[bioportal-announce] NCBO BioPortal 4.6 Released!

We are happy to announce the release of BioPortal 4.6. We have had a
number of "silent releases" since the 4.0 release last September. These
releases were concentrated mainly on performance and stability issues for
the new system and included only a few user-visible changes. We are
pleased to announce the latest BioPortal release and fill you in on
features that have been released silently in the interim:

 

-          Improved Search Result Display - Many ontologies contain
classes that are references to a canonical ontology that "owns" the class.
The system now automatically tries to identify the "owning" ontology and
emphasize it in the results while displaying the ontologies that contain
references to that ontology as subordinate (for that class). This feature
is easier to try out than to explain. Type in "cancer" into the search box
on the Search Tab and scan through the results to see what it is all
about. This sort of display has been requested by a number of users for
quite a while and we are happy to finally provide it.

-          Implemented Search for ID (URI), UMLS CUI, UMLS TUI, and
skos:notation - The search system now will use the input search to find a
class URI, a class skos:notation field ("short id" in the old system) or a
UMLS "concept unique identifier" or semantic type. All of these fields are
available through the default search mechanism. There is still an optional
"all properties" parameter to search these property values along with all
other property values.

-          Released New Version of BioMixer visualization system - The
BioMixer system has been updated to improve performance and be more
robust. (Work performed by our University of Victoria collaborators.)

-          Implemented New Mapping Visualization - Mappings system now
allows a user to visualize the strength of mappings relationships between
ontologies. Go to the mappings tab, select an ontology, and hit the
visualization radio button to try this out. (Work performed by our
University of Victoria collaborators.)

-          Implemented Configurable REST API calls - The Annotator and
Search REST calls now allow a user specify which fields of a class the
system should return. The user can also specify "all" to get everything. 

-          Updated UMLS Ontologies - All UMLS ontologies have been updated
to the latest (2013 AB) version.

-          Improved Autocomplete - The autocomplete in the ontology "Jump
To" box, and in the widgets, now works more reliably with results that are
more intuitive than previously.

-          Provide Access Control for Mappings - We have implemented
access control to prevent people other than the author from deleting a
mapping.

-          Reimplemented Annotator "Longest Only" Parameter - We have
reimplemented the annotator "longest only" parameter to work in all
situations. This parameter allows the user to limit the returned results
to only those matches which are longer than other matches for a given
ontology. In the old system this parameter did not work correctly.

-          Reimplemented Widgets to not use Flash - We have reimplemented
the widgets to not use the Adobe Flash technology. Requiring the use of
this technology was unpopular among our user community.

-          Enabled Upload and Download Large Ontologies - We have fixed
various timeout problems which prevented users from uploading or
downloading large ontologies.

-          Fixed Bugs! - Fixed a very large number of bugs, some new with
the new system, and some carried forward from the old system.

 

 

We have today shut down access to the old BioPortal REST API and will be
turning off the old system entirely in the near future. We have provided 7
months for application developers to move to the new system and the vast
majority have already done so. The overwhelming response from developers
has been the that new system is now (after a few post release glitches!)
much easier to use and much more reliable than the old system.
Documentation for the new API is available at:

 <http://data.bioontology.org/documentation>
http://data.bioontology.org/documentation

 

Please try out the new features and let us know what you think.

 

The NCBO BioPortal Team