BioPortal Release Notes

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)