BioPortal Release Notes

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).

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

June 19, 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.

*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*

* 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*

* 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

* 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*

* 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)