NCBO Wiki - User contributions [en]

User talk:Marcosmr

2015-03-20T18:50:35Z

Fergerson: Welcome!

'''Welcome to ''NCBO Wiki''!'''
We hope you will contribute much and well.
You will probably want to read the [[Help:Contents|help pages]].
Again, welcome and have fun! [[User:Fergerson|Fergerson]] ([[User talk:Fergerson|talk]]) 11:50, 20 March 2015 (PDT)

User:Marcosmr

2015-03-20T18:50:34Z

Fergerson: Creating user page for new user.

User talk:JenniferVendetti

2015-02-24T00:39:21Z

Fergerson: Welcome!

User:JenniferVendetti

2015-02-24T00:39:20Z

Fergerson: Creating user page for new user.

BioPortal Release Notes

2014-06-13T00:41:03Z

Fergerson: /* BioPortal Release 4.0 (Sep 2013) */

== BioPortal Release 4.6 (May 2014) ==

* Improved Search Result Display – Many ontologies contain classes that are references to a canonical ontology that “owns” the class. The system now automatically tries to identify the “owning” ontology and emphasize it in the results while displaying the ontologies that contain references to that ontology as subordinate (for that class). This feature is easier to try out than to explain. Type in “cancer” into the search box on the Search Tab and scan through the results to see what it is all about. This sort of display has been requested by a number of users for quite a while and we are happy to finally provide it.
* Implemented Search for ID (URI), UMLS CUI, UMLS TUI, and skos:notation – The search system now will use the input search to find a class URI, a class skos:notation field (“short id” in the old system) or a UMLS “concept unique identifier” or semantic type. All of these fields are available through the default search mechanism. There is still an optional “all properties” parameter to search these property values along with all other property values.
* Released New Version of BioMixer visualization system – The BioMixer system has been updated to improve performance and be more robust. (Work performed by our University of Victoria collaborators.)
* Implemented New Mapping Visualization – Mappings system now allows a user to visualize the strength of mappings relationships between ontologies. Go to the mappings tab, select an ontology, and hit the visualization radio button to try this out. (Work performed by our University of Victoria collaborators.)
* Implemented Configurable REST API calls – The Annotator and Search REST calls now allow a user specify which fields of a class the system should return. The user can also specify “all” to get everything.
* Updated UMLS Ontologies – All UMLS ontologies have been updated to the latest (2013 AB) version.
* Improved Autocomplete – The autocomplete in the ontology “Jump To” box, and in the widgets, now works more reliably with results that are more intuitive than previously.
* Provide Access Control for Mappings – We have implemented access control to prevent people other than the author from deleting a mapping.
* Reimplemented Annotator “Longest Only” Parameter – We have reimplemented the annotator “longest only” parameter to work in all situations. This parameter allows the user to limit the returned results to only those matches which are longer than other matches for a given ontology. In the old system this parameter did not work correctly.
* Reimplemented Widgets to not use Flash – We have reimplemented the widgets to not use the Adobe Flash technology. Requiring the use of this technology was unpopular among our user community.
* Enabled Upload and Download Large Ontologies – We have fixed various timeout problems which prevented users from uploading or downloading large ontologies.
* Fixed Bugs! – Fixed a very large number of bugs, some new with the new system, and some carried forward from the old system.

We have today shut down access to the old BioPortal REST API and will be turning off the old system entirely in the near future. We have provided 7 months for application developers to move to the new system and the vast majority have already done so. The overwhelming response from developers has been the that new system is now (after a few post release glitches!) much easier to use and much more reliable than the old system. Documentation for the new API is available at:
http://data.bioontology.org/documentation

== BioPortal Release 4.0 (September 2013) ==

The primary distinguishing feature of this release is the replacement of several backend storage and caching mechanisms with a single triple-store based backend built with on the open source 4store platform. In addition we are simultaneously releasing a new version of the BioPortal REST API. This API is also built on top of the triple store. It provides a much more uniform and REST-full interface to the underlying BioPortal data than our previous REST API.

The old API will continue to function through the end of 2013. This API will only be able to access “old content” (that is, ontologies submitted or updated before today). We encourage API users to transition as quickly as possible to the new API. The new API is the only way to access both new content (submitted after today) and old content. The reports from beta users of the new API have been uniformly positive. Draft documentation for the new API is available at
http://data.bioontology.org/documentation

BioPortal users will note a few changes from the previous version. Some of these changes are temporary (we didn’t quite get everything done…) while others are permanent. There are also a number of minor and cosmetic changes. The list of the more important changes is available below.

With a release of this size, it is inevitable that some bugs have crept in. Please report any that you run across to the support@bioontology.org mailing list. Have confidence that we will be working diligently to prioritize and fix the problems that arise.

Temporary Changes
* All handling of obsolete classes in UI and API is not supported yet. Obsolete classes are currently indistinguishable from normal classes.
* “Slices” and ontology sets (user defined lists of ontologies of interest) are not supported yet
* The tree browse UI does not yet distinguish between is-a and part-of relations for OBO ontologies. Previously (and probably in the future) icons next to the class name indicated the relationship type.
* We do not yet have a VM version for this release. We expect to produce a new VM version by the end of the year. This VM will include the triple-store based storage mechanism. In addition VM users will be able to query the VM triple-store directly with SPARQL.
* Parsing of new ontologies and new versions remains disabled for the next few days. We will re-enable parsing by early next week.

Permanent Additions
* New ontologies and new versions of ontologies will be typically available for text annotation the next day after submission. Previously the process took several weeks to several months.
* We now have the latest versions UMLS ontologies. Previously we updated UMLS ontologies on request only, which left us with some very old versions. Going forward we will try to update our set of UMLS ontologies within a month of the UMLS release.

Permanent Subtractions
* Programmatic and browse access to classes in non-current versions of ontologies is removed. We still retain metadata about older versions of ontologies and we still allow you to download the source files for old versions.
* We no longer support Protégé Frames format ontologies. Owners of these ontologies will need to convert them to OWL or OBO to load them.
* We now use the owlAPI (http://owlapi.sourceforge.net/) to load OWL and OBO ontologies. This API supports OWL version 2.0. For almost all features, OWL 2.0 is a superset of OWL 1.0. There are some edge cases though where ontologies that marginally parsed with an OWL 1.0 parser will not parse at all with the OWL 2.0 parser. We leave it to OWL ontology owners to provide valid OWL 2.0 ontologies.

== BioPortal Release 3.12 ==
* Implemented the display of the OBO part-of relationship in the term neighborhood visualization.
* Improved some default layouts in the visualization system.
* Updated automated mappings for all ontologies.
* Regenerated the annotator hierarchy database. The versions of ontologies in this database are now much more current.
* Implemented support for federated queries in the [http://sparql.bioontology.org BioPortal SPARQL endpoint].
* Moved the mappings from the BioPortal endpoint into a separate public endpoint. This change allows us to update automated mappings more cleanly.
* Added the following resources to the Resource Index. All of these resources are the results of our collaboration with the [http://www.neuinfo.org/ Neuroscience Information Framework] (NIF) group.
** NIF PubMed Health: Tests
** NIF Drug Related Gene Database
** NIF Gemma
** NIF Integrated Disease View
* Fixed “Maximum Depth” metric for a number of ontologies. Was incorrectly displaying “1” in some cases.
* Fixed web service failure when attempting to retrieve all concepts from several ontologies.
* Fixed annotator to return all ancestor terms. Was missing some ancestors for some ontologies.
* Fixed Search to work correctly in MeSH.
* Fixed problem with SPARQL query to BioPortal endpoint on queries that include ORDER and LIMIT clauses

(Release February 2013)

== BioPortal Release 3.10 ==
* Revised UI for the Resource Index. This new UI supports the BioPortal slice mechanism. The new UI is also much faster than the previous one.
* Updated ontologies available for use with the Annotator which includes newer ontologies and more recent versions of existing ontologies.
* Fixed a longstanding bug in the Annotator that caused paths from a term to root nodes to occasionally be truncated.
* Allow submission of Notes on ontology terms by anonymous users. Previously a user had to be logged in to submit a note.

(Release July 2012)

== BioPortal Release 3.9 ==
* We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better” ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support@bioontology.org. *

* We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *

* We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).

<nowiki>*</nowiki> This item was requested via the User Support mailing list. Thank you for your comments and suggestions!

(Release June 2012)

== BioPortal Release 3.8 ==
* We have regenerated all mappings based on UMLS CUIs. Thus terms in different UMLS ontologies which share the same CUI are now mapped to each other. The mapping created is of type skos:closeMatch. There are now 3,000,000 of these UMLS CUI mappings in the system.*

* We have regenerated all mappings based on xrefs (OBO cross-reference) in OBO ontologies. A mapping is now generated when a term in an OBO ontology has an xref to a term in another ontology. The mapping created is of type skos:relatedMatch. There are 35,000 of these xref mappings in the system.*

* We have regenerated all mappings based on terms which have identical unique identifiers (IRIs). A mapping is now generated when term in an ontology has a unique identifier that is identical to the identifier of a term in another ontology. The mapping created is of type skos:exactMatch. There are 700,000 of these identical IRI mappings in the system.*

We also fixed a number of bugs which were causing performance, stability, and ontology upload problems.

<nowiki>*</nowiki>This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release May 2012)

== BioPortal Release 3.7 ==
* Updated term mappings generated by LOOM
* Added boolean functionality to Search Web service and UI
* Updated ontology content for the Resource Index
* BioPortal SPARQL endpoint beta release, http://sparql.bioontology.org
* Modified response of Annotator UI to not fail if input text contains returns or results do not have any term matches*
* Bug fix for Term Autocomplete widget to remove namespace collision with jQuery widgets*

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release April 2012)

== BioPortal Release 3.6 ==
* Created “alternate entry points” for BioPortal. These URL’s limit the ontologies that are visible in BioPortal, allowing users to focus on a shared, smaller set of ontologies. The entry points which are currently available are:
** OBO-Foundry: http://obo-foundry.bioportal.bioontology.org
** Unified Medical Language Systems: http://umls.bioportal.bioontology.org
** Cancer Biomedical Informatics Grid: http://cabig.bioportal.bioontology.org
** Clinical and Translational Science Awards: http://ctsa.bioportal.bioontology.org
** CTSA Health Ontology Mapper: http://ctsa-hom.bioportal.bioontology.org
** Proteomics Standards Initiative: http://psi.bioportal.bioontology.org
** WHO Family of International Classifications: http://who-fic.bioportal.bioontology.org
** Consultative Group on Intl Agricultural Research: http://cgiar.bioportal.bioontology.org
** Please contact us on the support mailing list if you would like us to configure an entry point for another set of ontologies.
* Major Updates and Fixes
** Updated the ontologies used by the Annotator Web Services*
** Improved the reliability and robustness of the parsing of OWL 2 ontologies*

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release January 2012)

== BioPortal Release 3.5 ==
* Added ability for logged-in users to filter which ontologies appear in their BioPortal display
* Updated Annotator page to simplify the selection of options, to clarify the annotation results, and to remove Flash from the implementation
* Improved Annotator Web service response performance by 5-10x*
* Added ability for the ontology Web services API to optionally return JSON (rather than XML)*
* Updated Ontology Recommender algorithm to provide better recommendations*
* Added display of matched terms for Ontology Recommender*
* Added Web service to get all namespaces for an ontology*
* Bug Fixes
** Display user-friendly names for RxNorm ontology properties

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release December 2011)

== BioPortal Release 3.4 ==
* Revised the Term Mappings tab to ease the creation of term-to-term mappings*
* Limited access to “Private” ontologies via the Browse and Search pages
* Added backend support to allow multiple administrators for a single ontology*
* Added ability to copy to the clipboard a permanent link to any BioPortal term*
* Bug Fixes
** Resolved issue causing search to not display all matching terms*
** Fixed Term Mappings tab display for IE 7 & 8*
** Fixed RDF Ontology Download Web service
** Fixed link to the list of resources included in the Resource Index*

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release October 2011)

== BioPortal Release 3.3 ==
New features include updates to the Web interface and Web services:
* Added Get Properties Web service, http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Property_Services
* Updated Search page to remove Flash
* Handling of obsolete terms, part 2 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OWL ontologies.
* Added Help documentation
* Implemented a feature to allow ontology submitters to flag their ontology as “licensed”. This feature allows the ontology submitter to require users to provide license information before they are allowed to access the ontology.
* Bug Fix
** Fixed the Filter by Account on the Mappings tab

(Release date September 2011)

== BioPortal Release 3.2 ==
New features include updates to the Web interface and Web services:
* Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender
** Web service documentation: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service
** Sample client information: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Client_Examples
* Added support for access control for viewing ontologies
* Added link to subscribe to BioPortal Notes emails
* Synchronized “Jump To” feature with ontology parsing and display
* Added documentation on Ontology Groups
* Annotator Web service – disabled use of “longest only” parameter when also selecting “ontologies to expand” parameter
* Removed the metric "Number of classes without an author"
* Handling of obsolete terms, part 1 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OBO and RRF ontologies. This feature will be extended to cover OWL ontologies in a subsequent release.
* Bug Fix
** Fixed calculation of “Classes with no definition” metric
** Added re-direct from old BioPortal URL format to new URL format to provide working links from archived search results

'''''Firefox Extension for NCBO API Key''''':
To make it easier to test Web service calls from your browser, we have released the NCBO API Key Firefox Extension. This extension will automatically add your API Key to NCBO REST URLs any time you visit them in Firefox. The extension is available at Mozilla's Add-On site. To use the extension, follow the installation directions, restart Firefox, and add your API Key into the “Options” dialog menu on the Add-Ons management screen. After that, the extension will automatically append your stored API Key any time you visit http://rest.bioontology.org.

'''''Upcoming software license change''''':
The next release of NCBO software will be under the two-clause BSD license rather than under the currently used three-clause BSD license. This change should not affect anyone’s use of NCBO software and this change is to a less restrictive license. More information about these licenses is available at the site: http://www.opensource.org/licenses. Please contact support@bioontology.org with any questions concerning this change.

== BioPortal Release 3.1 ==
New features include updates to the Web interface and Web services:
* Support for loading OWL 2 ontologies
* Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key.
* Browsing of ontologies that contain large numbers of sibling terms
* Icons for is_a and part_of are displayed for OBO format ontologies
* Display of the “occurs_in” relationship used in the Extended version of the Gene Ontology
Bug Fix
* Added informative error message when incompatible parameter values are used in the Annotator Web service and updated Perl client to capture this error response

(Release date July 8, 2011)

== BioPortal Release 3.0 ==
New features include updates to the Web interface and Web services:
* Web interface updates
* Browse page now displays ontology features, e.g. size of the ontology, number of notes added to the ontology, number of projects that use the ontology, and number of reviews of the ontology
* New ontology summary details page highlights the ontology metrics, reviews, projects, and derived views of the ontology
* Security Framework, part 1 - Added apikey parameter to all Web services. The apikey parameter is optional until June 15, 2011, after this time the apikey parameter will be required for usage of the Web services. Login to BioPortal to get your API key.
* Provisional Term Web service - New term proposals now receive a provisional term id. Additional Web services are now available for submitting provisional terms. For more details, see: http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms
* Form auto-complete Widget - Option to include term definition in display
* Resource Index
** Data indexed with new ontologies from BioPortal
** PubMed data now available for abstracts published in 2010

(Release date May 19, 2011)

== BioPortal Release 2.6.4 ==
New features include additional Web services and Web interface enhancements:
* Mapping Web services - Access to ontology term mappings, including UMLS, OBO DbXref, and LOOM mappings ( http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service ) ''Please note, the prototype Mapping Web service will be removed March 23''
* RDF Download Web service - Access any BioPortal ontology in RDF ( http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Term_Service and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Download_Service )
* Notes - Ability to archive Notes, e.g. accepted term proposals, and filter from display
* Annotator
** Updated ontology content
** Offsets corrected for non-ASCII characters
** Link to Annotator Web interface using parameters
** Web interface enhancements
* Display of ontology development status
* Hyperlinks on term details page
* Ability to add comments on Mappings

(Release date February 2011)

== BioPortal Release 2.5 ==
New features in this release include the following:
* Support for structured notes and term requests: Users can now use BioPortal to request that content developers add new terms or update other ontology content. BioPortal provides a structured template for making such requests, allowing users to suggest preferred names, synonyms, and definitions for the requested terms. BioPortal stores the requests as structured notes that are attached to the ontology and that other ontology tools, such as Protégé, will be able to use.

* Support for email notifications to interested parties whenever a BioPortal user creates new notes for an ontology of interest. (If you would like to subscribe to notifications about a particular ontology, please send email to support at bioontology.org. We will have an interactive form to sign-up for notifications shortly.)

* Prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation [1] for details).

* Prototype end-point for SPARQL access to all ontologies in BioPortal: http://sparql.bioontology.org

* Web services for retrieving instance information for OWL ontologies [1]. We are planning to release a user interface for viewing instances shortly.

* New ontology widgets that developers can embed on their Web sites, including an ontology tree widget that allows Web-site authors to present a display of an ontology or an ontology subtree for any BioPortal ontology in any Web page.

* Preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings

[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services

(Release date June 9, 2010)

BioPortal Release Notes

2014-06-13T00:40:47Z

Fergerson: /* BioPortal Release 4.0 */

== BioPortal Release 4.6 (May 2014) ==

* Improved Search Result Display – Many ontologies contain classes that are references to a canonical ontology that “owns” the class. The system now automatically tries to identify the “owning” ontology and emphasize it in the results while displaying the ontologies that contain references to that ontology as subordinate (for that class). This feature is easier to try out than to explain. Type in “cancer” into the search box on the Search Tab and scan through the results to see what it is all about. This sort of display has been requested by a number of users for quite a while and we are happy to finally provide it.
* Implemented Search for ID (URI), UMLS CUI, UMLS TUI, and skos:notation – The search system now will use the input search to find a class URI, a class skos:notation field (“short id” in the old system) or a UMLS “concept unique identifier” or semantic type. All of these fields are available through the default search mechanism. There is still an optional “all properties” parameter to search these property values along with all other property values.
* Released New Version of BioMixer visualization system – The BioMixer system has been updated to improve performance and be more robust. (Work performed by our University of Victoria collaborators.)
* Implemented New Mapping Visualization – Mappings system now allows a user to visualize the strength of mappings relationships between ontologies. Go to the mappings tab, select an ontology, and hit the visualization radio button to try this out. (Work performed by our University of Victoria collaborators.)
* Implemented Configurable REST API calls – The Annotator and Search REST calls now allow a user specify which fields of a class the system should return. The user can also specify “all” to get everything.
* Updated UMLS Ontologies – All UMLS ontologies have been updated to the latest (2013 AB) version.
* Improved Autocomplete – The autocomplete in the ontology “Jump To” box, and in the widgets, now works more reliably with results that are more intuitive than previously.
* Provide Access Control for Mappings – We have implemented access control to prevent people other than the author from deleting a mapping.
* Reimplemented Annotator “Longest Only” Parameter – We have reimplemented the annotator “longest only” parameter to work in all situations. This parameter allows the user to limit the returned results to only those matches which are longer than other matches for a given ontology. In the old system this parameter did not work correctly.
* Reimplemented Widgets to not use Flash – We have reimplemented the widgets to not use the Adobe Flash technology. Requiring the use of this technology was unpopular among our user community.
* Enabled Upload and Download Large Ontologies – We have fixed various timeout problems which prevented users from uploading or downloading large ontologies.
* Fixed Bugs! – Fixed a very large number of bugs, some new with the new system, and some carried forward from the old system.

We have today shut down access to the old BioPortal REST API and will be turning off the old system entirely in the near future. We have provided 7 months for application developers to move to the new system and the vast majority have already done so. The overwhelming response from developers has been the that new system is now (after a few post release glitches!) much easier to use and much more reliable than the old system. Documentation for the new API is available at:
http://data.bioontology.org/documentation

== BioPortal Release 4.0 (Sep 2013) ==

The primary distinguishing feature of this release is the replacement of several backend storage and caching mechanisms with a single triple-store based backend built with on the open source 4store platform. In addition we are simultaneously releasing a new version of the BioPortal REST API. This API is also built on top of the triple store. It provides a much more uniform and REST-full interface to the underlying BioPortal data than our previous REST API.

The old API will continue to function through the end of 2013. This API will only be able to access “old content” (that is, ontologies submitted or updated before today). We encourage API users to transition as quickly as possible to the new API. The new API is the only way to access both new content (submitted after today) and old content. The reports from beta users of the new API have been uniformly positive. Draft documentation for the new API is available at
http://data.bioontology.org/documentation

BioPortal users will note a few changes from the previous version. Some of these changes are temporary (we didn’t quite get everything done…) while others are permanent. There are also a number of minor and cosmetic changes. The list of the more important changes is available below.

