relatedMatch</tt> is used to state an associative mapping link between two concepts; <tt>skos:relatedMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>. <br />
** '''Symmetry''': <tt>skos:relatedMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:relatedMatch <conceptB> .<br />
<conceptB> skos:relatedMatch <conceptA> .<br />
<br />
* '''close match''': [http://www.w3.org/2004/02/skos#closeMatch skos:closeMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property. The <tt>skos:closeMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:closeMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:closeMatch <conceptB> .<br />
<conceptB> skos:closeMatch <conceptA> .<br />
<br />
* '''exact match''': [http://www.w3.org/2004/02/skos#exactMatch skos:exactMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. The <tt>skos:exactMatch</tt> it is a sub-property of <tt>skos:closeMatch</tt> and, in addition, it is an instance of <tt>owl:TransitiveProperty</tt>. Also, <tt>skos:exactMatch</tt> is disjoint with each of the properties <tt>skos:relatedMatch</tt>, <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt>.<br />
** '''Symmetry''': <tt>skos:exactMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:exactMatch <conceptB> .<br />
<conceptB> skos:exactMatch <conceptA> .<br />
<br />
* '''broad match''': [http://www.w3.org/2004/02/skos/core#broadMatch skos:broadMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:broadMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:broadMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:narrowMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:broadMatch <conceptB> .<br />
<conceptB> skos:narrowMatch <conceptA> .<br />
<br />
* '''narrow match''': [http://www.w3.org/2004/02/skos/core#narrowMatch skos:narrowMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:narrowMatch</tt> and <tt>skos:broadMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:narrowMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:narrowMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:broadMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:narrowMatch <conceptB> .<br />
<conceptB> skos:broadMatch <conceptA> .<br />
<br />
* '''homologous to''' (for anatomical terms): ''not defined yet''<br />
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).<br />
<br />
= Survey of BioPortal Mappings =<br />
The table below presents the statistics and examples of BioPortal mappings as of July 2010.<br />
<br />
{| border="1" cellpadding="2"<br />
| align="center" style="background:#f0f0f0;"|'''relationship'''<br />
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''<br />
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''<br />
| align="center" style="background:#f0f0f0;"|'''Source'''<br />
| align="center" style="background:#f0f0f0;"|'''Total mappings'''<br />
| width="1025" align="center" style="background:#f0f0f0;"|'''Notes'''<br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||LEXEVS_UMLS_MAPPER||2,028,186||Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings<br />
<br />
<tt>select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||LOOM||1,449,303||Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "lexical similarity";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||||2,562||Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings<br />
<br />
<tt>select * from mappings where map_source = "exact match or synonym match";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Manual||||628||Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology<br />
<br />
<tt>select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";</tt><br />
|-<br />
| owl:sameAs||shared id||Manual||||271,000||Mappings between the terms that share the same ID<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "direct reference";</tt><br />
|-<br />
| rdfs:seeAlso||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms<br />
<br />
<tt>select * from mappings where map_source = "OBO xref";</tt><br />
|-<br />
| skos:exactMatch||Dbxref||Manual||||7,028||Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs<br />
<br />
<tt>select * from mappings where map_source = "DbXref";</tt><br />
|-<br />
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO<br />
<br />
<tt>select * from mappings where map_source = "Upload"; </tt><br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";</tt><br />
|-<br />
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface<br />
<br />
<tt>select * from mappings where map_source = "BioPortal UI"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT <br />
<br />
<tt>select * from mappings where map_source = "NCICB"</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT<br />
<br />
<tt>select * from mappings where map_source = "NLM"</tt><br />
|}</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Mappings&diff=12104BioPortal Mappings2012-04-27T05:35:47Z<p>Darren Weber: Added additional skos mapping types, updated links to skos recommended edition, added notes about symmetry with examples of bidirectional mappings.</p>
<hr />
<div>This page defines common mapping types in the [http://bioportal.bioontology.org NCBO BioPortal] and provides examples of different mappings that already exist in BioPortal. We welcome comments on this set of mapping relations. Please send email to [mailto:support@bioontology.org support@bioontology.org].<br />
<br />
= BioPortal Mapping Types =<br />
