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[bioportal-announce] NCBO BioPortal 4.14 Released!

From: Ray Fergerson <ray.fergerson@stanford.edu>
Date: Mon, 23 Feb 2015 14:56:28 -0800 (PST)
To: <bioportal-announce@lists.stanford.edu>
Message-ID: <f3cd028b.00000600.0000000a@BMIR-WIN8L-RF1.stanford.edu>
We are happy to announce the release of BioPortal 4.14. We have had a
number of "silent releases" since the last announced 4.10 release in
September 2014. We are pleased to announce the latest BioPortal release
and fill you in on features that have been released silently in the
interim. This release in particular contains a number of features that
people have requested over the past few years. 


.         The ontology summary page for each ontology now has a graph of
recent history of the level of user-interface (UI) web traffic (number of
page views) for that ontology. This graph is available under the "Metrics"
box. See, for example,
http://bioportal.bioontology.org/ontologies/SNOMEDCT . The raw data is
also available for download in CSV format from the same location. 

.         The BioPortal home page now has a link that displays all
ontologies in the system and the number of UI views for each ontology.
Previously usage of only the top 5 ontologies were available. 

.         Users of our virtual machine now have the ability to plug in
alternate concept recognizers for use by the annotator. To support these
custom annotators, arbitrary parameters can be passed via the rest
interface to the underlying concept recognizer. Documentation for how to
make use of this feature is available at: 
tom-Concept-Recognizer . 
Previously the "mgrep" concept recognizer was hardwired into the system
and code modifications were required to employ another recognizer. 

.         Ontologies views can now be used for annotation. Previously only
top level ontologies were available for use by the annotation system. 

.         All of PubMed has been indexed for use by the Resource Index for
all terms in all ontologies in BioPortal. Previously only 18 months of
PubMed data was indexed. 

.         We now provide for download, for all resources in BioPortal,
files containing counts for term occurrence and co-occurrence (occurrence
of pairs of terms in a document). These files can be used for research in
enrichment analysis. Documentation of the files and how they might be used
is available at:

.         The ontology browse page now has a faceted interface that allows
the list of displayed ontologies to be narrowed as desired. Previously all
ontologies appeared in an alphabetical list but this became unwieldy with
the 400+ ontologies that we now have. 

.         There is now a user-interface for displaying all of the
properties in an ontology. If the properties were created in a hierarchy
then this hierarchy is displayed. Previously only the class hierarchy was
displayed. Properties were available programmatically though the REST
interface but this information was not surfaced in the UI.

.         Ontologies defined using SKOS are now supported. For these
ontologies, the hierarchy is determined by the SKOS "broader" and
"narrower" properties.

.         We now allow download of all publically available ontologies in
RDF. UMLS ontologies with restrictive licenses are excluded.

.         We fixed a number of non-parsing ontologies and removed a bunch
of low-content ("test") ontologies.

.         The system now contains the latest versions (2014AB) of all UMLS

.         We now treat all OBO synonym types as a BioPortal synonyms.
Previously only the OBO "exact" synonym type was treated as a BioPortal

.         We now notify by email the ontology authors if the nightly pull
of their ontology fails. 




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Received on Monday, 23 February 2015 22:57:10 UTC

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