With a release of this size, it is inevitable that some bugs have crept in. Please report any that you run across to the support@bioontology.org mailing list. Have confidence that we will be working diligently to prioritize and fix the problems that arise.

Temporary Changes
* All handling of obsolete classes in UI and API is not supported yet. Obsolete classes are currently indistinguishable from normal classes.
* “Slices” and ontology sets (user defined lists of ontologies of interest) are not supported yet
* The tree browse UI does not yet distinguish between is-a and part-of relations for OBO ontologies. Previously (and probably in the future) icons next to the class name indicated the relationship type.
* We do not yet have a VM version for this release. We expect to produce a new VM version by the end of the year. This VM will include the triple-store based storage mechanism. In addition VM users will be able to query the VM triple-store directly with SPARQL.
* Parsing of new ontologies and new versions remains disabled for the next few days. We will re-enable parsing by early next week.

Permanent Additions
* New ontologies and new versions of ontologies will be typically available for text annotation the next day after submission. Previously the process took several weeks to several months.
* We now have the latest versions UMLS ontologies. Previously we updated UMLS ontologies on request only, which left us with some very old versions. Going forward we will try to update our set of UMLS ontologies within a month of the UMLS release.

Permanent Subtractions
* Programmatic and browse access to classes in non-current versions of ontologies is removed. We still retain metadata about older versions of ontologies and we still allow you to download the source files for old versions.
* We no longer support Protégé Frames format ontologies. Owners of these ontologies will need to convert them to OWL or OBO to load them.
* We now use the owlAPI (http://owlapi.sourceforge.net/) to load OWL and OBO ontologies. This API supports OWL version 2.0. For almost all features, OWL 2.0 is a superset of OWL 1.0. There are some edge cases though where ontologies that marginally parsed with an OWL 1.0 parser will not parse at all with the OWL 2.0 parser. We leave it to OWL ontology owners to provide valid OWL 2.0 ontologies.

== BioPortal Release 3.12 ==
* Implemented the display of the OBO part-of relationship in the term neighborhood visualization.
* Improved some default layouts in the visualization system.
* Updated automated mappings for all ontologies.
* Regenerated the annotator hierarchy database. The versions of ontologies in this database are now much more current.
* Implemented support for federated queries in the [http://sparql.bioontology.org BioPortal SPARQL endpoint].
* Moved the mappings from the BioPortal endpoint into a separate public endpoint. This change allows us to update automated mappings more cleanly.
* Added the following resources to the Resource Index. All of these resources are the results of our collaboration with the [http://www.neuinfo.org/ Neuroscience Information Framework] (NIF) group.
** NIF PubMed Health: Tests
** NIF Drug Related Gene Database
** NIF Gemma
** NIF Integrated Disease View
* Fixed “Maximum Depth” metric for a number of ontologies. Was incorrectly displaying “1” in some cases.
* Fixed web service failure when attempting to retrieve all concepts from several ontologies.
* Fixed annotator to return all ancestor terms. Was missing some ancestors for some ontologies.
* Fixed Search to work correctly in MeSH.
* Fixed problem with SPARQL query to BioPortal endpoint on queries that include ORDER and LIMIT clauses

(Release February 2013)

== BioPortal Release 3.10 ==
* Revised UI for the Resource Index. This new UI supports the BioPortal slice mechanism. The new UI is also much faster than the previous one.
* Updated ontologies available for use with the Annotator which includes newer ontologies and more recent versions of existing ontologies.
* Fixed a longstanding bug in the Annotator that caused paths from a term to root nodes to occasionally be truncated.
* Allow submission of Notes on ontology terms by anonymous users. Previously a user had to be logged in to submit a note.

(Release July 2012)

== BioPortal Release 3.9 ==
* We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better” ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support@bioontology.org. *

* We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *

* We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).

<nowiki>*</nowiki> This item was requested via the User Support mailing list. Thank you for your comments and suggestions!

(Release June 2012)

== BioPortal Release 3.8 ==
* We have regenerated all mappings based on UMLS CUIs. Thus terms in different UMLS ontologies which share the same CUI are now mapped to each other. The mapping created is of type skos:closeMatch. There are now 3,000,000 of these UMLS CUI mappings in the system.*

* We have regenerated all mappings based on xrefs (OBO cross-reference) in OBO ontologies. A mapping is now generated when a term in an OBO ontology has an xref to a term in another ontology. The mapping created is of type skos:relatedMatch. There are 35,000 of these xref mappings in the system.*

* We have regenerated all mappings based on terms which have identical unique identifiers (IRIs). A mapping is now generated when term in an ontology has a unique identifier that is identical to the identifier of a term in another ontology. The mapping created is of type skos:exactMatch. There are 700,000 of these identical IRI mappings in the system.*

We also fixed a number of bugs which were causing performance, stability, and ontology upload problems.

<nowiki>*</nowiki>This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release May 2012)

== BioPortal Release 3.7 ==
* Updated term mappings generated by LOOM
* Added boolean functionality to Search Web service and UI
* Updated ontology content for the Resource Index
* BioPortal SPARQL endpoint beta release, http://sparql.bioontology.org
* Modified response of Annotator UI to not fail if input text contains returns or results do not have any term matches*
* Bug fix for Term Autocomplete widget to remove namespace collision with jQuery widgets*

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release April 2012)

== BioPortal Release 3.6 ==
* Created “alternate entry points” for BioPortal. These URL’s limit the ontologies that are visible in BioPortal, allowing users to focus on a shared, smaller set of ontologies. The entry points which are currently available are:
** OBO-Foundry: http://obo-foundry.bioportal.bioontology.org
** Unified Medical Language Systems: http://umls.bioportal.bioontology.org
** Cancer Biomedical Informatics Grid: http://cabig.bioportal.bioontology.org
** Clinical and Translational Science Awards: http://ctsa.bioportal.bioontology.org
** CTSA Health Ontology Mapper: http://ctsa-hom.bioportal.bioontology.org
** Proteomics Standards Initiative: http://psi.bioportal.bioontology.org
** WHO Family of International Classifications: http://who-fic.bioportal.bioontology.org
** Consultative Group on Intl Agricultural Research: http://cgiar.bioportal.bioontology.org
** Please contact us on the support mailing list if you would like us to configure an entry point for another set of ontologies.
* Major Updates and Fixes
** Updated the ontologies used by the Annotator Web Services*
** Improved the reliability and robustness of the parsing of OWL 2 ontologies*

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release January 2012)

== BioPortal Release 3.5 ==
* Added ability for logged-in users to filter which ontologies appear in their BioPortal display
* Updated Annotator page to simplify the selection of options, to clarify the annotation results, and to remove Flash from the implementation
* Improved Annotator Web service response performance by 5-10x*
* Added ability for the ontology Web services API to optionally return JSON (rather than XML)*
* Updated Ontology Recommender algorithm to provide better recommendations*
* Added display of matched terms for Ontology Recommender*
* Added Web service to get all namespaces for an ontology*
* Bug Fixes
** Display user-friendly names for RxNorm ontology properties

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release December 2011)

== BioPortal Release 3.4 ==
* Revised the Term Mappings tab to ease the creation of term-to-term mappings*
* Limited access to “Private” ontologies via the Browse and Search pages
* Added backend support to allow multiple administrators for a single ontology*
* Added ability to copy to the clipboard a permanent link to any BioPortal term*
* Bug Fixes
** Resolved issue causing search to not display all matching terms*
** Fixed Term Mappings tab display for IE 7 & 8*
** Fixed RDF Ontology Download Web service
** Fixed link to the list of resources included in the Resource Index*

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release October 2011)

== BioPortal Release 3.3 ==
New features include updates to the Web interface and Web services:
* Added Get Properties Web service, http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Property_Services
* Updated Search page to remove Flash
* Handling of obsolete terms, part 2 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OWL ontologies.
* Added Help documentation
* Implemented a feature to allow ontology submitters to flag their ontology as “licensed”. This feature allows the ontology submitter to require users to provide license information before they are allowed to access the ontology.
* Bug Fix
** Fixed the Filter by Account on the Mappings tab

(Release date September 2011)

== BioPortal Release 3.2 ==
New features include updates to the Web interface and Web services:
* Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender
** Web service documentation: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service
** Sample client information: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Client_Examples
* Added support for access control for viewing ontologies
* Added link to subscribe to BioPortal Notes emails
* Synchronized “Jump To” feature with ontology parsing and display
* Added documentation on Ontology Groups
* Annotator Web service – disabled use of “longest only” parameter when also selecting “ontologies to expand” parameter
* Removed the metric "Number of classes without an author"
* Handling of obsolete terms, part 1 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OBO and RRF ontologies. This feature will be extended to cover OWL ontologies in a subsequent release.
* Bug Fix
** Fixed calculation of “Classes with no definition” metric
** Added re-direct from old BioPortal URL format to new URL format to provide working links from archived search results

'''''Firefox Extension for NCBO API Key''''':
To make it easier to test Web service calls from your browser, we have released the NCBO API Key Firefox Extension. This extension will automatically add your API Key to NCBO REST URLs any time you visit them in Firefox. The extension is available at Mozilla's Add-On site. To use the extension, follow the installation directions, restart Firefox, and add your API Key into the “Options” dialog menu on the Add-Ons management screen. After that, the extension will automatically append your stored API Key any time you visit http://rest.bioontology.org.

'''''Upcoming software license change''''':
The next release of NCBO software will be under the two-clause BSD license rather than under the currently used three-clause BSD license. This change should not affect anyone’s use of NCBO software and this change is to a less restrictive license. More information about these licenses is available at the site: http://www.opensource.org/licenses. Please contact support@bioontology.org with any questions concerning this change.

== BioPortal Release 3.1 ==
New features include updates to the Web interface and Web services:
* Support for loading OWL 2 ontologies
* Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key.
* Browsing of ontologies that contain large numbers of sibling terms
* Icons for is_a and part_of are displayed for OBO format ontologies
* Display of the “occurs_in” relationship used in the Extended version of the Gene Ontology
Bug Fix
* Added informative error message when incompatible parameter values are used in the Annotator Web service and updated Perl client to capture this error response

(Release date July 8, 2011)

== BioPortal Release 3.0 ==
New features include updates to the Web interface and Web services:
* Web interface updates
* Browse page now displays ontology features, e.g. size of the ontology, number of notes added to the ontology, number of projects that use the ontology, and number of reviews of the ontology
* New ontology summary details page highlights the ontology metrics, reviews, projects, and derived views of the ontology
* Security Framework, part 1 - Added apikey parameter to all Web services. The apikey parameter is optional until June 15, 2011, after this time the apikey parameter will be required for usage of the Web services. Login to BioPortal to get your API key.
* Provisional Term Web service - New term proposals now receive a provisional term id. Additional Web services are now available for submitting provisional terms. For more details, see: http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms
* Form auto-complete Widget - Option to include term definition in display
* Resource Index
** Data indexed with new ontologies from BioPortal
** PubMed data now available for abstracts published in 2010

(Release date May 19, 2011)

== BioPortal Release 2.6.4 ==
New features include additional Web services and Web interface enhancements:
* Mapping Web services - Access to ontology term mappings, including UMLS, OBO DbXref, and LOOM mappings ( http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service ) ''Please note, the prototype Mapping Web service will be removed March 23''
* RDF Download Web service - Access any BioPortal ontology in RDF ( http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Term_Service and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Download_Service )
* Notes - Ability to archive Notes, e.g. accepted term proposals, and filter from display
* Annotator
** Updated ontology content
** Offsets corrected for non-ASCII characters
** Link to Annotator Web interface using parameters
** Web interface enhancements
* Display of ontology development status
* Hyperlinks on term details page
* Ability to add comments on Mappings

(Release date February 2011)

== BioPortal Release 2.5 ==
New features in this release include the following:
* Support for structured notes and term requests: Users can now use BioPortal to request that content developers add new terms or update other ontology content. BioPortal provides a structured template for making such requests, allowing users to suggest preferred names, synonyms, and definitions for the requested terms. BioPortal stores the requests as structured notes that are attached to the ontology and that other ontology tools, such as Protégé, will be able to use.

* Support for email notifications to interested parties whenever a BioPortal user creates new notes for an ontology of interest. (If you would like to subscribe to notifications about a particular ontology, please send email to support at bioontology.org. We will have an interactive form to sign-up for notifications shortly.)

* Prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation [1] for details).

* Prototype end-point for SPARQL access to all ontologies in BioPortal: http://sparql.bioontology.org

* Web services for retrieving instance information for OWL ontologies [1]. We are planning to release a user interface for viewing instances shortly.

* New ontology widgets that developers can embed on their Web sites, including an ontology tree widget that allows Web-site authors to present a display of an ontology or an ontology subtree for any BioPortal ontology in any Web page.

* Preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings

[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services

(Release date June 9, 2010)

BioPortal Release Notes

2014-06-13T00:39:25Z

Fergerson: /* BioPortal Release 4.6 (May 8, 2014) */

== BioPortal Release 4.6 (May 2014) ==

* Improved Search Result Display – Many ontologies contain classes that are references to a canonical ontology that “owns” the class. The system now automatically tries to identify the “owning” ontology and emphasize it in the results while displaying the ontologies that contain references to that ontology as subordinate (for that class). This feature is easier to try out than to explain. Type in “cancer” into the search box on the Search Tab and scan through the results to see what it is all about. This sort of display has been requested by a number of users for quite a while and we are happy to finally provide it.
* Implemented Search for ID (URI), UMLS CUI, UMLS TUI, and skos:notation – The search system now will use the input search to find a class URI, a class skos:notation field (“short id” in the old system) or a UMLS “concept unique identifier” or semantic type. All of these fields are available through the default search mechanism. There is still an optional “all properties” parameter to search these property values along with all other property values.
* Released New Version of BioMixer visualization system – The BioMixer system has been updated to improve performance and be more robust. (Work performed by our University of Victoria collaborators.)
* Implemented New Mapping Visualization – Mappings system now allows a user to visualize the strength of mappings relationships between ontologies. Go to the mappings tab, select an ontology, and hit the visualization radio button to try this out. (Work performed by our University of Victoria collaborators.)
* Implemented Configurable REST API calls – The Annotator and Search REST calls now allow a user specify which fields of a class the system should return. The user can also specify “all” to get everything.
* Updated UMLS Ontologies – All UMLS ontologies have been updated to the latest (2013 AB) version.
* Improved Autocomplete – The autocomplete in the ontology “Jump To” box, and in the widgets, now works more reliably with results that are more intuitive than previously.
* Provide Access Control for Mappings – We have implemented access control to prevent people other than the author from deleting a mapping.
* Reimplemented Annotator “Longest Only” Parameter – We have reimplemented the annotator “longest only” parameter to work in all situations. This parameter allows the user to limit the returned results to only those matches which are longer than other matches for a given ontology. In the old system this parameter did not work correctly.
* Reimplemented Widgets to not use Flash – We have reimplemented the widgets to not use the Adobe Flash technology. Requiring the use of this technology was unpopular among our user community.
* Enabled Upload and Download Large Ontologies – We have fixed various timeout problems which prevented users from uploading or downloading large ontologies.
* Fixed Bugs! – Fixed a very large number of bugs, some new with the new system, and some carried forward from the old system.

We have today shut down access to the old BioPortal REST API and will be turning off the old system entirely in the near future. We have provided 7 months for application developers to move to the new system and the vast majority have already done so. The overwhelming response from developers has been the that new system is now (after a few post release glitches!) much easier to use and much more reliable than the old system. Documentation for the new API is available at:
http://data.bioontology.org/documentation

== BioPortal Release 4.0 ==

The primary distinguishing feature of this release is the replacement of several backend storage and caching mechanisms with a single triple-store based backend built with on the open source 4store platform. In addition we are simultaneously releasing a new version of the BioPortal REST API. This API is also built on top of the triple store. It provides a much more uniform and REST-full interface to the underlying BioPortal data than our previous REST API.

The old API will continue to function through the end of 2013. This API will only be able to access “old content” (that is, ontologies submitted or updated before today). We encourage API users to transition as quickly as possible to the new API. The new API is the only way to access both new content (submitted after today) and old content. The reports from beta users of the new API have been uniformly positive. Draft documentation for the new API is available at
http://data.bioontology.org/documentation

BioPortal users will note a few changes from the previous version. Some of these changes are temporary (we didn’t quite get everything done…) while others are permanent. There are also a number of minor and cosmetic changes. The list of the more important changes is available below.

With a release of this size, it is inevitable that some bugs have crept in. Please report any that you run across to the support@bioontology.org mailing list. Have confidence that we will be working diligently to prioritize and fix the problems that arise.

Temporary Changes
* All handling of obsolete classes in UI and API is not supported yet. Obsolete classes are currently indistinguishable from normal classes.
* “Slices” and ontology sets (user defined lists of ontologies of interest) are not supported yet
* The tree browse UI does not yet distinguish between is-a and part-of relations for OBO ontologies. Previously (and probably in the future) icons next to the class name indicated the relationship type.
* We do not yet have a VM version for this release. We expect to produce a new VM version by the end of the year. This VM will include the triple-store based storage mechanism. In addition VM users will be able to query the VM triple-store directly with SPARQL.
* Parsing of new ontologies and new versions remains disabled for the next few days. We will re-enable parsing by early next week.

Permanent Additions
* New ontologies and new versions of ontologies will be typically available for text annotation the next day after submission. Previously the process took several weeks to several months.
* We now have the latest versions UMLS ontologies. Previously we updated UMLS ontologies on request only, which left us with some very old versions. Going forward we will try to update our set of UMLS ontologies within a month of the UMLS release.

Permanent Subtractions
* Programmatic and browse access to classes in non-current versions of ontologies is removed. We still retain metadata about older versions of ontologies and we still allow you to download the source files for old versions.
* We no longer support Protégé Frames format ontologies. Owners of these ontologies will need to convert them to OWL or OBO to load them.
* We now use the owlAPI (http://owlapi.sourceforge.net/) to load OWL and OBO ontologies. This API supports OWL version 2.0. For almost all features, OWL 2.0 is a superset of OWL 1.0. There are some edge cases though where ontologies that marginally parsed with an OWL 1.0 parser will not parse at all with the OWL 2.0 parser. We leave it to OWL ontology owners to provide valid OWL 2.0 ontologies.

== BioPortal Release 3.12 ==
* Implemented the display of the OBO part-of relationship in the term neighborhood visualization.
* Improved some default layouts in the visualization system.
* Updated automated mappings for all ontologies.
* Regenerated the annotator hierarchy database. The versions of ontologies in this database are now much more current.
* Implemented support for federated queries in the [http://sparql.bioontology.org BioPortal SPARQL endpoint].
* Moved the mappings from the BioPortal endpoint into a separate public endpoint. This change allows us to update automated mappings more cleanly.
* Added the following resources to the Resource Index. All of these resources are the results of our collaboration with the [http://www.neuinfo.org/ Neuroscience Information Framework] (NIF) group.
** NIF PubMed Health: Tests
** NIF Drug Related Gene Database
** NIF Gemma
** NIF Integrated Disease View
* Fixed “Maximum Depth” metric for a number of ontologies. Was incorrectly displaying “1” in some cases.
* Fixed web service failure when attempting to retrieve all concepts from several ontologies.
* Fixed annotator to return all ancestor terms. Was missing some ancestors for some ontologies.
* Fixed Search to work correctly in MeSH.
* Fixed problem with SPARQL query to BioPortal endpoint on queries that include ORDER and LIMIT clauses

(Release February 2013)

== BioPortal Release 3.10 ==
* Revised UI for the Resource Index. This new UI supports the BioPortal slice mechanism. The new UI is also much faster than the previous one.
* Updated ontologies available for use with the Annotator which includes newer ontologies and more recent versions of existing ontologies.
* Fixed a longstanding bug in the Annotator that caused paths from a term to root nodes to occasionally be truncated.
* Allow submission of Notes on ontology terms by anonymous users. Previously a user had to be logged in to submit a note.

(Release July 2012)

== BioPortal Release 3.9 ==
* We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better” ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support@bioontology.org. *

* We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *

* We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).

<nowiki>*</nowiki> This item was requested via the User Support mailing list. Thank you for your comments and suggestions!

(Release June 2012)

== BioPortal Release 3.8 ==
* We have regenerated all mappings based on UMLS CUIs. Thus terms in different UMLS ontologies which share the same CUI are now mapped to each other. The mapping created is of type skos:closeMatch. There are now 3,000,000 of these UMLS CUI mappings in the system.*

* We have regenerated all mappings based on xrefs (OBO cross-reference) in OBO ontologies. A mapping is now generated when a term in an OBO ontology has an xref to a term in another ontology. The mapping created is of type skos:relatedMatch. There are 35,000 of these xref mappings in the system.*

* We have regenerated all mappings based on terms which have identical unique identifiers (IRIs). A mapping is now generated when term in an ontology has a unique identifier that is identical to the identifier of a term in another ontology. The mapping created is of type skos:exactMatch. There are 700,000 of these identical IRI mappings in the system.*

We also fixed a number of bugs which were causing performance, stability, and ontology upload problems.

