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BioPortal 3.4

November 4, 2011

The following is a release announcement made by Trish Whetzel, PhD

The National Center for Biomedical Ontology is pleased to announce the release of BioPortal 3.4. New features include updates to the Web interface and Web services:

  • 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 snf 8
    • Fixed RDF Ontology Download Web service
    • Fixed link to the list of resources included in the Resource Index

BioPortal 3.3

September 6, 2011

The following is a release announcement made by Trish Whetzel, PhD

The National Center for Biomedical Ontology is pleased to announce the release of BioPortal 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 simplify UI and remove Flash implementation
  • Extended flagging of obsolete terms to OWL ontologies. Obsolete terms are displayed in italics and are grayed out.
  • Changed search UI to indicate obsolete terms
  • Implemented Help system and created Help documentation
  • Implemented a feature to allow ontology submitters to restrict access to their ontology by requiring that the user provide their license to access the ontology.
  • Bug Fix - Fixed the Filter by Account on the Mappings tab

BioPortal 3.2

September 6, 2011

The following is a release announcement made by Trish Whetzel, PhD

The National Center for Biomedical Ontology is pleased to announce the release of BioPortal 3.2. New features include updates to the Web interface and Web services:

  • Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender
  • 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 3.1

July 8, 2011

The following is a release announcement made by Trish Whetzel, PhD

The National Center for Biomedical Ontology is pleased to announce the release of BioPortal 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

BioPortal 3.0

May 19, 2011

The following is a release announcement made by Trish Whetzel, PhD

The National Center for Biomedical Ontology is pleased to announce the release of BioPortal 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.
  • 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

BioPortal 2.5

July 9, 2010

The following is a release announcement made by Trish Whetzel, PhD

The National Center for Biomedical Ontology is pleased to announce the release of BioPortal 2.5, a Web-based platform for browsing, visualizing, mapping, and commenting on biomedical ontologies and terminologies. Our new release of BioPortal includes many new features, Web services, and bug fixes. BioPortal is a comprehensive repository of biomedical ontologies that enables users to access and share ontologies that are actively used in biomedical communities. Users can publish their ontologies in BioPortal, link ontologies to each other, review ontologies and comment on specific terms, list projects that use ontologies, annotate textual metadata with ontologies, and use Web services to incorporate ontologies or their components into their software applications.

Major 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. 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@bioontology.org. We will have an interactive form to sign-up for notifications shortly.)
  • A set of prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation for details).
  • A set of Web services for retrieving instance information for OWL ontologies. 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.
  • A preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings