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BioPortal 2.1 Release PDF Print E-mail
Written by Virginia Gonzalez   
Friday, 08 May 2009 18:53

The National Center for Biomedical Ontology announces the release of BioPortal 2.1. Highlights of this release are:

-Annotator: a service that identifies mentions of biomedical ontology concepts in text that users submit. You can use the annotator service to tag automatically any item of interest with terms from UMLS and BioPortal ontologies. The Annotator is accessible via the BioPortal user interface [1] and as a REST service [2]

-Advanced user interface for searching ontologies [3] enables users to select which ontologies or categories of ontologies to search, specify search parameters, and filter and navigate easily through the search results

-Ontology-based projects: You can now describe your ontology-based projects, indicate which BioPortal ontologies you use, and provide reviews of those ontologies in the context of your project [4]

-Version management for OWL ontologies: you can download a diff between successive versions of an OWL ontology in tab-delimited format or as a set of RDF instances of the Protégé Change and Annotations ontology. See, for example, the details for the Biomedical Resource Ontology [5], to see a listing of diffs for its versions.

-Within-ontology search: you can use the search box at the top of each ontology tree to type in preferred name or a synonym and jump directly to one of the concepts that matches your search term (look for the "Jump to" box when you are exploring an ontology)

-Support for different hierarchy relations in OBO ontologies: just like in OBO-Edit, you will now see different icons when you browse the tree for an OBO ontologies, indicating the specific relationship between a child and a parent node (such as is-a or part-of)

Numerous improvements in user interaction:
-The new home page enables direct access to key BioPortal functionality, such as searching ontologies for terms, finding a specific ontology of interest, or searching the NCBO Resource index to find resources mentioning a particular concept of interest.
-New look and feel for BioPortal user interface
-Additional details on the ontology metadata page
-It is now easier to add and view reviews for a particular ontology
-Many other user interface improvements and fixes

Prototypes of upcoming features for accessing the NCBO Resource index:
-access to biomedical resources annotated with a specific ontology term when you are viewing the term in BioPortal (in the "Resources" tab)
-search through all resource annotations available in the NCBO Resource index
-the resources that NCBO currently indexes or provides access to include Conserved Domain Database, ArrayExpress, PharmGKB, UniProt KB, ARRS GoldMiner, Online Mendelian Inheritance in Man (OMIM), Reactome, Gene Expression Omnibus and NextBio (to check dynamically the list of resource that we currently have in the index, you can call the corresponding REST service [6]).