<nowiki>*</nowiki>This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release May 2012)

== BioPortal Release 3.7 ==
* Updated term mappings generated by LOOM
* Added boolean functionality to Search Web service and UI
* Updated ontology content for the Resource Index
* BioPortal SPARQL endpoint beta release, http://sparql.bioontology.org
* Modified response of Annotator UI to not fail if input text contains returns or results do not have any term matches*
* Bug fix for Term Autocomplete widget to remove namespace collision with jQuery widgets*

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release April 2012)

== BioPortal Release 3.6 ==
* Created “alternate entry points” for BioPortal. These URL’s limit the ontologies that are visible in BioPortal, allowing users to focus on a shared, smaller set of ontologies. The entry points which are currently available are:
** OBO-Foundry: http://obo-foundry.bioportal.bioontology.org
** Unified Medical Language Systems: http://umls.bioportal.bioontology.org
** Cancer Biomedical Informatics Grid: http://cabig.bioportal.bioontology.org
** Clinical and Translational Science Awards: http://ctsa.bioportal.bioontology.org
** CTSA Health Ontology Mapper: http://ctsa-hom.bioportal.bioontology.org
** Proteomics Standards Initiative: http://psi.bioportal.bioontology.org
** WHO Family of International Classifications: http://who-fic.bioportal.bioontology.org
** Consultative Group on Intl Agricultural Research: http://cgiar.bioportal.bioontology.org
** Please contact us on the support mailing list if you would like us to configure an entry point for another set of ontologies.
* Major Updates and Fixes
** Updated the ontologies used by the Annotator Web Services*
** Improved the reliability and robustness of the parsing of OWL 2 ontologies*

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release January 2012)

== BioPortal Release 3.5 ==
* Added ability for logged-in users to filter which ontologies appear in their BioPortal display
* Updated Annotator page to simplify the selection of options, to clarify the annotation results, and to remove Flash from the implementation
* Improved Annotator Web service response performance by 5-10x*
* Added ability for the ontology Web services API to optionally return JSON (rather than XML)*
* Updated Ontology Recommender algorithm to provide better recommendations*
* Added display of matched terms for Ontology Recommender*
* Added Web service to get all namespaces for an ontology*
* Bug Fixes
** Display user-friendly names for RxNorm ontology properties

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release December 2011)

== BioPortal Release 3.4 ==
* Revised the Term Mappings tab to ease the creation of term-to-term mappings*
* Limited access to “Private” ontologies via the Browse and Search pages
* Added backend support to allow multiple administrators for a single ontology*
* Added ability to copy to the clipboard a permanent link to any BioPortal term*
* Bug Fixes
** Resolved issue causing search to not display all matching terms*
** Fixed Term Mappings tab display for IE 7 & 8*
** Fixed RDF Ontology Download Web service
** Fixed link to the list of resources included in the Resource Index*

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release October 2011)

== BioPortal Release 3.3 ==
New features include updates to the Web interface and Web services:
* Added Get Properties Web service, http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Property_Services
* Updated Search page to remove Flash
* Handling of obsolete terms, part 2 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OWL ontologies.
* Added Help documentation
* Implemented a feature to allow ontology submitters to flag their ontology as “licensed”. This feature allows the ontology submitter to require users to provide license information before they are allowed to access the ontology.
* Bug Fix
** Fixed the Filter by Account on the Mappings tab

(Release date September 2011)

== BioPortal Release 3.2 ==
New features include updates to the Web interface and Web services:
* Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender
** Web service documentation: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service
** Sample client information: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Client_Examples
* Added support for access control for viewing ontologies
* Added link to subscribe to BioPortal Notes emails
* Synchronized “Jump To” feature with ontology parsing and display
* Added documentation on Ontology Groups
* Annotator Web service – disabled use of “longest only” parameter when also selecting “ontologies to expand” parameter
* Removed the metric "Number of classes without an author"
* Handling of obsolete terms, part 1 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OBO and RRF ontologies. This feature will be extended to cover OWL ontologies in a subsequent release.
* Bug Fix
** Fixed calculation of “Classes with no definition” metric
** Added re-direct from old BioPortal URL format to new URL format to provide working links from archived search results

'''''Firefox Extension for NCBO API Key''''':
To make it easier to test Web service calls from your browser, we have released the NCBO API Key Firefox Extension. This extension will automatically add your API Key to NCBO REST URLs any time you visit them in Firefox. The extension is available at Mozilla's Add-On site. To use the extension, follow the installation directions, restart Firefox, and add your API Key into the “Options” dialog menu on the Add-Ons management screen. After that, the extension will automatically append your stored API Key any time you visit http://rest.bioontology.org.

'''''Upcoming software license change''''':
The next release of NCBO software will be under the two-clause BSD license rather than under the currently used three-clause BSD license. This change should not affect anyone’s use of NCBO software and this change is to a less restrictive license. More information about these licenses is available at the site: http://www.opensource.org/licenses. Please contact support@bioontology.org with any questions concerning this change.

== BioPortal Release 3.1 ==
New features include updates to the Web interface and Web services:
* Support for loading OWL 2 ontologies
* Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key.
* Browsing of ontologies that contain large numbers of sibling terms
* Icons for is_a and part_of are displayed for OBO format ontologies
* Display of the “occurs_in” relationship used in the Extended version of the Gene Ontology
Bug Fix
* Added informative error message when incompatible parameter values are used in the Annotator Web service and updated Perl client to capture this error response

(Release date July 8, 2011)

== BioPortal Release 3.0 ==
New features include updates to the Web interface and Web services:
* Web interface updates
* Browse page now displays ontology features, e.g. size of the ontology, number of notes added to the ontology, number of projects that use the ontology, and number of reviews of the ontology
* New ontology summary details page highlights the ontology metrics, reviews, projects, and derived views of the ontology
* Security Framework, part 1 - Added apikey parameter to all Web services. The apikey parameter is optional until June 15, 2011, after this time the apikey parameter will be required for usage of the Web services. Login to BioPortal to get your API key.
* Provisional Term Web service - New term proposals now receive a provisional term id. Additional Web services are now available for submitting provisional terms. For more details, see: http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms
* Form auto-complete Widget - Option to include term definition in display
* Resource Index
** Data indexed with new ontologies from BioPortal
** PubMed data now available for abstracts published in 2010

(Release date May 19, 2011)

== BioPortal Release 2.6.4 ==
New features include additional Web services and Web interface enhancements:
* Mapping Web services - Access to ontology term mappings, including UMLS, OBO DbXref, and LOOM mappings ( http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service ) ''Please note, the prototype Mapping Web service will be removed March 23''
* RDF Download Web service - Access any BioPortal ontology in RDF ( http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Term_Service and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Download_Service )
* Notes - Ability to archive Notes, e.g. accepted term proposals, and filter from display
* Annotator
** Updated ontology content
** Offsets corrected for non-ASCII characters
** Link to Annotator Web interface using parameters
** Web interface enhancements
* Display of ontology development status
* Hyperlinks on term details page
* Ability to add comments on Mappings

(Release date February 2011)

== BioPortal Release 2.5 ==
New features in this release include the following:
* Support for structured notes and term requests: Users can now use BioPortal to request that content developers add new terms or update other ontology content. BioPortal provides a structured template for making such requests, allowing users to suggest preferred names, synonyms, and definitions for the requested terms. BioPortal stores the requests as structured notes that are attached to the ontology and that other ontology tools, such as Protégé, will be able to use.

* Support for email notifications to interested parties whenever a BioPortal user creates new notes for an ontology of interest. (If you would like to subscribe to notifications about a particular ontology, please send email to support at bioontology.org. We will have an interactive form to sign-up for notifications shortly.)

* Prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation [1] for details).

* Prototype end-point for SPARQL access to all ontologies in BioPortal: http://sparql.bioontology.org

* Web services for retrieving instance information for OWL ontologies [1]. We are planning to release a user interface for viewing instances shortly.

* New ontology widgets that developers can embed on their Web sites, including an ontology tree widget that allows Web-site authors to present a display of an ontology or an ontology subtree for any BioPortal ontology in any Web page.

* Preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings

[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services

(Release date June 9, 2010)

BioPortal Release Notes

2014-06-13T00:38:53Z

Fergerson:

== BioPortal Release 4.6 (May 8, 2014) ==

* Improved Search Result Display – Many ontologies contain classes that are references to a canonical ontology that “owns” the class. The system now automatically tries to identify the “owning” ontology and emphasize it in the results while displaying the ontologies that contain references to that ontology as subordinate (for that class). This feature is easier to try out than to explain. Type in “cancer” into the search box on the Search Tab and scan through the results to see what it is all about. This sort of display has been requested by a number of users for quite a while and we are happy to finally provide it.
* Implemented Search for ID (URI), UMLS CUI, UMLS TUI, and skos:notation – The search system now will use the input search to find a class URI, a class skos:notation field (“short id” in the old system) or a UMLS “concept unique identifier” or semantic type. All of these fields are available through the default search mechanism. There is still an optional “all properties” parameter to search these property values along with all other property values.
* Released New Version of BioMixer visualization system – The BioMixer system has been updated to improve performance and be more robust. (Work performed by our University of Victoria collaborators.)
* Implemented New Mapping Visualization – Mappings system now allows a user to visualize the strength of mappings relationships between ontologies. Go to the mappings tab, select an ontology, and hit the visualization radio button to try this out. (Work performed by our University of Victoria collaborators.)
* Implemented Configurable REST API calls – The Annotator and Search REST calls now allow a user specify which fields of a class the system should return. The user can also specify “all” to get everything.
* Updated UMLS Ontologies – All UMLS ontologies have been updated to the latest (2013 AB) version.
* Improved Autocomplete – The autocomplete in the ontology “Jump To” box, and in the widgets, now works more reliably with results that are more intuitive than previously.
* Provide Access Control for Mappings – We have implemented access control to prevent people other than the author from deleting a mapping.
* Reimplemented Annotator “Longest Only” Parameter – We have reimplemented the annotator “longest only” parameter to work in all situations. This parameter allows the user to limit the returned results to only those matches which are longer than other matches for a given ontology. In the old system this parameter did not work correctly.
* Reimplemented Widgets to not use Flash – We have reimplemented the widgets to not use the Adobe Flash technology. Requiring the use of this technology was unpopular among our user community.
* Enabled Upload and Download Large Ontologies – We have fixed various timeout problems which prevented users from uploading or downloading large ontologies.
* Fixed Bugs! – Fixed a very large number of bugs, some new with the new system, and some carried forward from the old system.

We have today shut down access to the old BioPortal REST API and will be turning off the old system entirely in the near future. We have provided 7 months for application developers to move to the new system and the vast majority have already done so. The overwhelming response from developers has been the that new system is now (after a few post release glitches!) much easier to use and much more reliable than the old system. Documentation for the new API is available at:
http://data.bioontology.org/documentation

== BioPortal Release 4.0 ==

The primary distinguishing feature of this release is the replacement of several backend storage and caching mechanisms with a single triple-store based backend built with on the open source 4store platform. In addition we are simultaneously releasing a new version of the BioPortal REST API. This API is also built on top of the triple store. It provides a much more uniform and REST-full interface to the underlying BioPortal data than our previous REST API.

The old API will continue to function through the end of 2013. This API will only be able to access “old content” (that is, ontologies submitted or updated before today). We encourage API users to transition as quickly as possible to the new API. The new API is the only way to access both new content (submitted after today) and old content. The reports from beta users of the new API have been uniformly positive. Draft documentation for the new API is available at
http://data.bioontology.org/documentation

BioPortal users will note a few changes from the previous version. Some of these changes are temporary (we didn’t quite get everything done…) while others are permanent. There are also a number of minor and cosmetic changes. The list of the more important changes is available below.

With a release of this size, it is inevitable that some bugs have crept in. Please report any that you run across to the support@bioontology.org mailing list. Have confidence that we will be working diligently to prioritize and fix the problems that arise.

Temporary Changes
* All handling of obsolete classes in UI and API is not supported yet. Obsolete classes are currently indistinguishable from normal classes.
* “Slices” and ontology sets (user defined lists of ontologies of interest) are not supported yet
* The tree browse UI does not yet distinguish between is-a and part-of relations for OBO ontologies. Previously (and probably in the future) icons next to the class name indicated the relationship type.
* We do not yet have a VM version for this release. We expect to produce a new VM version by the end of the year. This VM will include the triple-store based storage mechanism. In addition VM users will be able to query the VM triple-store directly with SPARQL.
* Parsing of new ontologies and new versions remains disabled for the next few days. We will re-enable parsing by early next week.

Permanent Additions
* New ontologies and new versions of ontologies will be typically available for text annotation the next day after submission. Previously the process took several weeks to several months.
* We now have the latest versions UMLS ontologies. Previously we updated UMLS ontologies on request only, which left us with some very old versions. Going forward we will try to update our set of UMLS ontologies within a month of the UMLS release.

Permanent Subtractions
* Programmatic and browse access to classes in non-current versions of ontologies is removed. We still retain metadata about older versions of ontologies and we still allow you to download the source files for old versions.
* We no longer support Protégé Frames format ontologies. Owners of these ontologies will need to convert them to OWL or OBO to load them.
* We now use the owlAPI (http://owlapi.sourceforge.net/) to load OWL and OBO ontologies. This API supports OWL version 2.0. For almost all features, OWL 2.0 is a superset of OWL 1.0. There are some edge cases though where ontologies that marginally parsed with an OWL 1.0 parser will not parse at all with the OWL 2.0 parser. We leave it to OWL ontology owners to provide valid OWL 2.0 ontologies.

== BioPortal Release 3.12 ==
* Implemented the display of the OBO part-of relationship in the term neighborhood visualization.
* Improved some default layouts in the visualization system.
* Updated automated mappings for all ontologies.
* Regenerated the annotator hierarchy database. The versions of ontologies in this database are now much more current.
* Implemented support for federated queries in the [http://sparql.bioontology.org BioPortal SPARQL endpoint].
* Moved the mappings from the BioPortal endpoint into a separate public endpoint. This change allows us to update automated mappings more cleanly.
* Added the following resources to the Resource Index. All of these resources are the results of our collaboration with the [http://www.neuinfo.org/ Neuroscience Information Framework] (NIF) group.
** NIF PubMed Health: Tests
** NIF Drug Related Gene Database
** NIF Gemma
** NIF Integrated Disease View
* Fixed “Maximum Depth” metric for a number of ontologies. Was incorrectly displaying “1” in some cases.
* Fixed web service failure when attempting to retrieve all concepts from several ontologies.
* Fixed annotator to return all ancestor terms. Was missing some ancestors for some ontologies.
* Fixed Search to work correctly in MeSH.
* Fixed problem with SPARQL query to BioPortal endpoint on queries that include ORDER and LIMIT clauses

(Release February 2013)

== BioPortal Release 3.10 ==
* Revised UI for the Resource Index. This new UI supports the BioPortal slice mechanism. The new UI is also much faster than the previous one.
* Updated ontologies available for use with the Annotator which includes newer ontologies and more recent versions of existing ontologies.
* Fixed a longstanding bug in the Annotator that caused paths from a term to root nodes to occasionally be truncated.
* Allow submission of Notes on ontology terms by anonymous users. Previously a user had to be logged in to submit a note.

(Release July 2012)

== BioPortal Release 3.9 ==
* We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better” ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support@bioontology.org. *

* We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *

* We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).

<nowiki>*</nowiki> This item was requested via the User Support mailing list. Thank you for your comments and suggestions!

(Release June 2012)

== BioPortal Release 3.8 ==
* We have regenerated all mappings based on UMLS CUIs. Thus terms in different UMLS ontologies which share the same CUI are now mapped to each other. The mapping created is of type skos:closeMatch. There are now 3,000,000 of these UMLS CUI mappings in the system.*

* We have regenerated all mappings based on xrefs (OBO cross-reference) in OBO ontologies. A mapping is now generated when a term in an OBO ontology has an xref to a term in another ontology. The mapping created is of type skos:relatedMatch. There are 35,000 of these xref mappings in the system.*

* We have regenerated all mappings based on terms which have identical unique identifiers (IRIs). A mapping is now generated when term in an ontology has a unique identifier that is identical to the identifier of a term in another ontology. The mapping created is of type skos:exactMatch. There are 700,000 of these identical IRI mappings in the system.*

We also fixed a number of bugs which were causing performance, stability, and ontology upload problems.

<nowiki>*</nowiki>This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release May 2012)

== BioPortal Release 3.7 ==
* Updated term mappings generated by LOOM
* Added boolean functionality to Search Web service and UI
* Updated ontology content for the Resource Index
* BioPortal SPARQL endpoint beta release, http://sparql.bioontology.org
* Modified response of Annotator UI to not fail if input text contains returns or results do not have any term matches*
* Bug fix for Term Autocomplete widget to remove namespace collision with jQuery widgets*

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release April 2012)

== BioPortal Release 3.6 ==
* Created “alternate entry points” for BioPortal. These URL’s limit the ontologies that are visible in BioPortal, allowing users to focus on a shared, smaller set of ontologies. The entry points which are currently available are:
** OBO-Foundry: http://obo-foundry.bioportal.bioontology.org
** Unified Medical Language Systems: http://umls.bioportal.bioontology.org
** Cancer Biomedical Informatics Grid: http://cabig.bioportal.bioontology.org
** Clinical and Translational Science Awards: http://ctsa.bioportal.bioontology.org
** CTSA Health Ontology Mapper: http://ctsa-hom.bioportal.bioontology.org
** Proteomics Standards Initiative: http://psi.bioportal.bioontology.org
** WHO Family of International Classifications: http://who-fic.bioportal.bioontology.org
** Consultative Group on Intl Agricultural Research: http://cgiar.bioportal.bioontology.org
** Please contact us on the support mailing list if you would like us to configure an entry point for another set of ontologies.
* Major Updates and Fixes
** Updated the ontologies used by the Annotator Web Services*
** Improved the reliability and robustness of the parsing of OWL 2 ontologies*

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release January 2012)

== BioPortal Release 3.5 ==
* Added ability for logged-in users to filter which ontologies appear in their BioPortal display
* Updated Annotator page to simplify the selection of options, to clarify the annotation results, and to remove Flash from the implementation
* Improved Annotator Web service response performance by 5-10x*
* Added ability for the ontology Web services API to optionally return JSON (rather than XML)*
* Updated Ontology Recommender algorithm to provide better recommendations*
* Added display of matched terms for Ontology Recommender*
* Added Web service to get all namespaces for an ontology*
* Bug Fixes
** Display user-friendly names for RxNorm ontology properties

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release December 2011)

== BioPortal Release 3.4 ==
* Revised the Term Mappings tab to ease the creation of term-to-term mappings*
* Limited access to “Private” ontologies via the Browse and Search pages
* Added backend support to allow multiple administrators for a single ontology*
* Added ability to copy to the clipboard a permanent link to any BioPortal term*
* Bug Fixes
** Resolved issue causing search to not display all matching terms*
** Fixed Term Mappings tab display for IE 7 & 8*
** Fixed RDF Ontology Download Web service
** Fixed link to the list of resources included in the Resource Index*

<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release October 2011)

== BioPortal Release 3.3 ==
New features include updates to the Web interface and Web services:
* Added Get Properties Web service, http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Property_Services
* Updated Search page to remove Flash
* Handling of obsolete terms, part 2 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OWL ontologies.
* Added Help documentation
* Implemented a feature to allow ontology submitters to flag their ontology as “licensed”. This feature allows the ontology submitter to require users to provide license information before they are allowed to access the ontology.
* Bug Fix
** Fixed the Filter by Account on the Mappings tab

(Release date September 2011)

== BioPortal Release 3.2 ==
New features include updates to the Web interface and Web services:
* Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender
** Web service documentation: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service
** Sample client information: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Client_Examples
* Added support for access control for viewing ontologies
* Added link to subscribe to BioPortal Notes emails
* Synchronized “Jump To” feature with ontology parsing and display
* Added documentation on Ontology Groups
* Annotator Web service – disabled use of “longest only” parameter when also selecting “ontologies to expand” parameter
* Removed the metric "Number of classes without an author"
* Handling of obsolete terms, part 1 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OBO and RRF ontologies. This feature will be extended to cover OWL ontologies in a subsequent release.
* Bug Fix
** Fixed calculation of “Classes with no definition” metric
** Added re-direct from old BioPortal URL format to new URL format to provide working links from archived search results

'''''Firefox Extension for NCBO API Key''''':
To make it easier to test Web service calls from your browser, we have released the NCBO API Key Firefox Extension. This extension will automatically add your API Key to NCBO REST URLs any time you visit them in Firefox. The extension is available at Mozilla's Add-On site. To use the extension, follow the installation directions, restart Firefox, and add your API Key into the “Options” dialog menu on the Add-Ons management screen. After that, the extension will automatically append your stored API Key any time you visit http://rest.bioontology.org.

