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[protege-discussion] BioPortal 2.1 Release

Trish Whetzel plwhetzel at
Tue May 5 18:32:56 PDT 2009

The National Center for Biomedical Ontology is pleased to announce 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
-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]).

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