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[bioontology-support] [bioportal-announce] Announcing BioPortal Release 3.12

Ray Fergerson ray.fergerson at
Wed Feb 6 10:46:38 PST 2013

We are happy to announce the release of BioPortal 3.12. 


Our development team remains primarily focused on replacing the BioPortal
backend infrastructure with an RDF triple store and revising the BioPortal
API. Little of this infrastructure work is visible yet but it will become
more so in the coming months. For now we continue with small monthly
releases on the current system infrastructure. These releases are limited
mostly to improvements to the visualization system (BioMixer) and small
bug fixes.


The notable changes since the last announced release are:

-          Implemented the display of the OBO part-of relationship in the
term neighborhood visualization.

-          Improved some default layouts in the visualization system.

-          Updated automated mappings for all ontologies.

-          Regenerated the annotator hierarchy database. The versions of
ontologies in this database are now much more current.

-          Implemented support for federated queries in the BioPortal
SPARQL endpoint. 

-          Moved the mappings from the BioPortal endpoint into a separate
public endpoint. This change allows us to update automated mappings more

-          Added the following resources to the Resource Index. All of
these resources are the results of our collaboration with the Neuroscience
Information Framework (NIF) group.

o   NIF PubMed Health: Tests

o   NIF Drug Related Gene Database

o   NIF Gemma

o   NIF Integrated Disease View

-          Fixed "Maximum Depth" metric for a number of ontologies. Was
incorrectly displaying "1" in some cases.

-          Fixed web service failure when attempting to retrieve all
concepts from several ontologies.

-          Fixed annotator to return all ancestor terms. Was missing some
ancestors for some ontologies.

-          Fixed Search to work correctly in MeSH.

-          Fixed problem with SPARQL query to BioPortal endpoint on
queries that include ORDER and LIMIT clauses.




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