'''''Upcoming software license change''''':
The next release of NCBO software will be under the two-clause BSD license rather than under the currently used three-clause BSD license. This change should not affect anyone’s use of NCBO software and this change is to a less restrictive license. More information about these licenses is available at the site: http://www.opensource.org/licenses. Please contact support@bioontology.org with any questions concerning this change.

== BioPortal Release 3.1 ==
New features include updates to the Web interface and Web services:
* Support for loading OWL 2 ontologies
* Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key.
* Browsing of ontologies that contain large numbers of sibling terms
* Icons for is_a and part_of are displayed for OBO format ontologies
* Display of the “occurs_in” relationship used in the Extended version of the Gene Ontology
Bug Fix
* Added informative error message when incompatible parameter values are used in the Annotator Web service and updated Perl client to capture this error response

(Release date July 8, 2011)

== BioPortal Release 3.0 ==
New features include updates to the Web interface and Web services:
* Web interface updates
* Browse page now displays ontology features, e.g. size of the ontology, number of notes added to the ontology, number of projects that use the ontology, and number of reviews of the ontology
* New ontology summary details page highlights the ontology metrics, reviews, projects, and derived views of the ontology
* Security Framework, part 1 - Added apikey parameter to all Web services. The apikey parameter is optional until June 15, 2011, after this time the apikey parameter will be required for usage of the Web services. Login to BioPortal to get your API key.
* Provisional Term Web service - New term proposals now receive a provisional term id. Additional Web services are now available for submitting provisional terms. For more details, see: http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms
* Form auto-complete Widget - Option to include term definition in display
* Resource Index
** Data indexed with new ontologies from BioPortal
** PubMed data now available for abstracts published in 2010

(Release date May 19, 2011)

== BioPortal Release 2.6.4 ==
New features include additional Web services and Web interface enhancements:
* Mapping Web services - Access to ontology term mappings, including UMLS, OBO DbXref, and LOOM mappings ( http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service ) ''Please note, the prototype Mapping Web service will be removed March 23''
* RDF Download Web service - Access any BioPortal ontology in RDF ( http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Term_Service and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Download_Service )
* Notes - Ability to archive Notes, e.g. accepted term proposals, and filter from display
* Annotator
** Updated ontology content
** Offsets corrected for non-ASCII characters
** Link to Annotator Web interface using parameters
** Web interface enhancements
* Display of ontology development status
* Hyperlinks on term details page
* Ability to add comments on Mappings

(Release date February 2011)

== BioPortal Release 2.5 ==
New features in this release include the following:
* Support for structured notes and term requests: Users can now use BioPortal to request that content developers add new terms or update other ontology content. BioPortal provides a structured template for making such requests, allowing users to suggest preferred names, synonyms, and definitions for the requested terms. BioPortal stores the requests as structured notes that are attached to the ontology and that other ontology tools, such as Protégé, will be able to use.

* Support for email notifications to interested parties whenever a BioPortal user creates new notes for an ontology of interest. (If you would like to subscribe to notifications about a particular ontology, please send email to support at bioontology.org. We will have an interactive form to sign-up for notifications shortly.)

* Prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation [1] for details).

* Prototype end-point for SPARQL access to all ontologies in BioPortal: http://sparql.bioontology.org

* Web services for retrieving instance information for OWL ontologies [1]. We are planning to release a user interface for viewing instances shortly.

* New ontology widgets that developers can embed on their Web sites, including an ontology tree widget that allows Web-site authors to present a display of an ontology or an ontology subtree for any BioPortal ontology in any Web page.

* Preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings

[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services

(Release date June 9, 2010)

BioPortal Mappings

2014-04-07T22:05:11Z

Fergerson: /* Survey of BioPortal Mappings */

BioPortal Mappings

2014-04-07T22:04:26Z

Fergerson: /* Mapping Relationships */

= BioPortal Mapping Notes =

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].

== Related Mapping Documents ==

* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service REST Service for Mappings]
* [http://bioportal.bioontology.org/mappings BioPortal Mappings]

= Mapping Sources =

* [http://www.bioontology.org/ The National Center for Biomedical Ontology (NCBO)]
** '''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. These mappings are represented by the mapping relationship '''skos:closeMatch'''.
** '''NCBO Identical URI (loom)''': Mapping for terms with the same URI from different ontologies. These mappings are represented by the mapping relationship '''skos:exactMatch'''.

* [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS)]
** '''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. These mappings are represented by the mapping relationship '''skos:closeMatch'''.
** '''NLM UMLS (MRMAP)''': Mappings between terms from the UMLS MRMAP.RRF data. These mappings are represented by the mapping relationship '''skos:closeMatch'''.

* [http://obofoundry.org/ The Open Biological and Biomedical Ontologies (OBO)]
** '''OBO xref''': Mappings between ontology terms related by an OBO xref property. These mappings are represented by the mapping relationship '''skos:relatedMatch'''.
** See also, [http://obofoundry.org/index.cgi?show=mappings OBO mappings]

= Mapping Relationships =

There are mappings of the following types in BioPortal:

* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]
** '''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

* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]
** '''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.

* '''related match''': [http://www.w3.org/2004/02/skos/core#relatedMatch skos:relatedMatch]
** '''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>.
** '''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>:

<conceptA> skos:relatedMatch <conceptB> .
<conceptB> skos:relatedMatch <conceptA> .

* '''close match''': [http://www.w3.org/2004/02/skos#closeMatch skos:closeMatch]
** '''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>.
** '''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>:

<conceptA> skos:closeMatch <conceptB> .
<conceptB> skos:closeMatch <conceptA> .

* '''exact match''': [http://www.w3.org/2004/02/skos#exactMatch skos:exactMatch]
** '''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>.
** '''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>:

<conceptA> skos:exactMatch <conceptB> .
<conceptB> skos:exactMatch <conceptA> .

= Survey of BioPortal Mappings =
The table below presents the statistics and examples of BioPortal mappings as of July 2010.

{| border="1" cellpadding="2"
| align="center" style="background:#f0f0f0;"|'''relationship'''
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''
| align="center" style="background:#f0f0f0;"|'''Source'''
| align="center" style="background:#f0f0f0;"|'''Total mappings'''
| width="1025" align="center" style="background:#f0f0f0;"|'''Notes'''
|-
| 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

<tt>select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";</tt>
|-
| 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

<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>
|-
| 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

<tt>select * from mappings where map_source = "exact match or synonym match";</tt>
|-
| 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

<tt>select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";</tt>
|-
| owl:sameAs||shared id||Manual||||271,000||Mappings between the terms that share the same ID

<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>
|-
| skos:relatedMatch||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms

<tt>select * from mappings where map_source = "OBO xref";</tt>
|-
| 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

<tt>select * from mappings where map_source = "DbXref";</tt>
|-
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO

<tt>select * from mappings where map_source = "Upload"; </tt>
|-
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings

<tt>select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";</tt>
|-
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface

<tt>select * from mappings where map_source = "BioPortal UI"</tt>
|-
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT

<tt>select * from mappings where map_source = "NCICB"</tt>
|-
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity

<tt>select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"</tt>
|-
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT

<tt>select * from mappings where map_source = "NLM"</tt>
|}

Lexicon Builder

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== Introduction ==

The LexiconBuilder project has been undertaken for creating a Web service that allows building of custom lexicons from BioPortal ontologies. The custom lexicons built by our system can be used for a variety of natural language processing and other ontology related tasks.

While generating the custom lexicons, several features of our system can be utilized for ease of creation, integration and maintainence of such lexicons. The users can specify ontology mappings in order to identify and retrieve relevant concepts in other ontologies which they might not otherwise know about, in order to assist in enriching the custom lexicons. It also facilitates the interpretation of datasets using the concept mappings between particular datasets. They can also make use of the visualization services provided by NCBO to view and understand the ontology structure retrieved, which otherwise can be a daunting task. Additionally, users can also retrieve identifiers for concepts etc using the lexicon builder and can then utilize the hierarchy services using those ids to identify and visualize the hierarchies(using the visualization service) in the lexicon and can then subsequently make changes to their lexicon building parameters, until they narrow down to their exact requirements. Our system also simplifies the task of performing version management of the custom lexicons. When changes occur to the underlying data, new data is added to the ontologies or old data is changed/deleted, the users can simply retrieve a newer version of their lexicon using our services.

The custom lexicons generated by using our system can help users in a variety of tasks, some exemplified by the users of our system. These lexicons can be used for domain or requirement specific text annotation tasks. e.g. annotation of protein mutations with disease terms. They can also be very useful for ontology related tasks such as ontology learning especially information extraction and also for the task of ontology enrichment. One of our users want to use our service for compiling a disease dictionary, which has actually served as our driving use case. They can also be employed for the purpose of tagging elements for enhancing the user browsing experience for domain specific information e.g. For the task of assisting the user when they are browsing the Web especially for documents related to the biomedical domain we could possible tag elements related to say Tumors and add more context specific information using a Tumor lexicon generated using our system. Another example comes from our user who are using our system to create workflow specific lexicons for concept recognition tasks.

== Code location ==

The prototype Lexicon Builder code and REST services are no longer available. We plan to reimplement the Lexicon Builder in 2014-2015.

== Publication ==

The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies
Gautam Kumar Parai, Clement Jonquet, Rong Xu, Mark A. Musen and Nigam H. Shah
AMIA Annu Symp Proc. 2010

[[Media:LexiconBuilder.pdf]]

== Usage ==
===Inclusion Criteria===

'''Ontologies''' [default: all]
(i.e., list of ontologies you want to use to expand separated with comma (without spaces) e.g., SNOMEDCT,NCI,MSH.

'''Parent Concept''' [default: all]
(i.e. localConceptID of the concept to retrieve children concepts.

'''Synonyms''' true false [default: true]
(i.e., do you want the synonyms of the concept too?)

'''Semantic Types For Concepts''' [default: all]
(i.e., list of UMLS semantic types you want to use separated with comma (without spaces) e.g., T000,T047,T048.

'''Mapping Types For Mapped Concepts''' [default: none]
(i.e., list of mapping types you want to use for the mapping expansion component separated with comma (without spaces) e.g., inter-cui,from-mrrel.)

'''MEDLINE Counts''' [default: all]
(i.e., MEDLINE count of the concepts retrieved is greater than the specified count e.g. 10000)

'''Result Offset''' [default: None]
(i.e., Retrieve results starting from this result. If Result Offset and NO Result Count then returns the top 'Result Offset' results)
Result Count [default: None]
(i.e., Number of results you want to retrieve starting from the offset.)
e.g. 'Result Offset' = 0 'Result Count' = 100 For retrieving the top 100 results.

===Exclusion Criteria===

'''stopWords''' [default: empty]
(i.e., list of stop words to use (i.e., not to use for annotation) separated with comma (without spaces) e.g., in,am,be,is.

'''withDefaultStopWords''' true false [default: false]
(i.e., do you want to use our default stop word list available here: /obs/stopwords . This cancel the above one.)

===Output Criteria===

'''Output Columns''' (i.e., the columns you want in the results.)
LocalConceptID
LocalOntologyID
OntologyName
OntologyVersion
OntologyDescription
TermName
LocalSemanticTypeID
LocalSemanticTypeName
MappedLocalConceptID
MappingType

'''Unique Column''' (i.e., the unique column on which to group the results. e.g. using Concept will give one row for each unique concept.)
LocalConceptID
TermName
The 'unique column' parameters are available only if you choose them in the Output Columns section too.

'''Output Format''' (i.e., the format of the results.) [default: asXml]
asXML
asText
asTabDelimited

'''Compressed Output''' (Yes: Dictionary as a compressed ZIP file. No: Dictionary displayed on browser. ) [default: No]
Yes
No

== Workflow ==

[[Image:Example.png]]

Annotator User Guide

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This service has been replaced. Instead please see:

http://data.bioontology.org/documentation#nav_annotator

Main Page

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Main Page

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Main Page

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Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, dissemination events conducted by the NCBO and publically shared materials from the NCBO.
Please visit our [http://www.bioontology.org Main Site] for more information and materials.

{| class="wikitable"
|-
! style="background:#efefef;" | NCBO Links
! style="background:#efefef;" | Shared Materials
! style="background:#efefef;" | NCBC Links
|-
| [http://www.bioontology.org/ Home page]
| [[Public Requirements Redirect|Public Requirements]]
| [http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]
|-
| [http://www.bioontology.org/wiki/index.php/NCBO_FAQ FAQ]
| [[Shared Materials]]
| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]
|-
| [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination]
|-
| [http://www.bioontology.org/wiki/index.php/News_Events_Publications News, Events and Publications]
| [[Evaluation Activities]]
| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]
|}

=== Software ===
*[http://bioportal.bioontology.org NCBO BioPortal] - Home page for BioPortal Web site
* [http://sparql.bioontology.org/ NCBO BioPortal SPARQL Endpoint] - Access BioPortal via SPARQL queries
* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Resource Index.
* [http://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes BioPortal Software Release Announcements]
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.

=== User Support Documentation ===
*[[BioPortal Help]] - General BioPortal help documentation.
* [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in Your Project] - Documentation on how to use NCBO Technology in your project

=== Technical Documentation ===
* [http://data.bioontology.org/documentation NCBO REST Web services] - Listing of all NCBO web services with usage documentation
* [http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal BioPortal SPARQL Endpoint] - BioPortal SPARQL documentation
* [[BioPortal UI URLs]] - Documentation on how to link back to BioPortal UI pages
* [http://www.bioontology.org/wiki/index.php/SampleCodeCookbook Code samples] - Sample code for common tasks with BioPortal Web services
* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Resource Index.
* ''Retired'' -> See [[BioPortal REST services]] for access to UMLS content. [[UMLS_REST_Services]] - Documentation on how to use our ''prototype'' UMLS services (NetKernel)

=== Ontology Development Projects ===
Below are links for ontology development projects that NCBO is involved in.
*[[BRO:Main_Page]] - Biomedical Resource Ontology
*[[TMO:]] - Translational Medicine Ontology
*[[NPO:Main_Page]] - NanoParticle Ontology
*[[PATO:Main_Page]] - An ontology of phenotypic qualities
*[[RO:Main_Page]] - OBO Relations ontology
*[[CARO:Main_Page]] - Reference anatomical ontology
*[[CL:Main_Page]] - OBO Cell ontology
*[[SO:Main_Page]] - Sequence Ontology
*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders
*[[OCI:Main_Page]] - Ontology of Clinical Investigation

=== Research projects and Prototypes ===
*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores (Nipun Bhatia)
*[[Path to Root]] - Project for consuming the path to root and other OBS rest services (Nipun Bhatia)
*[[PURL Server]] - Instructions on how to set-up a PURL server and create Master-Slave architecture for redundancy (Nipun Bhatia)
*[[Annotation Summarizer]] - Project utilizing OBS REST services to derive information from datasets referencing ontologies in BioPortal (Rob Tirrell)
*[[Lexicon Builder]] - Project for creating a service that allows building of custom lexicons from bioportal ontologies. (Gautam Parai)
*[[Medline Analysis]] - Project for applying natural language processing methods on Medline to analyze the frequency and syntactic type distribution of ontology terms. (Rong Xu)
*[[MetaMap Installation]] - Project to install a custom MetaMap using the NCBO data in order to integrate it in the [[Annotator Web service]] workflow. (Tejaswi Tenneti)

BioPortal REST services

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NCBO BioPortal v4.0 REST services are documented at: http://data.bioontology.org/documentation

BioPortal Help

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== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

To '''find a term in any ontology''' enter the name of 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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

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].

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]

If you know of a publicly available biomedical resource that you would like to see in the Resource Index please send a request to include it to support@bioontology.org.

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

=== Visualizing concepts and mappings ===
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].

== Programing with the BioPortal API ==
Documentation about how to use the BioPortal REST API to access information is available here:

http://www.bioontology.org/wiki/index.php/NCBO_REST_services

== Glossary ==
; 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.
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term: synonym for "obsolete term" in some ontologies.
; group: a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings: Set of mappings for a given term to terms other ontologies.
; term resources: Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
=== NCBO ===
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.

=== BioPortal ===
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.

=== SPARQL Endpoint ===
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.

Main Page

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Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, dissemination events conducted by the NCBO and publically shared materials from the NCBO.
Please visit our [http://www.bioontology.org Main Site] for more information and materials.

{| class="wikitable"
|-
! style="background:#efefef;" | NCBO Links
! style="background:#efefef;" | Shared Materials
! style="background:#efefef;" | NCBC Links
|-
| [http://www.bioontology.org/ Home page]
| [[Public Requirements Redirect|Public Requirements]]
| [http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]
|-
| [http://www.bioontology.org/wiki/index.php/NCBO_FAQ FAQ]
| [[Shared Materials]]
| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]
|-
| [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination]
|-
| [http://www.bioontology.org/wiki/index.php/News_Events_Publications News, Events and Publications]
| [[Evaluation Activities]]
| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]
|}

=== Software ===
*[http://bioportal.bioontology.org NCBO BioPortal] - Home page for BioPortal Web site
* [http://sparql.bioontology.org/ NCBO BioPortal SPARQL Endpoint] - Access BioPortal via SPARQL queries
* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Resource Index.
* [http://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes BioPortal Software Release Announcements]
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.

=== User Support Documentation ===
*[[BioPortal Help]] - General BioPortal help documentation.
* [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in Your Project] - Documentation on how to use NCBO Technology in your project

=== Technical Documentation ===
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO REST Web services] - Listing of all NCBO web services with usage documentation
* [http://www.bioontology.org/wiki/index.php/View_Extraction Ontology Subset Extraction Web service] - Documentation on how to extract subtree views from ontologies
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Term Mappings Web service] - Documentation & information about accessing term mapping data
* [http://www.bioontology.org/wiki/index.php/Ontology_Notes Term Proposal Web service] - Documentation & information about posting and accessing comments and new term proposals
* [[Annotator Web service]] - Documentation & information about the NCBO Annotator
* [[Ontology Recommender Web service]] - Documentation & information about the NCBO Ontology Recommender
* [[Resource Index]] - Documentation & information about the annotation-based NCBO biomedical Resources Index
* [http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal BioPortal SPARQL Endpoint] - BioPortal SPARQL documentation
* [[BioPortal UI URLs]] - Documentation on how to link back to BioPortal UI pages
* [http://www.bioontology.org/wiki/index.php/SampleCodeCookbook Code samples] - Sample code for common tasks with BioPortal Web services
* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Resource Index.
* ''Retired'' -> See [[BioPortal REST services]] for access to UMLS content. [[UMLS_REST_Services]] - Documentation on how to use our ''prototype'' UMLS services (NetKernel)

=== Ontology Development Projects ===
Below are links for ontology development projects that NCBO is involved in.
*[[BRO:Main_Page]] - Biomedical Resource Ontology
*[[TMO:]] - Translational Medicine Ontology
*[[NPO:Main_Page]] - NanoParticle Ontology
*[[PATO:Main_Page]] - An ontology of phenotypic qualities
*[[RO:Main_Page]] - OBO Relations ontology
*[[CARO:Main_Page]] - Reference anatomical ontology
*[[CL:Main_Page]] - OBO Cell ontology
*[[SO:Main_Page]] - Sequence Ontology
*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders
*[[OCI:Main_Page]] - Ontology of Clinical Investigation

=== Research projects and Prototypes ===
*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores (Nipun Bhatia)
*[[Path to Root]] - Project for consuming the path to root and other OBS rest services (Nipun Bhatia)
*[[PURL Server]] - Instructions on how to set-up a PURL server and create Master-Slave architecture for redundancy (Nipun Bhatia)
*[[Annotation Summarizer]] - Project utilizing OBS REST services to derive information from datasets referencing ontologies in BioPortal (Rob Tirrell)
*[[Lexicon Builder]] - Project for creating a service that allows building of custom lexicons from bioportal ontologies. (Gautam Parai)
*[[Medline Analysis]] - Project for applying natural language processing methods on Medline to analyze the frequency and syntactic type distribution of ontology terms. (Rong Xu)
*[[MetaMap Installation]] - Project to install a custom MetaMap using the NCBO data in order to integrate it in the [[Annotator Web service]] workflow. (Tejaswi Tenneti)

BioPortal REST services

2013-07-17T18:26:46Z

Fergerson: /* Get paths to root/leaves from a concept in the latest version of a given ontology */

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].

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

* '''Note''': 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.

* '''''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.

* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs.

= Overview - Using NCBO Technology in Your Project =
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]].

= Sample Code Cookbook =
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]
**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

*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

*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.

= BioPortal Announce Mailing List =
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.

