[ontolog-forum] BioPortal 2.1 Release

[Trish Whetzel <plwhetzel@xxxxxxxxx>]

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 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]).
 
[1] http://bioportal.bioontology.org/annotate
[2] http://bioontology.org/wiki/index.php/Annotator_Web_service









[3] http://bioportal.bioontology.org/search
[4] http://bioportal.bioontology.org/projects








[5] http://bioportal.bioontology.org/ontologies/39521
[6] http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources

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