<br />
There are mappings of the following types in BioPortal:<br />
<br />
* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]<br />
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual<br />
<br />
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]<br />
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource. <br />
<br />
* '''related match''': [http://www.w3.org/2004/02/skos/core#relatedMatch skos:relatedMatch]<br />
** '''Definition''': (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:relatedMatch</tt> is used to state an associative mapping link between two concepts; <tt>skos:relatedMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>. <br />
** '''Symmetry''': <tt>skos:relatedMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:relatedMatch <conceptB> .<br />
<conceptB> skos:relatedMatch <conceptA> .<br />
<br />
* '''close match''': [http://www.w3.org/2004/02/skos#closeMatch skos:closeMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property. The <tt>skos:closeMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:closeMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:closeMatch <conceptB> .<br />
<conceptB> skos:closeMatch <conceptA> .<br />
<br />
* '''exact match''': [http://www.w3.org/2004/02/skos#exactMatch skos:exactMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. The <tt>skos:exactMatch</tt> it is a sub-property of <tt>skos:closeMatch</tt> and, in addition, it is an instance of <tt>owl:TransitiveProperty</tt>. Also, <tt>skos:exactMatch</tt> is disjoint with each of the properties <tt>skos:relatedMatch</tt>, <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt>.<br />
** '''Symmetry''': <tt>skos:exactMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:exactMatch <conceptB> .<br />
<conceptB> skos:exactMatch <conceptA> .<br />
<br />
* '''broad match''': [http://www.w3.org/2004/02/skos/core#broadMatch skos:broadMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:broadMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:broadMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:narrowMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:broadMatch <conceptB> .<br />
<conceptB> skos:narrowMatch <conceptA> .<br />
<br />
* '''narrow match''': [http://www.w3.org/2004/02/skos/core#narrowMatch skos:narrowMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:narrowMatch</tt> and <tt>skos:broadMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:narrowMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:narrowMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:broadMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:narrowMatch <conceptB> .<br />
<conceptB> skos:broadMatch <conceptA> .<br />
<br />
* '''homologous to''' (for anatomical terms): ''not defined yet''<br />
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).<br />
<br />
= Survey of BioPortal Mappings =<br />
The table below presents the statistics and examples of BioPortal mappings as of July 2010.<br />
<br />
{| border="1" cellpadding="2"<br />
| align="center" style="background:#f0f0f0;"|'''relationship'''<br />
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''<br />
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''<br />
| align="center" style="background:#f0f0f0;"|'''Source'''<br />
| align="center" style="background:#f0f0f0;"|'''Total mappings'''<br />
| width="1025" align="center" style="background:#f0f0f0;"|'''Notes'''<br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||LEXEVS_UMLS_MAPPER||2,028,186||Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings<br />
<br />
<tt>select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||LOOM||1,449,303||Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "lexical similarity";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||||2,562||Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings<br />
<br />
<tt>select * from mappings where map_source = "exact match or synonym match";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Manual||||628||Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology<br />
<br />
<tt>select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";</tt><br />
|-<br />
| owl:sameAs||shared id||Manual||||271,000||Mappings between the terms that share the same ID<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "direct reference";</tt><br />
|-<br />
| rdfs:seeAlso||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms<br />
<br />
<tt>select * from mappings where map_source = "OBO xref";</tt><br />
|-<br />
| skos:exactMatch||Dbxref||Manual||||7,028||Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs<br />
<br />
<tt>select * from mappings where map_source = "DbXref";</tt><br />
|-<br />
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO<br />
<br />
<tt>select * from mappings where map_source = "Upload"; </tt><br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";</tt><br />
|-<br />
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface<br />
<br />
<tt>select * from mappings where map_source = "BioPortal UI"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT <br />
<br />
<tt>select * from mappings where map_source = "NCICB"</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT<br />
<br />
<tt>select * from mappings where map_source = "NLM"</tt><br />
|}</div>Darren Weberhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=12103BioPortal Help2012-04-27T00:31:26Z<p>Darren Weber: /* Mappings Tab */</p>