= Service Output Formats =
''JSON output scheduled for mid-December release''
Currently, BioPortal services allow for two output formats: XML (default) and JSON (currently works only for ontology and concept services).

* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as application/xml.
* '''JSON''': requires an "Accept" request-header with the following value: application/json.

If both application/xml and application/json 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

'''NOTE:''' JSON output is currently not available for Annotator Service.

= Services to access ontologies and ontology versions =

== List all the latest version of ontologies ==

* '''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.
* '''Signature''': ./ontologies?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey
** NOTE: The element <id> contains the value for the ontology version identifier.
Ontology files that were successfully parsed have a value of 3 for the <statusId> attribute in the XML response.

== Get a specific ontology based on a version id ==
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey

== Download an ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.
* '''Signature''': ./ontologies/download/{ontology version id}?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey
* '''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.

== Download the latest ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.
* '''Signature''': ./virtual/download/{ontology id}?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey

== Get all versions of an ontology from a virtual ontology id ==
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey
* '''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.

== Get latest version of an ontology id ==
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey

== Get Metrics for an ontology version ==
* '''Signature''': ./ontologies/metrics/{ontology version id}?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40133?apikey=YourAPIKey
* More documentation: http://www.bioontology.org/wiki/index.php/Ontology_Metrics

== Get all the namespace prefixes for an ontology version ==
* '''Signature''': ./ontologies/namespaces/{ontology version id}?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/namespaces/44450?apikey=YourAPIKey

== List all ontology categories ==
* '''Signature''': ./categories?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/categories?apikey=YourAPIKey

== List all ontology groups ==
* '''Signature''': ./groups?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/groups?apikey=YourAPIKey

= Services to access ontology views and ontology view versions =

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

== Download a specific ontology view based on the ontology view version id ==
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey
* '''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.

== Get all view versions of a virtual view ==

* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey

However, there are a few Web services that are distinct for views.

== List the latest version of all Views ==
* '''Signature''': ./views?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey

== Get all versions of views from a virtual ontology id ==
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey

= Search services =

== Search BioPortal ==
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey

* '''Boolean Search Options:'''
** () parentheses allow to enclose multiple terms joined by OR
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre>
** - the minus sign preceding a term indicates NOT
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre>
** No prefix means MUST (required).

* '''Optional Arguments:'''
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)
** isexactmatch=[1/0] – match the entire concept name (default: 0)
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.
** 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.
* '''Description:'''
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).

In phrase searches (multiple words), the wildcard character is appended to the 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).

* '''Field Values'''
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".

* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8"?>
<success>
<accessedResource>/bioportal/search/</accessedResource>
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>1</numPages>
<pageSize>2</pageSize>
<numResultsPage>2</numResultsPage>
<numResultsTotal>2</numResultsTotal>
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean">
<searchResultList>
<searchBean>
<ontologyVersionId>47638</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel>
<recordType>apreferredname</recordType>
<objectType>class</objectType>
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId>
<conceptIdShort>Gene</conceptIdShort>
<preferredName>Gene</preferredName>
<contents>Gene</contents>
<isObsolete>0</isObsolete>
</searchBean>
<searchBean>
<ontologyVersionId>47638</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel>
<recordType>csynonym</recordType>
<objectType>class</objectType>
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId>
<conceptIdShort>Gene_Object</conceptIdShort>
<preferredName>Gene Object</preferredName>
<contents>Gene</contents>
<isObsolete>1</isObsolete>
</searchBean>
</searchResultList>
<ontologyHitList>
<ontologyHitBean>
<ontologyVersionId>47638</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel>
<numHits>2</numHits>
</ontologyHitBean>
</ontologyHitList>
<numHitsTotal>3</numHitsTotal>
</contents>
</page>
</data>
</success>
</pre>

= Term services =
(formerly referred to as Concept services)

== Get term, including its properties, subclasses, and superclasses ==
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}/{concept id}&apikey={YourAPIKey}
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}?conceptid={uri-encoded concept id}
** 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.
* '''Optional arguments:'''
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.
** 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.

Examples using Alt Signature
* http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey
* http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey

Examples using Alt Virtual Signature (uses ontology id and uri-encoded concept id)
* http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD10%2FO80-O84.9&apikey=YourAPIKey
* http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=http%3A%2F%2Fbioontology.org%2Fontologies%2FBiomedicalResourceOntology.owl%23Software&apikey=YourAPIKey

* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8"?>
<success>
<accessedResource>/bioportal/concepts/44103</accessedResource>
<accessDate>2010-12-08 16:57:43.763 PST</accessDate>
<data>
<classBean>
<id>O80-O84.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId>

<label>Delivery</label>
<type>Class</type>
<relations>
<entry>
<string>SubClass</string>
<list>
<classBean>

<id>O84</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId>
<label>Multiple delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>

<int>5</int>
</entry>
</relations>
</classBean>
<classBean>
<id>O83</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId>

<label>Other assisted single delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>7</int>
</entry>

</relations>
</classBean>
<classBean>
<id>O82</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId>
<label>Single delivery by caesarean section</label>
<type>Class</type>

<relations>
<entry>
<string>ChildCount</string>
<int>5</int>
</entry>
</relations>
</classBean>
<classBean>

<id>O81</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId>
<label>Single delivery by forceps and vacuum extractor</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>

<int>6</int>
</entry>
</relations>
</classBean>
<classBean>
<id>O80</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId>

<label>Single spontaneous delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>4</int>
</entry>

</relations>
</classBean>
</list>
</entry>
<entry>
<string>PAR</string>
<list>
<classBean>

<id>O00-O99.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId>
<label>Pregnancy, childbirth and the puerperium</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>

<int>8</int>
</entry>
</relations>
</classBean>
</list>
</entry>
<entry>
<string>ChildCount</string>

<int>5</int>
</entry>
<entry>
<string>Semantic_Type</string>
<list>
<string>Therapeutic or Preventive Procedure</string>
</list>

</entry>
<entry>
<string>TUI</string>
<list>
<string>T061</string>
</list>
</entry>
<entry>

<string>UMLS_CUI</string>
<list>
<string>C0011209</string>
</list>
</entry>
<entry>
<string>SuperClass</string>

<list>
<classBean>
<id>O00-O99.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId>
<label>Pregnancy, childbirth and the puerperium</label>
<type>Class</type>
<relations>

<entry>
<string>ChildCount</string>
<int>8</int>
</entry>
</relations>
</classBean>
</list>
</entry>

</relations>
</classBean>
</data>
</success>
</pre>

== Get all root terms for an ontology version id ==
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey

== Get a path between a term and the root ==

* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey

* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey
* 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.
* 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]].

== Get all terms using the specific ontology version id ==

'''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.

* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}
* '''Examples''':
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey
* '''Arguments:'''
** '''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)
** '''pagenum:''' An integer indicating which page of results to return.
** '''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.

== Get all terms using the virtual ontology id ==

'''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.

* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey
* '''Arguments:'''
** '''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)
** '''pagenum:''' An integer indicating which page of results to return.
** '''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.

== Changes to the Get all terms service ==

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.

* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500

* '''Signature'''
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:
*** '''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)
*** '''pagenum:''' An integer indicating which page of results to return.
*** '''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.

* '''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.

= View Extraction Service =
* 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.

= Property Services =

== Get all available ontology properties using the specific ontology version id ==
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey
* '''Description''': returns all properties for a given ontology version.
* '''Sample Output:'''
<pre>
<success>
<accessedResource>/bioportal/ontologies/properties/38801
</accessedResource>
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate>
<data>
<list>
<propertyBean>
<id>has_value</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value
</fullId>
<label>has_value</label>
<type>property</type>
<isObsolete>0</isObsolete>
<relations />
</propertyBean>
<propertyBean>
<id>has_description</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description
</fullId>
<label>has_description</label>
<type>property</type>
<isObsolete>0</isObsolete>
<relations />
</propertyBean>
<propertyBean>
<id>has_pages</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages
</fullId>
<label>has_pages</label>
<type>property</type>
<isObsolete>0</isObsolete>
<relations>
<entry>
<string>Domain</string>
<classBean>
<id>BibliographicReference</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference
</fullId>
<label>BibliographicReference</label>
<type>class</type>
<isObsolete>0</isObsolete>
<relations />
</classBean>
</entry>
</relations>
</propertyBean>
</list>
</data>
</success>
</pre>

= Instance Services =

== Get all direct instances for a given term ==
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey}
* '''Optional arguments:'''
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)

* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey
* '''Description''': returns all direct instances for a given term.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/instances/38801
</accessedResource>
<accessDate>20100408 18:17:21.226 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>5</numPages>
<pageSize>1</pageSize>
<numResultsPage>1</numResultsPage>
<numResultsTotal>5</numResultsTotal>
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean">
<list>
<instanceBean>
<id>unknown_substrate_type</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</fullId>
<label>unknown_substrate_type</label>
<relations>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>

<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_484</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>

<list>
<string>SubstrateType of unknown type.</string>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</contents>
</page>
</data>
</success>
</pre>

== Get an instance and its property/value pairs ==
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}

* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey
* '''Description''': returns information about an instance and a list of property/value pairs.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/instance/38801
</accessedResource>
<accessDate>20100408 18:10:48.760 PDT</accessDate>
<data>
<instanceBean>
<id>glass</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</fullId>
<label>glass</label>
<relations>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_742</string>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>
<list>
<string>The array is made on a glass slide.</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</data>
</success>
</pre>

= Hierarchy Services =

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.

* '''NOTE: 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.'''

== Get paths to root/leaves from a concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/C3224?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/C3262?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/C3224?apikey=YourAPIKey
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).
* '''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 '''NOTE''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].

= Bio2RDF Dump Service =

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.

* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey

= Annotator Service =

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

The Annotator can be tested via a Web interface available through [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.

= Ontology Recommender =
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.

= Resource Index Service =

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

= RDF Term Service =

* '''Signature''': ./bioportal/rdf/{ontology version id}/?conceptid={concept id}&apikey=YourAPIKey
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id}&apikey=YourAPIKey
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id},{concept id},...,{concept id}&apikey=YourAPIKey
** '''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.
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/?conceptid=NEMO_0000024&apikey=YourAPIKey
** http://rest.bioontology.org/bioportal/rdf/47799/?conceptid=NEMO_1398000&apikey=YourAPIKey
* '''Required arguments:'''
** ontology version id
** concept id
* '''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].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki>
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki>
* '''Sample Output:'''
<pre>
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"
xml:base="http://purl.bioontology.org/ontology/NEMO"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#">
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO">
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name>
<ontology:acronym>NEMO</ontology:acronym>
<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>
<BPMetadata:id>45141</BPMetadata:id>
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/>
</owl:Ontology>



<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/>
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/>
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/>





<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/>



<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024">
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/>
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel>
<skos:notation>NEMO_0000024</skos:notation>
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label>
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/>
</owl:Class>
</rdf:RDF>



</pre>

= RDF Download Service =

* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files.
* '''Required arguments:'''
** ontology version id
* '''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].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}

= Notes Service (Term Proposals and Comments) =
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.

= Mapping Service =
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service.



= XML Schema Definitions for the REST services =

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.

BioPortal REST services

2013-07-17T18:25:40Z

Fergerson: /* Get paths to root/leaves from a concept in the latest version of a given ontology */

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].

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

* '''Note''': 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.

* '''''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.

* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs.

= Overview - Using NCBO Technology in Your Project =
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]].

= Sample Code Cookbook =
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]
**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

*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

*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.

= BioPortal Announce Mailing List =
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.

= Service Output Formats =
''JSON output scheduled for mid-December release''
Currently, BioPortal services allow for two output formats: XML (default) and JSON (currently works only for ontology and concept services).

* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as application/xml.
* '''JSON''': requires an "Accept" request-header with the following value: application/json.

If both application/xml and application/json 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

'''NOTE:''' JSON output is currently not available for Annotator Service.

= Services to access ontologies and ontology versions =

== List all the latest version of ontologies ==

* '''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.
* '''Signature''': ./ontologies?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey
** NOTE: The element <id> contains the value for the ontology version identifier.
Ontology files that were successfully parsed have a value of 3 for the <statusId> attribute in the XML response.

== Get a specific ontology based on a version id ==
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey

== Download an ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.
* '''Signature''': ./ontologies/download/{ontology version id}?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey
* '''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.

== Download the latest ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.
* '''Signature''': ./virtual/download/{ontology id}?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey

== Get all versions of an ontology from a virtual ontology id ==
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey
* '''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.

== Get latest version of an ontology id ==
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey

== Get Metrics for an ontology version ==
* '''Signature''': ./ontologies/metrics/{ontology version id}?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40133?apikey=YourAPIKey
* More documentation: http://www.bioontology.org/wiki/index.php/Ontology_Metrics

== Get all the namespace prefixes for an ontology version ==
* '''Signature''': ./ontologies/namespaces/{ontology version id}?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/namespaces/44450?apikey=YourAPIKey

== List all ontology categories ==
* '''Signature''': ./categories?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/categories?apikey=YourAPIKey

== List all ontology groups ==
* '''Signature''': ./groups?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/groups?apikey=YourAPIKey

= Services to access ontology views and ontology view versions =

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

== Download a specific ontology view based on the ontology view version id ==
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey
* '''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.

== Get all view versions of a virtual view ==

* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey

However, there are a few Web services that are distinct for views.

== List the latest version of all Views ==
* '''Signature''': ./views?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey

== Get all versions of views from a virtual ontology id ==
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey

= Search services =

== Search BioPortal ==
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey

* '''Boolean Search Options:'''
** () parentheses allow to enclose multiple terms joined by OR
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre>
** - the minus sign preceding a term indicates NOT
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre>
** No prefix means MUST (required).

* '''Optional Arguments:'''
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)
** isexactmatch=[1/0] – match the entire concept name (default: 0)
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.
** 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.
* '''Description:'''
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).

In phrase searches (multiple words), the wildcard character is appended to the 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).

* '''Field Values'''
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".

* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8"?>
<success>
<accessedResource>/bioportal/search/</accessedResource>
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>1</numPages>
<pageSize>2</pageSize>
<numResultsPage>2</numResultsPage>
<numResultsTotal>2</numResultsTotal>
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean">
<searchResultList>
<searchBean>
<ontologyVersionId>47638</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel>
<recordType>apreferredname</recordType>
<objectType>class</objectType>
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId>
<conceptIdShort>Gene</conceptIdShort>
<preferredName>Gene</preferredName>
<contents>Gene</contents>
<isObsolete>0</isObsolete>
</searchBean>
<searchBean>
<ontologyVersionId>47638</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel>
<recordType>csynonym</recordType>
<objectType>class</objectType>
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId>
<conceptIdShort>Gene_Object</conceptIdShort>
<preferredName>Gene Object</preferredName>
<contents>Gene</contents>
<isObsolete>1</isObsolete>
</searchBean>
</searchResultList>
<ontologyHitList>
<ontologyHitBean>
<ontologyVersionId>47638</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel>
<numHits>2</numHits>
</ontologyHitBean>
</ontologyHitList>
<numHitsTotal>3</numHitsTotal>
</contents>
</page>
</data>
</success>
</pre>

= Term services =
(formerly referred to as Concept services)

== Get term, including its properties, subclasses, and superclasses ==
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}/{concept id}&apikey={YourAPIKey}
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}?conceptid={uri-encoded concept id}
** 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.
* '''Optional arguments:'''
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.
** 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.

Examples using Alt Signature
* http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey
* http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey

Examples using Alt Virtual Signature (uses ontology id and uri-encoded concept id)
* http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD10%2FO80-O84.9&apikey=YourAPIKey
* http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=http%3A%2F%2Fbioontology.org%2Fontologies%2FBiomedicalResourceOntology.owl%23Software&apikey=YourAPIKey

* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8"?>
<success>
<accessedResource>/bioportal/concepts/44103</accessedResource>
<accessDate>2010-12-08 16:57:43.763 PST</accessDate>
<data>
<classBean>
<id>O80-O84.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId>

<label>Delivery</label>
<type>Class</type>
<relations>
<entry>
<string>SubClass</string>
<list>
<classBean>

<id>O84</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId>
<label>Multiple delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>

<int>5</int>
</entry>
</relations>
</classBean>
<classBean>
<id>O83</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId>

<label>Other assisted single delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>7</int>
</entry>

</relations>
</classBean>
<classBean>
<id>O82</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId>
<label>Single delivery by caesarean section</label>
<type>Class</type>

<relations>
<entry>
<string>ChildCount</string>
<int>5</int>
</entry>
</relations>
</classBean>
<classBean>

<id>O81</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId>
<label>Single delivery by forceps and vacuum extractor</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>

<int>6</int>
</entry>
</relations>
</classBean>
<classBean>
<id>O80</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId>

<label>Single spontaneous delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>4</int>
</entry>

</relations>
</classBean>
</list>
</entry>
<entry>
<string>PAR</string>
<list>
<classBean>

<id>O00-O99.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId>
<label>Pregnancy, childbirth and the puerperium</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>

<int>8</int>
</entry>
</relations>
</classBean>
</list>
</entry>
<entry>
<string>ChildCount</string>

<int>5</int>
</entry>
<entry>
<string>Semantic_Type</string>
<list>
<string>Therapeutic or Preventive Procedure</string>
</list>

</entry>
<entry>
<string>TUI</string>
<list>
<string>T061</string>
</list>
</entry>
<entry>

<string>UMLS_CUI</string>
<list>
<string>C0011209</string>
</list>
</entry>
<entry>
<string>SuperClass</string>

<list>
<classBean>
<id>O00-O99.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId>
<label>Pregnancy, childbirth and the puerperium</label>
<type>Class</type>
<relations>

<entry>
<string>ChildCount</string>
<int>8</int>
</entry>
</relations>
</classBean>
</list>
</entry>

</relations>
</classBean>
</data>
</success>
</pre>

== Get all root terms for an ontology version id ==
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey

== Get a path between a term and the root ==

* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey

* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey
* 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.
* 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]].

== Get all terms using the specific ontology version id ==

'''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.

* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}
* '''Examples''':
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey
* '''Arguments:'''
** '''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)
** '''pagenum:''' An integer indicating which page of results to return.
** '''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.

== Get all terms using the virtual ontology id ==

'''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.

* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey
* '''Arguments:'''
** '''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)
** '''pagenum:''' An integer indicating which page of results to return.
** '''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.

== Changes to the Get all terms service ==

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.

* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500

* '''Signature'''
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:
*** '''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)
*** '''pagenum:''' An integer indicating which page of results to return.
*** '''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.

* '''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.

= View Extraction Service =
* 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.

= Property Services =

== Get all available ontology properties using the specific ontology version id ==
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey
* '''Description''': returns all properties for a given ontology version.
* '''Sample Output:'''
<pre>
<success>
<accessedResource>/bioportal/ontologies/properties/38801
</accessedResource>
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate>
<data>
<list>
<propertyBean>
<id>has_value</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value
</fullId>
<label>has_value</label>
<type>property</type>
<isObsolete>0</isObsolete>
<relations />
</propertyBean>
<propertyBean>
<id>has_description</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description
</fullId>
<label>has_description</label>
<type>property</type>
<isObsolete>0</isObsolete>
<relations />
</propertyBean>
<propertyBean>
<id>has_pages</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages
</fullId>
<label>has_pages</label>
<type>property</type>
<isObsolete>0</isObsolete>
<relations>
<entry>
<string>Domain</string>
<classBean>
<id>BibliographicReference</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference
</fullId>
<label>BibliographicReference</label>
<type>class</type>
<isObsolete>0</isObsolete>
<relations />
</classBean>
</entry>
</relations>
</propertyBean>
</list>
</data>
</success>
</pre>

= Instance Services =

== Get all direct instances for a given term ==
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey}
* '''Optional arguments:'''
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)

* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey
* '''Description''': returns all direct instances for a given term.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/instances/38801
</accessedResource>
<accessDate>20100408 18:17:21.226 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>5</numPages>
<pageSize>1</pageSize>
<numResultsPage>1</numResultsPage>
<numResultsTotal>5</numResultsTotal>
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean">
<list>
<instanceBean>
<id>unknown_substrate_type</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</fullId>
<label>unknown_substrate_type</label>
<relations>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>

<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_484</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>

<list>
<string>SubstrateType of unknown type.</string>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</contents>
</page>
</data>
</success>
</pre>

== Get an instance and its property/value pairs ==
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}

* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey
* '''Description''': returns information about an instance and a list of property/value pairs.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/instance/38801
</accessedResource>
<accessDate>20100408 18:10:48.760 PDT</accessDate>
<data>
<instanceBean>
<id>glass</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</fullId>
<label>glass</label>
<relations>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_742</string>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>
<list>
<string>The array is made on a glass slide.</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</data>
</success>
</pre>

= Hierarchy Services =

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.

* '''NOTE: 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.'''

== Get paths to root/leaves from a concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/C3224?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/C3262?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/C3224?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).
* '''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 '''NOTE''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].

= Bio2RDF Dump Service =

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.

* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey

= Annotator Service =

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

The Annotator can be tested via a Web interface available through [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.

= Ontology Recommender =
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.

= Resource Index Service =

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

= RDF Term Service =

* '''Signature''': ./bioportal/rdf/{ontology version id}/?conceptid={concept id}&apikey=YourAPIKey
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id}&apikey=YourAPIKey
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id},{concept id},...,{concept id}&apikey=YourAPIKey
** '''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.
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/?conceptid=NEMO_0000024&apikey=YourAPIKey
** http://rest.bioontology.org/bioportal/rdf/47799/?conceptid=NEMO_1398000&apikey=YourAPIKey
* '''Required arguments:'''
** ontology version id
** concept id
* '''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].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki>
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki>
* '''Sample Output:'''
<pre>
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"
xml:base="http://purl.bioontology.org/ontology/NEMO"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#">
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO">
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name>
<ontology:acronym>NEMO</ontology:acronym>
<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>
<BPMetadata:id>45141</BPMetadata:id>
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/>
</owl:Ontology>



<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/>
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/>
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/>





<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/>



<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024">
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/>
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel>
<skos:notation>NEMO_0000024</skos:notation>
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label>
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/>
</owl:Class>
</rdf:RDF>



</pre>

= RDF Download Service =

* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files.
* '''Required arguments:'''
** ontology version id
* '''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].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}

= Notes Service (Term Proposals and Comments) =
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.

= Mapping Service =
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service.



= XML Schema Definitions for the REST services =

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.

Resource Index REST Web Service User Guide

2013-07-09T20:30:32Z

Fergerson: /* Introduction */

===Introduction===
The Resource Index API is available through a REST web services interface.

This documentation describes the current version of the API. Some changes may append in the future.

The Resource index API is based on the web service that returns annotations from the Resource Index (called via a REST post). Additionally some simplified REST get services returned simplified results.

----

===Sample HTTP Client for the Resource Index REST Web Service===

* Test HTML Page : http://rest.bioontology.org/resource_index/test

* Test HTML Page ('''element per concept(s)''') : http://rest.bioontology.org/resource_index/test/search

=== List of Resource Index Resources ===
* Resources Page : http://rest.bioontology.org/resource_index/resources/list/

===Service endpoints===
* To retrieve "annotations" either per element or per concept(s) : http://rest.bioontology.org/resource_index/

* To retrieve "element" per concept(s) : http://rest.bioontology.org/resource_index/search

=== Resource Index Web service Validation ===
* '''Note''': 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.

* '''''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.

=== POST calls ===

POST your requests at the service endpoints.

====Parameters====

The Resource Index web service offers a set of parameters that allows a user to customize the annotations returned according to his specific requirements. For example, the annotations returned can be limited to a specific set of ontology and a specific set of semantic types. Plus, the expanded annotations can be filtered.

Please see below for the list of parameters and the possible values.

'''Note** :''' ''Parameter '''apikey''' and '''applicationid''' applies to all POST and GET calls.''

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''apikey**'''
|width="10%"|{apikey}
|width="10%"|default: null
|width="70%"|User identification query parameter with the pattern of "apikey=YourAPIKey". This parameter replaces the email parameter. The parameter will be required in June 2011.

|-valign="top"
|width="10%"|'''applicationid**'''
|width="10%"|{applicationid}
|width="10%"|default: null
|width="70%"|Identifies the application calling the REST service. To receive your "applicationid" please request one from [mailto:support@bioontology.org Support].

|-valign="top"
|width="10%"|'''ontologiesToKeepInResult'''
|width="10%"|{localOntology1,...,localOntologyN}
|width="10%"|default: empty (i.e. all ontologies)
|width="70%"|Specifies the list of ontologies you want to filter in the result from the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces)
* For example, 42789,42838,42142.

|-valign="top"
|width="10%"|'''semanticTypes'''
|width="10%"|{semanticType1,...,semanticTypeN}
|width="10%"|default: empty (i.e. all semanticTypes)
|width="70%"|Specifies the list of UMLS semantic types to use in the annotation process. The list of semantic types that can be used is available at the /obs/semanticTypes URL. Note that the restriction to semantic types is also applied during the semantic expansion steps.
* For example, T047,T048,T191.

|-valign="top"
|width="10%"|'''levelMax'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step.
* For example, an annotation done with levelMax=3 will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. An annotation done with levelMax=0 is equivalent to disable the is_a transitive closure expansion step.

|-valign="top"
|width="10%"|'''mappingTypes'''
|width="10%"|{null,mappingType1,...,mappingTypeN}
|width="10%"|default: empty (i.e. all mappingTypes)
|width="70%"|Specifies the list of mapping types to use during the mapping expansion step. The list of rmapping types that can be used is available at the /obs/mappingTypes URL. The current list is described in section Mapping types.
* For example, Automatic,Manual.
* Note that the use of the key word "'''null'''" in the mappingTypes list disables the mapping expansion component.

|-valign="top"
|width="10%"|'''filterNumber'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.

|-valign="top"
|width="10%"|'''minTermSize'''
|width="10%"|{integer}
|width="10%"|default: 0
|width="70%"|Specifies the minimum length of the term to be included in the annotations.

|-valign="top"
|width="10%"|'''withSynonyms'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name.

|-valign="top"
|width="10%"|'''additionalStopWords'''
|width="10%"|{stopWord1,...,stopWordN}
|width="10%"|default: empty (i.e. none)
|width="70%"|Specifies the list of additional stop words to use. Already used stop words are available here: [[http://rest.bioontology.org/obs/stopwords]]

|-valign="top"
|width="10%"|'''isStopWordsCaseSenstive '''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies whether stopwords are case-sensitive or not.

|-valign="top"
|width="10%"|'''conceptids'''
|width="10%"|{conceptid1,...,conceptidn}
|width="10%"|default: empty (i.e. all concepts)
|width="70%"|Specifies the list of concept to use to query the Resource index (i.e., get the annotations done with this list). This parameter must be jointly specified with the mode parameter. If conceptids contains only one element then the mode parameter can be ignored. The values are separated with comma (without spaces).
* For example, 40401/D008545,4513/Virtual_surface.

|-valign="top"
|width="10%"|'''isVirtualOntologyId'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the list of ontologies are all BioPortal virtual ontology ids. This parameter applies to both conceptids and ontologiesToKeepInResult parameters.

|-valign="top"
|width="10%"|'''mode'''
|width="10%"|{union, intersection}
|width="10%"|default: union
|width="70%"|Specifies the mode to use when querying the resource index with several concept (parameter conceptids ). The union mode returns the union of all the annotations (filtered eventually with other parameters) done with each specified conceptid. The intersection mode returns the intersection.

|-valign="top"
|width="10%"|'''elementid'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the identifier of the resource element for which annotations are requested. The elementid is defined by the original resource e.g., PMID for PubMed, NCT for ClinicalTrials. The full list of the elementid type is defined in Section Local element ID used.
* For example, NCT00001589 or GDS2735.

|-valign="top"
|width="10%"|'''resourceids'''
|width="10%"|
|width="10%"|default: all
|width="70%"|Specifies the resource to filter the annotations with. The resourceids identifies a resource in the Resource Index. They are defined in section Resource identifiers. The list of resourceids can be used is available at the /obs/resources URL.
* For example, GEO,CT,AE.

|-valign="top"
|width="10%"|'''elementDetails'''
|width="10%"|{true, false}
|width="10%"|default: false
|width="70%"|Specifies the if the returned resource elements to be detailed or not.

|-valign="top"
|width="10%"|'''withContext'''
|width="10%"|{true, false}
|width="10%"|default: true
|width="70%"|Specifies whether the annotations context information to be available or not. If turn to false, the set of annotations returned will be simplified and will not detail the context information for an annotation. Only the score will be returned.

|-valign="top"
|width="10%"|'''offset and limit'''
|width="10%"|{integer}
|width="10%"|default: 0/10 respectively
|width="70%"|Specifies an offset and limits the number of annotation results.

|-valign="top"
|width="10%"|'''format'''
|width="10%"|{text, tabDelimited, owl, rdf, xml}
|width="10%"|default: xml
|width="70%"|Specifies the desired format of the response. RDF and OWL outputs are defined according to a RDFS schema and OWL ontology respectively available here: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs and http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|}

===Web Service Response===

'''Response Format'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''text'''
|width="90%"| Returns plain text representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''tabDelimited'''
|width="90%"| Shorter version of "Text" format, returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').

|-valign="top"
|width="10%"|'''xml'''
|width="90%"| Returns XML representation of the ObrResultBean(Detailled).

|-valign="top"
|width="10%"|'''owl'''
|width="90%"| Returns OWL representation of the ObrResultBean(Detailled). The elementsof the result (dictionary, parameters, annotations, etc) are described as instances in the following ontology: http://obs.bioontology.org/ontologies/NCBO_OBS_ontology.owl

|-valign="top"
|width="10%"|'''rdf'''
|width="90%"| Returns RDF representation of the annotations in ObrResultBean(Detailled). The elements of the result are described as instances in the following ontology: http://obs.bioontology.org/ontologies/BioPortalAnnotation.rdfs
|}

'''Note :''' ''if request parameter withContext is true, then returns representation of the ObrResultBeanDetailed and if request parameter withContext is false, then returns representation of the ObrResultBean.''

'''Response Content: ObrResultBeanDetailed'''

Response ObrResultBeanDetailed contains all the contents of ObrResultBean. Those contents are described in section Response Content: ObrResultBean.

Following are remaining contents for ObrResultBeanDetailed :

{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''directAnnotations'''
|width="90%"| One '''annotation''' is represented by ''ObrAnnotationBean''.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"| One '''annotation''' is represented by ''ObrAnnotationBean''.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"| One '''annotation''' is represented by ''ObrAnnotationBean''.

|}

'''Note :''' ''Response contents of the ObrAnnotationBean are described in section ObrResultBean annotations''

'''Response Content: ObrResultBean'''
{| border="1" cellpadding="2"
|-valign="top"
|width="10%"|'''resultId'''
|width="90%"|
|-valign="top"
|width="10%"|'''dictionary'''
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. dictionaryId, dictionaryName, and dictionaryDate identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator Restlet service on time.
|-valign="top"
|width="10%"|'''resultStatistics'''
|width="90%"| Each '''statistics''' contains information on the number of annotations done for a given context. The contextName keyword identifies the type of context and annotationCount is the number of annotations of this type.
|-valign="top"
|width="10%"|'''parameters'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator Restlet service. Those parameters are described in section Service parameters
|-valign="top"
|width="10%"|'''ontologies'''
|width="90%"| To keep the model simple, we provide only the global ontology identifier, localOntologyId the name (ontologyName) and version (ontologyVersion). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: nbAnnotation, the number of annotation that have been made with concepts from this ontology. score, the sum of all the scores of the annotations done with concepts from this ontology (if parameter scored=true). Therefore, score represents the most accurate ontology to annotate the given text.
|-valign="top"
|width="10%"|'''annotations'''
|width="90%"| ''ObrAnnotationBean/ObrAnnotationBeanDetailed'' is a representation of one '''annotation/annotationDetailed'''. If ''elementDetails'' parameter is true the service return response of type '''annotation''', otherwise '''annotationDetailed'''. An annotation has a score which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a concept in a context.

'''Response Content: ObrAnnotationBeanDetailled'''

Response ObrAnnotationBeanDetailed contains all the contents of ObrAnnotationBean. Those contents are described in section Response Content: ObrAnnotationBean.

Following are remaining contents for ObrAnnotationBeanDetailed :

{| border="2" 

|-valign="top"
|width="10%"|'''element'''
|width="90%"|
* ''localElementId'' - Global identifier for the resource element.
* ''elementStructure'' - Represents Structure of an element for a given resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIds'''
|width="90%"|map contain ontologyIds for each context (as String).
|}

|}

'''Response Content: ObrAnnotationBean'''

{| border="2" 
|-valign="top"
|width="10%"|'''localElementId'''
|width="90%"| Identifier for resource element.
|-valign="top"
|width="10%"|'''score'''
|width="90%"|
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|
* ''localConceptId'' - global identifier for the concept in its original repository.
* ''localOntologyId'' - identifier for the ontology in which the concept is defined.
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology.
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository).
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred.
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999).
|-valign="top"
|width="10%"|'''context'''
|width="90%"| Context specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:
{| border="2" style="background:#ABCDEF;" 
|-valign="top"
|width="10%"|'''MGREP'''
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties:
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression. Attention, those values are in number of bytes, not characters e.g., ½ is a two-byte character, thus will count for 2 characters.
|-valign="top"
|width="10%"|'''ISA_CLOSURE'''
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:
* ''childConceptId'' - the concept from which the annotation was derived.
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.
|-valign="top"
|width="10%"|'''MAPPING'''
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties:
* mappedConceptId identifies the concept from which the annotation was derived.
* mappingType specifies the type of mapping.
* ''from'' and ''to'' - specify the character index in the given text for the matched expression.
|}
|}

|-valign="top"
|width="10%"|'''localElementId localConceptIds mode withContext elementDetails counts offsetStart offsetMax'''
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Resource Index Restlet service. Those parameters are described in section Service parameters

|}

===GET calls===
Following section describes all other simplified GET services available in Resource_Index_API.

====Annotation by Concept Service====
Returns the set of annotations done with a given localConceptId.

*GET Request Format : '''/byconcept/{ontologyid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42838/false/true/0/10?conceptid=Melanoma&apikey=YourAPIKey
*Old Request Format* :
**/byconcept/{ontologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''. If request parameter withContext is true, then returns representation of the '''resultDetailed''' and if request parameter withContext is false, then returns representation of the '''result'''.

====Annotation for BioPortal virtual ontology Concept Service ====
Returns the set of all annotations done with a given localConceptId using BioPortal virtual ontology id.

*GET Request Format : '''/byconcept/virtual/{virtual_ontology_id}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptid=Melanoma&apikey=YourAPIKey
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

====Annotation By Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptId for given resourceId.

*GET Request Format : '''/byconcept/{ontologyid}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/42838/AE/false/true/0/10?conceptid=Melanoma&apikey=YourAPIKey
*Old Request Format* :
**/byconcept/{ontologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/{ontologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

====Annotation for BioPortal virtual ontology Concept And Resource Service ====
Returns the set of all annotations done with a given localConceptId using BioPortal virtual ontology id and using particular resourceId.

*GET Request Format : '''/byconcept/virtual/{virtual_ontology_id}/{resourceid}/{withContext}/{counts}/{offset}/{limit}?conceptid={conceptid}'''
*Example : http://rest.bioontology.org/resource_index/byconcept/virtual/1032/AE/false/true/0/10?conceptid=Melanoma&apikey=YourAPIKey
*Old Request Format* :
**/byconcept/virtual/{virtualOntologyID}/{resourceID}/{withContext}/{counts}/{from}/{number}?conceptID={conceptID}
**/byconcept/virtual/{virtualOntologyID}/{conceptID}/{resourceID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

'''For Multiple resources using service at basis URL'''
*GET Request Format : '''/?conceptids={conceptids}&isVirtualOntologyId=true&resourceids={resourceids}&withContext={withContext}&counts={counts}&offset={offset}&limit={limit}&levelMax=2147483647&filterNumber=false'''
*Example : http://rest.bioontology.org/resource_index/?conceptids=1032/Melanoma&isVirtualOntologyId=true&resourceids=CT,DBK,OMIM,RXRD&withContext=true&counts=true&offset=0&limit=10&levelMax=2147483647&filterNumber=false&apikey=YourAPIKey

*Response Content : '''result/resultDetailed''' for each resource. ''ObrResultBean/ObrResultBeanDetailed'' is a representation of one '''result/resultDetailed'''

====Annotation By Resource Element Service ====
Returns the set of all annotations done with a given resource element localElementId for all the concepts.

*GET Request Format : '''/byelement/{resourceid}/{elementDetails}{withContext}/{counts}/{offset}/{limit}?elementid={elementid}'''
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/false/true/false/0/10?elementid=E-GEOD-18509&apikey=YourAPIKey
*Example 1 : http://rest.bioontology.org/resource_index/byelement/AE/true/true/false/0/10?elementid=E-GEOD-18509&apikey=YourAPIKey

*Old Request Format* :
**/byelement/{resourceID}/{withContext}/{counts}/{from}/{number}?elementID={localElementID}
**/byelement/{resourceID}/{localElementID}/{withContext}/{counts}/{from}/{number}

*Response Content : ''ObrResultBean/ObrResultBeanDetailed'' is a representation of '''result/resultDetailed'''.

====Annotation Details By Resource Element Service ====
Returns the set of all annotations details with a given resource element localElementId for given conceptId

*GET Request Format : '''/details/{elementDetails}/concept/{ontologyid}/resource/{resourceid}/{offset}/{limit}?conceptid={conceptid}&elementid={elementid}'''
*Example : http://rest.bioontology.org/resource_index/details/true/concept/42838/resource/AE/0/10?conceptid=Melanoma&elementid=E-GEOD-18509&apikey=YourAPIKey
*Old Request Format* :
**/details/{elementDetails}/concept/{ontologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/concept/{ontologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ''ObrAnnotationBean/ObrAnnotationBeanDetailed'' is a representation of one '''annotation/annotationDetailed'''. annotationDetailed if elementDetails is true otherwise annotation.

====Annotation Details By Resource Element Service for BioPortal Virtual OntologyID====
Returns the set of all annotations details with a given resource element localElementId for given conceptId of BioPortal virtual ontologyId

*GET Request Format : '''/details/{elementDetails}/virtual/concept/{virtual_ontology_id}/resource/{resourceid}/{offset}/{limit}?conceptid={conceptid}&elementid={elementid}'''
*Example : http://rest.bioontology.org/resource_index/details/true/virtual/concept/1032/resource/AE/0/10?conceptid=Melanoma&elementid=E-GEOD-18509&apikey=YourAPIKey
*Old Request Format* :
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/resource/{resourceID}?conceptID={conceptID}&elementID={localElementID}
**/details/{elementDetails}/virtual/concept/{virtualOntologyID}/{conceptID}/resource/{resourceID}/element/{localElementID}

*Response Content : ''ObrAnnotationBean/ObrAnnotationBeanDetailed'' is a representation of one '''annotation/annotationDetailed'''. annotationDetailed if elementDetails is true otherwise annotation.

====Resources Service ====
Returns the set of all resources available in resource index and information related to it.

*GET Request Format : ''/resources''
*Example: http://rest.bioontology.org/resource_index/resources?apikey=YourAPIKey

*Response Content : Resource is a representation of one resource
'''Response Content: Resource'''

{| border="2" 
|-valign="top"
|width="10%"|'''resourceName'''
|width="90%"| Name of the particular resource.

|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"| Identifier of the resource.

|-valign="top"
|width="10%"|'''mainContext'''
|width="90%"| Main context string for the resource.

|-valign="top"
|width="10%"|'''resourceURL'''
|width="90%"| Website URL for the resource

|-valign="top"
|width="10%"|'''resourceElementURL'''
|width="90%"| Base URL for getting elements for resource.

|-valign="top"
|width="10%"|'''resourceDescription'''
|width="90%"| Description of the resource.

|-valign="top"
|width="10%"|'''resourceLogo'''
|width="90%"| URL of logo image for the resource.

|-valign="top"
|width="10%"|'''resourceStructure'''
|width="90%"| Represents Structure of an element for the resource.

'''Response Content: Structure'''

{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|resource identifier for Resource.

|-valign="top"
|width="10%"|'''contexts'''
|width="90%"|list of context for resource.

|-valign="top"
|width="10%"|'''itemKeys'''
|width="90%"|list of itemKeys for resource.

|-valign="top"
|width="10%"|'''weights'''
|width="90%"|map contain weights (as double) for each context (as String).

|-valign="top"
|width="10%"|'''ontoIds'''
|width="90%"|map contain ontology ids for each context (as String).
|}

|}

====Resource Service ====
Returns the resource in resource index for given resource id and information related to it.

*GET Request Format : ''/resources/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/resources/AE?apikey=YourAPIKey
*Old Request Format* : /resources/{resourceID}
*Response Content : ''Resource'' is a representation of one '''resource'''.

====Resource Element Service ====
Service returns elementURL for given localElementId and redirect it to get resource element on the web.

*GET Request Format : ''/element/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/element/AE?elementid=E-GEOD-9118&apikey=YourAPIKey
*Old Request Format* : /element/{resourceID}?element={localElementID}
*Response Content : Web page containing details of the element.