<hr />
<div>== User Interface ==<br />
=== Home Page ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Resource Index Tab|search biomedical resources]] for a term<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://www.bioontology.org/wiki/index.php/NCBO_REST_services REST API documentation] for more information.<br />
<br />
=== Browse Tab ===<br />
<br />
Here you can browse our library of Biomedical ontologies and can also submit your own ontology. The system displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''find a particular ontology quickly''', begin typing the ontology name or abbreviation in the “Filter by Text” field. You can also narrow the list of ontologies shown by selecting a specific “category” (a domain) or a “group” to which the ontology belongs. To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology. You can subscribe to '''receive RSS updates''' when any ontology in the system changes by clicking the subscribe link. You can subscribe to updates for a particular ontology from the summary page for that ontology. To go to the summary page click on the ontology name link.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
To '''access ontologies programmatically''', see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Services_to_access_ontologies_and_ontology_versions Ontology REST API documentation].<br />
<br />
=== Search Tab ===<br />
<br />
The search capability allows you to enter some text and find terms across multiple terminologies that contain this text. The names, synonyms, properties for a term are searched for matches to the entered text.<br />
<br />
To '''find a term in any ontology''' enter the full or partial name the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches are returned. Usually this number is sufficient to cover matches in all names, ids, and synonyms.<br />
<br />
Some boolean search capability is available. Prefixing a term with "-" means NOT for that term. Thus "heart -attack" will search for terms with "heart" but not "attack" in the name. An OR capability is also available using parentheses. Thus "(heart attack)" means to find terms with either "heart" or "attack" in the name.<br />
<br />
To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].<br />
<br />
=== Mappings Tab ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].<br />
<br />
=== Recommender Tab ===<br />
<br />
The Ontology Recommender accepts text and returns a ranked set of ontologies that most closely match the text. The ranking takes into account how many terms from the text are in the ontology and the size of the ontology. <br />
<br />
The '''ontology ranking algorithm''' is described in the paper [http://bmir.stanford.edu/file_asset/index.php/1591/BMIR-2010-1432.pdf Building an Ontology Recommender Web Service].<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].<br />
<br />
=== Annotator Tab ===<br />
<br />
To '''annotate text directly with ontological terms''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''create annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
=== Resource Index Tab ===<br />
<br />
The resource index is a pre-calculated set of annotations of selected biomedical resources. We have annotated these resources with all terms in all ontologies in BioPortal. We did this by running the Annotator Web Service on the textual descriptions of individual items in each of these resources. To retrieve records annotated with a specific ontology term, enter the term in the search box and press the "Search" button. <br />
<br />
To '''access annotations for resources programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Resource_Index_REST_Web_Service_User_Guide Resource Index REST API documentation].<br />
<br />
Further information on ontology-based search and mining of biomedical resources is available in [http://www.ncbi.nlm.nih.gov/pubmed/21918645 Jonquet et al Web Semant. 2011 Sep 1;9(3):316-324], [http://www.ncbi.nlm.nih.gov/pubmed/21550421 LePendu et al J Biomed Inform. 2011 Dec;44 Suppl 1:S31-8] and [http://www.ncbi.nlm.nih.gov/pubmed/22494789 Liu et al J Am Med Inform Assoc. 2012 Apr 11]<br />
<br />
=== Projects Tab ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
== Glossary ==<br />
; class : A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept : (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI : Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term : synonym for "obsolete term" in some ontologies.<br />
; group : a collection of ontologies that are typically associated with some outside group or organization. <br />
; obsolete term : A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping : Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; property : Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource : Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; slice: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym : Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term : Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings : Set of mappings for a given term to terms other ontologies. <br />
; term resources : Set of resources that contain annotations for a given term.<br />
<br />
== How to cite NCBO and BioPortal ==<br />
Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W170-3. Epub 2009 May 29. PubMed PMID: 19483092; PubMed Central PMCID: PMC2703982.</div>Darren Weber