====Element details service by elementid ====
Returns detail for given element using resource id and element id

*GET Request Format : ''/elementDetails/{resourceid}?elementid={elementid}''
*Example: http://rest.bioontology.org/resource_index/elementDetails/AE?elementid=E-GEOD-9118&apikey=YourAPIKey

*Response Content : element

====Elements detail service by chronology ====
Retruns elements details for given resource id cronologically

*GET Request Format : ''/elements/{resourceid}?method={method}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/elements/AE?method=chronology&offset=0&limit=10&apikey=YourAPIKey

*Response Content : ''Element'' is a representation of one '''element'''.

====Resources Service with ontologies used for indexing ====
Returns the set of all resources available in resource index and list of onotolgies used for indexing them.

*GET Request Format : ''/resources?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources?withontologies=true&apikey=YourAPIKey
*Old Request Format* : /resources?withOntologies=true
*Response Content : ObrResourceBean is a representation of one resource with ontologies
'''Response Content: ObrResourceBean'''

Response ObrResourceBean contains all the contents of Resource. Those contents are described in section ''Response Content: Resource''.

Following are remaining contents for ObrResourceBean :

{| border="2" 
|-valign="top"
|width="10%"|'''ontologiesUsed'''
|width="90%"| Presents list of ontologies used for indexing. Each ontology of type OntologyBean.
'''Response Content: OntologyBean'''
{| border="2" style="background:#ABCDEF;"
|-valign="top"
|width="10%"|'''localOntologyId'''
|width="90%"|Local onotology id for Ontology.

|-valign="top"
|width="10%"|'''ontologyName'''
|width="90%"|name of the resource.

|-valign="top"
|width="10%"|'''ontologyVersion'''
|width="90%"|version number for resource.

|-valign="top"
|width="10%"|'''virtualOntologyId'''
|width="90%"|virtual ontology id for ontology.
|}
|}

====Resource Service with ontologies used for indexing ====
Returns the information about resources and list of onotolgies used for indexing it.

*GET Request Format : ''/resources/{resourceid}?withontologies=true''
*Example: http://rest.bioontology.org/resource_index/resources/AE?withOntologies=true&apikey=YourAPIKey
*Old Request Format : /resources/{resourceID}?withOntologies=true
*Response Content : '''resource''' is represented by ''ObrResourceBean''.

====Ontologies Service with resources indexed ====
Returns the set of all ontologies used in resource index with list of resources indexed by given ontology.

*GET Request Format : ''/ontologies?withresources=true''
*Example: http://rest.bioontology.org/resource_index/ontologies?withresources=true&apikey=YourAPIKey

*Response Content : Each '''ontology''' is represented by ''ObrOntologyBean''.

Response ObrOntologyBean contains all the contents of OntologyBean.Those contents are described in section Response Content: OntologyBean.

Following are remaining contents for ObrResourceBean :
{| border="2" 
|-valign="top"
|width="10%"|'''resources'''
|width="90%"| Represents list of resources. Response content for each '''resource''' is of type ''Resource''.
|}

====Ontology Service with resources indexed ====
Returns the information about given ontologies used in resource index with list of resources.

*GET Request Format : ''/ontologies/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/ontologies/42838?apikey=YourAPIKey

*Response Content : '''ontology''' is represented by ''ObrOntologyBean''.

====Virtual Ontology Service with resources indexed ====
Returns the ontology versions in resource index with list of resources for given virtual_ontology_id.

*GET Request Format : ''/virtual/ontology/{virtual_ontology_id}?withresources={true|false}''
*Example: http://rest.bioontology.org/resource_index/virtual/ontology/1032?withresources=true&apikey=YourAPIKey

*Response Content : List of '''ontology''' represented by ''ObrOntologyBean''.

====Concept Frequency Service====
Returns the get most used concepts for given resource id.

*GET Request Format : ''/most-used-concepts/{resourceid}?method={counts|score}&offset={offset}&limit={limit}''
*Example: http://rest.bioontology.org/resource_index/most-used-concepts/AE?method=counts&offset=0&limit=10&apikey=YourAPIKey

*Response Content : '''conceptFrequency''' with format ''ObrConceptFrequencyBean''.

'''Response Content: ObrConceptFrequencyBean'''

Following are contents for ObrConceptFrequencyBean:
{| border="2" 
|-valign="top"
|width="10%"|'''concept'''
|width="90%"|ConceptBean is a representation of concept

|-valign="top"
|width="10%"|'''counts'''
|width="90%"|Frequency counts for a concept .

|-valign="top"
|width="10%"|'''score'''
|width="90%"|score for a concept .

|}

====All Statistics Service====
Returns the information about number of all the annotations done in resource index.

*GET Request Format : ''/statistics/all''
*Example: http://rest.bioontology.org/resource_index/statistics/all?apikey=YourAPIKey

*Response Content : All '''statistics' represented by ''ObrStatisticsBean''.

'''Response Content: ObrStatisticsBean'''
Following are remaining contents for ObrStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''aggregatedAnnotations'''
|width="90%"|Sum of the number of rows in all the indexing tables

|-valign="top"
|width="10%"|'''mgrepAnnotations'''
|width="90%"|Number of mgrep annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''reportedAnnotations'''
|width="90%"|Number of reported annotations entries in direct annotation table.

|-valign="top"
|width="10%"|'''isaAnnotations'''
|width="90%"|Number of is-a annotations entries in extended annotation table.

|-valign="top"
|width="10%"|'''mappingAnnotations'''
|width="90%"|Number of mapping annotations entries in extended annotation table.

|}

====Ontology Statistics Service====
Returns the total statistics for given ontology for All resources.

*GET Request Format : ''/statistics/ontology/{ontologyid}''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42838?apikey=YourAPIKey

*Response Content : '''ontologyStatistics''' with format ''ObrOntologyStatisticsBean''.

'''Response Content: ObrOntologyStatisticsBean'''
Following are contents for ObrOntologyStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|Resource Id for resource.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|ObrStatisticsBean is a representation of statistics

|}

====Ontology Statistics Service by resources====
Returns the statistics for given ontology for each resource separately.

*GET Request Format : ''/statistics/ontology/{onotlogyid}?byresource=true''
*Example: http://rest.bioontology.org/resource_index/statistics/ontology/42838?byresource=true&apikey=YourAPIKey

*Response Content : '''ontologyStatistics''' with format ''ObrOntologyStatisticsBean''.

====Resource Statistics Service====
Returns the total statistics for given resource for All ontology.

*GET Request Format : ''/statistics/resource/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/CANANO?apikey=YourAPIKey

*Response Content : '''resourceStatistics''' with format ''ObrResourceStatisticsBean''.

'''Response Content: ObrResourceStatisticsBean'''
Following are contents for ObrResourceStatisticsBean:
{| border="2" 
|-valign="top"
|width="10%"|'''localOntologyId'''
|width="90%"|local ontology id for given ontology.

|-valign="top"
|width="10%"|'''statistics'''
|width="90%"|''ObrStatisticsBean'' is a representation of '''statistics'''.

|}

====Resource Statistics Service by ontologies====
Returns the statistics for given resource for each ontology separately.

*GET Request Format : ''/statistics/resource/{resourceid}?byontology=true ''
*Example: http://rest.bioontology.org/resource_index/statistics/resource/AE?byontology=true&apikey=YourAPIKey

*Response Content : '''resourceStatistics''' with format ''ObrResourceStatisticsBean''.

====All Executions Service====
Returns the information about all workflow executions done in resource index.

*GET Request Format : ''/executions''
*Web Page Request Format : ''/executions/list/''
*Examples:
**http://rest.bioontology.org/resource_index/executions?apikey=YourAPIKey
**http://rest.bioontology.org/resource_index/executions/list/?apikey=YourAPIKey

*Response Content : List of all '''execution'' represented by ''ObrExecutionBean''.

'''Response Content: ObrExecutionBean'''
Following are remaining contents for ObrExecutionBean:
{| border="2" 
|-valign="top"
|width="10%"|'''resourceId'''
|width="90%"|Identifier of the resource.

|-valign="top"
|width="10%"|'''dictionaryId'''
|width="90%"|Identifier of the dictionary used for execution.

|-valign="top"
|width="10%"|'''withCompleteDictionary'''
|width="90%"|Specifies if complete dictionary is used for execution or not (true/false).

|-valign="top"
|width="10%"|'''elementCount'''
|width="90%"|Number of elements updated/annotated in execution.

|-valign="top"
|width="10%"|'''firstExecution'''
|width="90%"|Boolean value specifies if execution is first execution.

|-valign="top"
|width="10%"|'''executionBeginning'''
|width="90%"|Specifies Date/Time at which execution started.

|-valign="top"
|width="10%"|'''executionEnd'''
|width="90%"|Specifies Date/Time at which execution ended..

|-valign="top"
|width="10%"|'''executionTime'''
|width="90%"|Time required (in HH:mm:ss format) to complete current execution.

|}

====Resource Executions Service====
Returns the information about workflow executions done for given resource in resource index.

*GET Request Format : ''/executions/{resourceid}''
*Example: http://rest.bioontology.org/resource_index/executions/WP?apikey=YourAPIKey

*Response Content : '''execution'' represented by ''ObrExecutionBean''.
----
'''Note* :''' ''Old Request Format not working anymore.''

----

User talk:Klortho

2013-06-12T23:07:44Z

Fergerson: Welcome!

User:Klortho

2013-06-12T23:07:43Z

Fergerson: Creating user page for new user.

User talk:Andrew Su

2013-03-22T00:47:35Z

Fergerson: Welcome!

BioPortal Help

2013-03-09T02:00:30Z

Fergerson: /* How to cite NCBO and BioPortal */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

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].

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]

If you know of a publicly available biomedical resource that you would like to see in the Resource Index please send a request to include it to support@bioontology.org.

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

=== Visualizing concepts and mappings ===
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].

== Programing with the BioPortal API ==
Documentation about how to use the BioPortal REST API to access information is available here:

http://www.bioontology.org/wiki/index.php/NCBO_REST_services

== Glossary ==
; 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.
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term: synonym for "obsolete term" in some ontologies.
; group: a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings: Set of mappings for a given term to terms other ontologies.
; term resources: Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
=== NCBO ===
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.

=== BioPortal ===
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.

=== SPARQL Endpoint ===
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.

Dissemination Wiki

2012-11-15T00:43:56Z

Fergerson: /* NCBO Dissemination and Outreach: Future Events */

== NCBO Dissemination and Outreach: Future Events ==
*'''[http://www.amia.org/amia2012/tutorials Clinical Classifications and Biomedical Ontologies: Terminology Evolution, Principles, and Practicalities]''', AMIA 2012 Annual Symposium, November 3, 2012 Chicago, IL. Presented by Christopher Chute, James Cimino, and Mark Musen.
*'''[[Media:NCBO_NCBC_Showcase_2.pdf|Overview Presentation for the NCBC Showcase]]''', November 8-9, 2012
*'''[https://www.nescent.org/sites/academy/Anatomy_ontologies Course on Anatomy Ontologies]''', July 30-August 3, 2012, [http://nescent.org National Evolutionary Synthesis Center], Durham, NC.

* '''NCBO Webinar Series'''
** The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]

* [[Example.ogg|Foo Bar]]

==Past Events==

*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''

== Educational Documents, Video and Audio Presentations ==

* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]

* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]

Dissemination Wiki

2012-11-15T00:37:22Z

Fergerson: /* NCBO Dissemination and Outreach: Future Events */

== NCBO Dissemination and Outreach: Future Events ==
*'''[http://www.amia.org/amia2012/tutorials Clinical Classifications and Biomedical Ontologies: Terminology Evolution, Principles, and Practicalities]''', AMIA 2012 Annual Symposium, November 3, 2012 Chicago, IL. Presented by Christopher Chute, James Cimino, and Mark Musen.
* [File:NCBO_NCBC_Showcase_2.pdf Overview Presentation for the NCBC Showcase], November 8-9, 2012
*'''[https://www.nescent.org/sites/academy/Anatomy_ontologies Course on Anatomy Ontologies]''', July 30-August 3, 2012, [http://nescent.org National Evolutionary Synthesis Center], Durham, NC.

* '''NCBO Webinar Series'''
** The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]

* [[Example.ogg|Foo Bar]]

==Past Events==

*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''

== Educational Documents, Video and Audio Presentations ==

* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]

* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]

Dissemination Wiki

2012-11-15T00:26:46Z

Fergerson:

== NCBO Dissemination and Outreach: Future Events ==
*'''[http://www.amia.org/amia2012/tutorials Clinical Classifications and Biomedical Ontologies: Terminology Evolution, Principles, and Practicalities]''', AMIA 2012 Annual Symposium, November 3, 2012 Chicago, IL. Presented by Christopher Chute, James Cimino, and Mark Musen.
* [[File:NCBO_NCBC_Showcase_2.pdf]]NCBO Overview Presentation for the NCBC Showcase, November 8-9, 2012
*'''[https://www.nescent.org/sites/academy/Anatomy_ontologies Course on Anatomy Ontologies]''', July 30-August 3, 2012, [http://nescent.org National Evolutionary Synthesis Center], Durham, NC.

* '''NCBO Webinar Series'''
** The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]

==Past Events==

*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''

== Educational Documents, Video and Audio Presentations ==

* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]

* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]

File:NCBO NCBC Showcase 2.pdf

2012-11-15T00:26:04Z

Fergerson:

Dissemination Wiki

2012-11-15T00:24:01Z

Fergerson: /* NCBO Dissemination and Outreach: Future Events */

== NCBO Dissemination and Outreach: Future Events ==
*'''[http://www.amia.org/amia2012/tutorials Clinical Classifications and Biomedical Ontologies: Terminology Evolution, Principles, and Practicalities]''', AMIA 2012 Annual Symposium, November 3, 2012 Chicago, IL. Presented by Christopher Chute, James Cimino, and Mark Musen.
* NCBO Overview Presentation for the NCBC Showcase, November 8-9, 2012
*'''[https://www.nescent.org/sites/academy/Anatomy_ontologies Course on Anatomy Ontologies]''', July 30-August 3, 2012, [http://nescent.org National Evolutionary Synthesis Center], Durham, NC.

* '''NCBO Webinar Series'''
** The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]

==Past Events==

*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''

== Educational Documents, Video and Audio Presentations ==

* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]

* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]

BioPortal Help

2012-10-25T00:56:52Z

Fergerson: /* Programing with the BioPortal API */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

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].

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]

If you know of a publicly available biomedical resource that you would like to see in the Resource Index please send a request to include it to support@bioontology.org.

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

== Programing with the BioPortal API ==
Documentation about how to use the BioPortal REST API to access information is available here:

http://www.bioontology.org/wiki/index.php/NCBO_REST_services

== Glossary ==
; 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.
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term: synonym for "obsolete term" in some ontologies.
; group: a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings: Set of mappings for a given term to terms other ontologies.
; term resources: Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
=== BioPortal ===
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.

=== NCBO ===
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.

=== SPARQL Endpoint ===
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.

BioPortal Help

2012-10-25T00:55:32Z

Fergerson: /* Programmatic Access */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

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].

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]

If you know of a publicly available biomedical resource that you would like to see in the Resource Index please send a request to include it to support@bioontology.org.

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

== Programing with the BioPortal API ==
Documentation about how to use the BioPortal REST API to access information is available here:

== Glossary ==
; 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.
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term: synonym for "obsolete term" in some ontologies.
; group: a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings: Set of mappings for a given term to terms other ontologies.
; term resources: Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
=== BioPortal ===
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.

=== NCBO ===
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.

=== SPARQL Endpoint ===
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.

BioPortal Help

2012-10-25T00:54:20Z

Fergerson: /* Glossary */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

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].

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]

If you know of a publicly available biomedical resource that you would like to see in the Resource Index please send a request to include it to support@bioontology.org.

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

== Programmatic Access ==

== Glossary ==
; 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.
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term: synonym for "obsolete term" in some ontologies.
; group: a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings: Set of mappings for a given term to terms other ontologies.
; term resources: Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
=== BioPortal ===
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.

=== NCBO ===
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.

=== SPARQL Endpoint ===
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.

BioPortal REST services

2012-10-25T00:52:12Z

Fergerson:

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].

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

* '''Note''': 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.

* '''''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.

* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs.

= Overview - Using NCBO Technology in Your Project =
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.

= Sample Code Cookbook =
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]
**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

*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

*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.

= BioPortal Announce Mailing List =
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.

= Service Output Formats =
''JSON output scheduled for mid-December release''
Currently, BioPortal services allow for two output formats: XML (default) and JSON (currently works only for ontology and concept services).

* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as application/xml.
* '''JSON''': requires an "Accept" request-header with the following value: application/json.

If both application/xml and application/json 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

'''NOTE:''' JSON output is currently not available for Annotator Service.

= Services to access ontologies and ontology versions =

== List all the latest version of ontologies ==

* '''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.
* '''Signature''': ./ontologies?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey
** NOTE: The element <id> contains the value for the ontology version identifier.

== Get a specific ontology based on a version id ==
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey

== Download an ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey
* '''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.

== Download the latest ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey

== Get all versions of an ontology from a virtual ontology id ==
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey
* '''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.

== Get latest version of an ontology id ==
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey

== Get Metrics for an ontology version ==
* '''Signature''': ./ontologies/metrics/{ontology version id}?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40133?apikey=YourAPIKey
* More documentation: http://www.bioontology.org/wiki/index.php/Ontology_Metrics

== Get all the namespace prefixes for an ontology version ==
* '''Signature''': ./ontologies/namespaces/{ontology version id}?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/namespaces/44450?apikey=YourAPIKey

== List all ontology categories ==
* '''Signature''': ./categories?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/categories?apikey=YourAPIKey

== List all ontology groups ==
* '''Signature''': ./groups?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/groups?apikey=YourAPIKey

= Services to access ontology views and ontology view versions =

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

== Download a specific ontology view based on the ontology view version id ==
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey
* '''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.

== Get all view versions of a virtual view ==

* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey

However, there are a few Web services that are distinct for views.

== List the latest version of all Views ==
* '''Signature''': ./views?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey

== Get all versions of views from a virtual ontology id ==
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey

= Search services =

== Search BioPortal ==
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey

* '''Boolean Search Options:'''
** () parentheses allow to enclose multiple terms joined by OR
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre>
** - the minus sign preceding a term indicates NOT
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre>
** No prefix means MUST (required).

* '''Optional Arguments:'''
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)
** isexactmatch=[1/0] – match the entire concept name (default: 0)
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.
** 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.
* '''Description:'''
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).

In phrase searches (multiple words), the wildcard character is appended to the 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).

* '''Field Values'''
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".

* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8"?>
<success>
<accessedResource>/bioportal/search/</accessedResource>
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>1</numPages>
<pageSize>2</pageSize>
<numResultsPage>2</numResultsPage>
<numResultsTotal>2</numResultsTotal>
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean">
<searchResultList>
<searchBean>
<ontologyVersionId>47638</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel>
<recordType>apreferredname</recordType>
<objectType>class</objectType>
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId>
<conceptIdShort>Gene</conceptIdShort>
<preferredName>Gene</preferredName>
<contents>Gene</contents>
<isObsolete>0</isObsolete>
</searchBean>
<searchBean>
<ontologyVersionId>47638</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel>
<recordType>csynonym</recordType>
<objectType>class</objectType>
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId>
<conceptIdShort>Gene_Object</conceptIdShort>
<preferredName>Gene Object</preferredName>
<contents>Gene</contents>
<isObsolete>1</isObsolete>
</searchBean>
</searchResultList>
<ontologyHitList>
<ontologyHitBean>
<ontologyVersionId>47638</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel>
<numHits>2</numHits>
</ontologyHitBean>
</ontologyHitList>
<numHitsTotal>3</numHitsTotal>
</contents>
</page>
</data>
</success>
</pre>

= Term services =
(formerly referred to as Concept services)

== Get term, including its properties, subclasses, and superclasses ==
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}
**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.
* '''Optional arguments:'''
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.
** 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.

* '''Example''': http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey

* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey

* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8"?>
<success>
<accessedResource>/bioportal/concepts/44103</accessedResource>
<accessDate>2010-12-08 16:57:43.763 PST</accessDate>
<data>
<classBean>
<id>O80-O84.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId>

<label>Delivery</label>
<type>Class</type>
<relations>
<entry>
<string>SubClass</string>
<list>
<classBean>

<id>O84</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId>
<label>Multiple delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>

<int>5</int>
</entry>
</relations>
</classBean>
<classBean>
<id>O83</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId>

<label>Other assisted single delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>7</int>
</entry>

</relations>
</classBean>
<classBean>
<id>O82</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId>
<label>Single delivery by caesarean section</label>
<type>Class</type>

<relations>
<entry>
<string>ChildCount</string>
<int>5</int>
</entry>
</relations>
</classBean>
<classBean>

<id>O81</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId>
<label>Single delivery by forceps and vacuum extractor</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>

<int>6</int>
</entry>
</relations>
</classBean>
<classBean>
<id>O80</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId>

<label>Single spontaneous delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>4</int>
</entry>

</relations>
</classBean>
</list>
</entry>
<entry>
<string>PAR</string>
<list>
<classBean>

<id>O00-O99.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId>
<label>Pregnancy, childbirth and the puerperium</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>

<int>8</int>
</entry>
</relations>
</classBean>
</list>
</entry>
<entry>
<string>ChildCount</string>

<int>5</int>
</entry>
<entry>
<string>Semantic_Type</string>
<list>
<string>Therapeutic or Preventive Procedure</string>
</list>

</entry>
<entry>
<string>TUI</string>
<list>
<string>T061</string>
</list>
</entry>
<entry>

<string>UMLS_CUI</string>
<list>
<string>C0011209</string>
</list>
</entry>
<entry>
<string>SuperClass</string>

<list>
<classBean>
<id>O00-O99.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId>
<label>Pregnancy, childbirth and the puerperium</label>
<type>Class</type>
<relations>

<entry>
<string>ChildCount</string>
<int>8</int>
</entry>
</relations>
</classBean>
</list>
</entry>

</relations>
</classBean>
</data>
</success>
</pre>

== Get all root terms for an ontology version id ==
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey

== Get a path between a term and the root ==

* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey

* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey
* 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.
* 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]].

== Get all terms using the specific ontology version id ==

'''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.

* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}
* '''Examples''':
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey
* '''Arguments:'''
** '''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)
** '''pagenum:''' An integer indicating which page of results to return.
** '''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.

== Get all terms using the virtual ontology id ==

'''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.

* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey
* '''Arguments:'''
** '''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)
** '''pagenum:''' An integer indicating which page of results to return.
** '''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.

== Changes to the Get all terms service ==

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.

* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500

* '''Signature'''
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:
*** '''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)
*** '''pagenum:''' An integer indicating which page of results to return.
*** '''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.

* '''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.

= View Extraction Service =
* 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.

= Property Services =

== Get all available ontology properties using the specific ontology version id ==
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey
* '''Description''': returns all properties for a given ontology version.
* '''Sample Output:'''
<pre>
<success>
<accessedResource>/bioportal/ontologies/properties/38801
</accessedResource>
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate>
<data>
<list>
<propertyBean>
<id>has_value</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value
</fullId>
<label>has_value</label>
<type>property</type>
<isObsolete>0</isObsolete>
<relations />
</propertyBean>
<propertyBean>
<id>has_description</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description
</fullId>
<label>has_description</label>
<type>property</type>
<isObsolete>0</isObsolete>
<relations />
</propertyBean>
<propertyBean>
<id>has_pages</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages
</fullId>
<label>has_pages</label>
<type>property</type>
<isObsolete>0</isObsolete>
<relations>
<entry>
<string>Domain</string>
<classBean>
<id>BibliographicReference</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference
</fullId>
<label>BibliographicReference</label>
<type>class</type>
<isObsolete>0</isObsolete>
<relations />
</classBean>
</entry>
</relations>
</propertyBean>
</list>
</data>
</success>
</pre>

= Instance Services =

== Get all direct instances for a given term ==
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey}
* '''Optional arguments:'''
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)

* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey
* '''Description''': returns all direct instances for a given term.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/instances/38801
</accessedResource>
<accessDate>20100408 18:17:21.226 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>5</numPages>
<pageSize>1</pageSize>
<numResultsPage>1</numResultsPage>
<numResultsTotal>5</numResultsTotal>
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean">
<list>
<instanceBean>
<id>unknown_substrate_type</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</fullId>
<label>unknown_substrate_type</label>
<relations>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>

<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_484</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>

<list>
<string>SubstrateType of unknown type.</string>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</contents>
</page>
</data>
</success>
</pre>

== Get an instance and its property/value pairs ==
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}

* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey
* '''Description''': returns information about an instance and a list of property/value pairs.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/instance/38801
</accessedResource>
<accessDate>20100408 18:10:48.760 PDT</accessDate>
<data>
<instanceBean>
<id>glass</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</fullId>
<label>glass</label>
<relations>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_742</string>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>
<list>
<string>The array is made on a glass slide.</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</data>
</success>
</pre>

= Hierarchy Services =

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.

* '''NOTE: 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.'''

== Get paths to root/leaves from a concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).
* '''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 '''NOTE''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].

= Bio2RDF Dump Service =

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.

* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey

= Annotator Service =

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

The Annotator can be tested via a Web interface available through [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.

= Ontology Recommender =
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.

= Resource Index Service =

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

= RDF Term Service =

* '''Signature''': ./bioportal/rdf/{ontology version id}/?conceptid={concept id}&apikey=YourAPIKey
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id}&apikey=YourAPIKey
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id},{concept id},...,{concept id}&apikey=YourAPIKey
** '''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.
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/?conceptid=NEMO_0000024&apikey=YourAPIKey
** http://rest.bioontology.org/bioportal/rdf/47799/?conceptid=NEMO_1398000&apikey=YourAPIKey
* '''Required arguments:'''
** ontology version id
** concept id
* '''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].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki>
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki>
* '''Sample Output:'''
<pre>
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"
xml:base="http://purl.bioontology.org/ontology/NEMO"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#">
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO">
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name>
<ontology:acronym>NEMO</ontology:acronym>
<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>
<BPMetadata:id>45141</BPMetadata:id>
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/>
</owl:Ontology>



<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/>
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/>
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/>





<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/>



<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024">
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/>
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel>
<skos:notation>NEMO_0000024</skos:notation>
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label>
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/>
</owl:Class>
</rdf:RDF>



</pre>

= RDF Download Service =

* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files.
* '''Required arguments:'''
** ontology version id
* '''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].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}

= Notes Service (Term Proposals and Comments) =
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.

= Mapping Service =
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service.



= XML Schema Definitions for the REST services =

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.

BioPortal Help

2012-10-19T22:27:02Z

Fergerson: /* How to cite NCBO and BioPortal */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

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].

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]

If you know of a publicly available biomedical resource that you would like to see in the Resource Index please send a request to include it to support@bioontology.org.

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

== Glossary ==
; 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.
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term: synonym for "obsolete term" in some ontologies.
; group: a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings: Set of mappings for a given term to terms other ontologies.
; term resources: Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
=== BioPortal ===
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.

=== NCBO ===
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.

=== SPARQL Endpoint ===
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.

BioPortal Help

2012-10-01T22:59:11Z

Fergerson: /* Resource Index Tab */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

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].

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]

If you know of a publicly available biomedical resource that you would like to see in the Resource Index please send a request to include it to support@bioontology.org.

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

== Glossary ==
; 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.
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term: synonym for "obsolete term" in some ontologies.
; group: a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings: Set of mappings for a given term to terms other ontologies.
; term resources: Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
=== BioPortal ===
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.

=== NCBO ===

Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.

BioPortal Help

2012-10-01T22:58:43Z

Fergerson: /* Resource Index Tab */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

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].

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]

If you know of a publicly available biomedical resource that you would like to see in the Resource Index please send a request to include it to support@bioontology.org

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

== Glossary ==
; 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.
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term: synonym for "obsolete term" in some ontologies.
; group: a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings: Set of mappings for a given term to terms other ontologies.
; term resources: Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
=== BioPortal ===
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.

=== NCBO ===

Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.

BioPortal REST services

2012-08-29T22:40:50Z

Fergerson: /* Get siblings of a given concept in the latest version of a given ontology */

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].

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

* '''Note''': 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.

* '''''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.

* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs.

= Overview - Using NCBO Technology in Your Project =
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.

= Sample Code Cookbook =
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]
**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

*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

*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.

= BioPortal Announce Mailing List =
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.

= Service Output Formats =
''JSON output scheduled for mid-December release''
Currently, BioPortal services allow for two output formats: XML (default) and JSON (currently works only for ontology and concept services).

* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as application/xml.
* '''JSON''': requires an "Accept" request-header with the following value: application/json.

If both application/xml and application/json 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

'''NOTE:''' JSON output is currently not available for Annotator Service.

= Services to access ontologies and ontology versions =

== List all the latest version of ontologies ==

* '''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.
* '''Signature''': ./ontologies?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey
** NOTE: The element <id> contains the value for the ontology version identifier.

== Get a specific ontology based on a version id ==
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey

== Download an ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey

== Download the latest ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey

== Get all versions of an ontology from a virtual ontology id ==
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey

== Get latest version of an ontology id ==
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey

== List all ontology categories ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./categories?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/categories

== List all ontology groups ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./groups?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/groups

= Services to access ontology views and ontology view versions =

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

== Download a specific ontology view based on the ontology view version id ==
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey

== Get all view versions of a virtual view ==

* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey

However, there are a few Web services that are distinct for views.

== List the latest version of all Views ==
* '''Signature''': ./views?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey

== Get all versions of views from a virtual ontology id ==
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey

= Search services =

== Search BioPortal ==
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey

* '''Boolean Search Options:'''
** () parentheses allow to enclose multiple terms joined by OR
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre>
** - the minus sign preceding a term indicates NOT
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre>
** No prefix means MUST (required).

* '''Optional Arguments:'''
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)
** isexactmatch=[1/0] – match the entire concept name (default: 0)
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.
** 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.
* '''Description:'''
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).

In phrase searches (multiple words), the wildcard character is appended to the 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).

* '''Field Values'''
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".

* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8"?>
<success>
<accessedResource>/bioportal/search/</accessedResource>
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>1</numPages>
<pageSize>2</pageSize>
<numResultsPage>2</numResultsPage>
<numResultsTotal>2</numResultsTotal>
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean">
<searchResultList>
<searchBean>
<ontologyVersionId>47638</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel>
<recordType>apreferredname</recordType>
<objectType>class</objectType>
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId>
<conceptIdShort>Gene</conceptIdShort>
<preferredName>Gene</preferredName>
<contents>Gene</contents>
<isObsolete>0</isObsolete>
</searchBean>
<searchBean>
<ontologyVersionId>47638</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel>
<recordType>csynonym</recordType>
<objectType>class</objectType>
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId>
<conceptIdShort>Gene_Object</conceptIdShort>
<preferredName>Gene Object</preferredName>
<contents>Gene</contents>
<isObsolete>1</isObsolete>
</searchBean>
</searchResultList>
<ontologyHitList>
<ontologyHitBean>
<ontologyVersionId>47638</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel>
<numHits>2</numHits>
</ontologyHitBean>
</ontologyHitList>
<numHitsTotal>3</numHitsTotal>
</contents>
</page>
</data>
</success>
</pre>

= Term services =
(formerly referred to as Concept services)

== Get term, including its properties, subclasses, and superclasses ==
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}/{concept id}
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology virtual id}?conceptid={uri-encoded concept id}
**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.
* '''Optional arguments:'''
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.
** 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.

* '''Example''': http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey

* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey

* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8"?>
<success>
<accessedResource>/bioportal/concepts/44103</accessedResource>
<accessDate>2010-12-08 16:57:43.763 PST</accessDate>
<data>
<classBean>
<id>O80-O84.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId>

<label>Delivery</label>
<type>Class</type>
<relations>
<entry>
<string>SubClass</string>
<list>
<classBean>

<id>O84</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId>
<label>Multiple delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>

<int>5</int>
</entry>
</relations>
</classBean>
<classBean>
<id>O83</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId>

<label>Other assisted single delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>7</int>
</entry>

</relations>
</classBean>
<classBean>
<id>O82</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId>
<label>Single delivery by caesarean section</label>
<type>Class</type>

<relations>
<entry>
<string>ChildCount</string>
<int>5</int>
</entry>
</relations>
</classBean>
<classBean>

<id>O81</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId>
<label>Single delivery by forceps and vacuum extractor</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>

<int>6</int>
</entry>
</relations>
</classBean>
<classBean>
<id>O80</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId>

<label>Single spontaneous delivery</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>
<int>4</int>
</entry>

</relations>
</classBean>
</list>
</entry>
<entry>
<string>PAR</string>
<list>
<classBean>

<id>O00-O99.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId>
<label>Pregnancy, childbirth and the puerperium</label>
<type>Class</type>
<relations>
<entry>
<string>ChildCount</string>

<int>8</int>
</entry>
</relations>
</classBean>
</list>
</entry>
<entry>
<string>ChildCount</string>

<int>5</int>
</entry>
<entry>
<string>Semantic_Type</string>
<list>
<string>Therapeutic or Preventive Procedure</string>
</list>

</entry>
<entry>
<string>TUI</string>
<list>
<string>T061</string>
</list>
</entry>
<entry>

<string>UMLS_CUI</string>
<list>
<string>C0011209</string>
</list>
</entry>
<entry>
<string>SuperClass</string>

<list>
<classBean>
<id>O00-O99.9</id>
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId>
<label>Pregnancy, childbirth and the puerperium</label>
<type>Class</type>
<relations>

<entry>
<string>ChildCount</string>
<int>8</int>
</entry>
</relations>
</classBean>
</list>
</entry>

</relations>
</classBean>
</data>
</success>
</pre>

== Get all root terms for an ontology version id ==
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey

== Get a path between a term and the root ==

* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey

* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey
* 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.
* 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]].

== Get all terms using the specific ontology version id ==

'''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.

* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}
* '''Examples''':
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey
* '''Arguments:'''
** '''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)
** '''pagenum:''' An integer indicating which page of results to return.
** '''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.

== Get all terms using the virtual ontology id ==

'''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.

* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey
* '''Arguments:'''
** '''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)
** '''pagenum:''' An integer indicating which page of results to return.
** '''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.

== Changes to the Get all terms service ==

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.

* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500

* '''Signature'''
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:
*** '''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)
*** '''pagenum:''' An integer indicating which page of results to return.
*** '''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.

* '''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.

= View Extraction Service =
* 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.

= Property Services =

== Get all available ontology properties using the specific ontology version id ==
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey
* '''Description''': returns all properties for a given ontology version.
* '''Sample Output:'''
<pre>
<success>
<accessedResource>/bioportal/ontologies/properties/38801
</accessedResource>
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate>
<data>
<list>
<propertyBean>
<id>has_value</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value
</fullId>
<label>has_value</label>
<type>property</type>
<isObsolete>0</isObsolete>
<relations />
</propertyBean>
<propertyBean>
<id>has_description</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description
</fullId>
<label>has_description</label>
<type>property</type>
<isObsolete>0</isObsolete>
<relations />
</propertyBean>
<propertyBean>
<id>has_pages</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages
</fullId>
<label>has_pages</label>
<type>property</type>
<isObsolete>0</isObsolete>
<relations>
<entry>
<string>Domain</string>
<classBean>
<id>BibliographicReference</id>
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference
</fullId>
<label>BibliographicReference</label>
<type>class</type>
<isObsolete>0</isObsolete>
<relations />
</classBean>
</entry>
</relations>
</propertyBean>
</list>
</data>
</success>
</pre>

= Instance Services =

== Get all direct instances for a given term ==
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey}
* '''Optional arguments:'''
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)

* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey
* '''Description''': returns all direct instances for a given term.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/instances/38801
</accessedResource>
<accessDate>20100408 18:17:21.226 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>5</numPages>
<pageSize>1</pageSize>
<numResultsPage>1</numResultsPage>
<numResultsTotal>5</numResultsTotal>
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean">
<list>
<instanceBean>
<id>unknown_substrate_type</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</fullId>
<label>unknown_substrate_type</label>
<relations>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>

<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_484</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>

<list>
<string>SubstrateType of unknown type.</string>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</contents>
</page>
</data>
</success>
</pre>

== Get an instance and its property/value pairs ==
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}

* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey
* '''Description''': returns information about an instance and a list of property/value pairs.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/instance/38801
</accessedResource>
<accessDate>20100408 18:10:48.760 PDT</accessDate>
<data>
<instanceBean>
<id>glass</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</fullId>
<label>glass</label>
<relations>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_742</string>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>
<list>
<string>The array is made on a glass slide.</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</data>
</success>
</pre>

= Hierarchy Services =

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.

* '''NOTE: 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.'''

== Get paths to root/leaves from a concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).
* '''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 '''NOTE''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].

= Bio2RDF Dump Service =

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.

* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey

= Annotator Service =

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

The Annotator can be tested via a Web interface available through [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.

= Ontology Recommender =
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.

= Resource Index Service =

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

= RDF Term Service =

* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?apikey=YourAPIKey
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?apikey=YourAPIKey
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?apikey=YourAPIKey
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_0000024?apikey=YourAPIKey
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_0000023?apikey=YourAPIKey
* '''Required arguments:'''
** ontology version id
** concept id
* '''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].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki>
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki>
* '''Sample Output:'''
<pre>
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"
xml:base="http://purl.bioontology.org/ontology/NEMO"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#">
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO">
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name>
<ontology:acronym>NEMO</ontology:acronym>
<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>
<BPMetadata:id>45141</BPMetadata:id>
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/>
</owl:Ontology>



<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/>
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/>
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/>
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/>





<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/>



<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024">
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/>
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel>
<skos:notation>NEMO_0000024</skos:notation>
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label>
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/>
</owl:Class>
</rdf:RDF>



</pre>

= RDF Download Service =

* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files.
* '''Required arguments:'''
** ontology version id
* '''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].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}

= Notes Service (Term Proposals and Comments) =
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.

= Mapping Service =
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service.



= XML Schema Definitions for the REST services =

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.

User talk:The CHISEL Group

2012-08-20T16:11:32Z

Fergerson: Welcome!

BioPortal Help

2012-07-15T17:40:08Z

Fergerson: /* How to cite NCBO and BioPortal */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

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].

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]

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

== Glossary ==
; 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.
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term: synonym for "obsolete term" in some ontologies.
; group: a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings: Set of mappings for a given term to terms other ontologies.
; term resources: Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
=== BioPortal ===
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.

=== NCBO ===

Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.

BioPortal Help

2012-07-15T17:37:51Z

Fergerson: /* How to cite NCBO and BioPortal */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

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].

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]

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

== Glossary ==
; 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.
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term: synonym for "obsolete term" in some ontologies.
; group: a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings: Set of mappings for a given term to terms other ontologies.
; term resources: Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
=== BioPortal ===
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.

=== NCBO ===

User talk:Kevin Peterson

2012-06-04T18:12:30Z

Fergerson: Welcome!

BioPortal Help

2012-05-02T00:49:44Z

Fergerson: /* Annotator Tab */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

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].

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]

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

== Glossary ==
; 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.
; concept : (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term : synonym for "obsolete term" in some ontologies.
; group : a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource : Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym : Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term : Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings : Set of mappings for a given term to terms other ontologies.
; term resources : Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
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.

BioPortal Help

2012-05-02T00:48:47Z

Fergerson: /* Annotator Tab */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

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].

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]

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

== Glossary ==
; 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.
; concept : (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term : synonym for "obsolete term" in some ontologies.
; group : a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource : Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym : Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term : Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings : Set of mappings for a given term to terms other ontologies.
; term resources : Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
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.

BioPortal Help

2012-05-02T00:46:41Z

Fergerson: /* Resource Index Tab */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

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].

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]

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

== Glossary ==
; 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.
; concept : (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term : synonym for "obsolete term" in some ontologies.
; group : a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource : Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym : Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term : Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings : Set of mappings for a given term to terms other ontologies.
; term resources : Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
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.

BioPortal Help

2012-05-02T00:41:30Z

Fergerson: /* Annotator Tab */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', 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.

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.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

=== Resource Index Tab ===

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.

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].

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]

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

== Glossary ==
; 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.
; concept : (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term : synonym for "obsolete term" in some ontologies.
; group : a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource : Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym : Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term : Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings : Set of mappings for a given term to terms other ontologies.
; term resources : Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
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.

BioPortal Help

2012-05-02T00:37:36Z

Fergerson: /* Recommender Tab */

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

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.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page 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.

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.

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
* logged in to BioPortal
* granted access to the ontology
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.

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].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

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.

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.

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.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

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]).

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.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

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.

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.

To '''create annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

=== Resource Index Tab ===

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.

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].

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]

=== Projects Tab ===

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.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

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.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

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.

=== Viewing and editing reviews ===
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.

== Glossary ==
; 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.
; concept : (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; 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.
; deprecated term : synonym for "obsolete term" in some ontologies.
; group : a collection of ontologies that are typically associated with some outside group or organization.
; 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.
; 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".
; 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.
; 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).
; resource : Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; 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.
; synonym : Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term : Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings : Set of mappings for a given term to terms other ontologies.
; term resources : Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
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.