Congratulations, Ray and the NCBO team! (01)
Fyi,. OOR folks ... (02)
---------- Forwarded message ----------
From: Ray Fergerson <ray.fergerson@xxxxxxxxxxxx>
Date: Thu, May 8, 2014 at 12:37 PM
Subject: [bioportal-announce] NCBO BioPortal 4.6 Released!
To: bioportal-announce@xxxxxxxxxxxxxxxxxx (03)
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: (04)
- 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. (05)
- 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. (06)
- 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.) (07)
- 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.) (08)
- 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. (09)
- Updated UMLS Ontologies – All UMLS ontologies have been
updated to the latest (2013 AB) version. (010)
- 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. (011)
- Provide Access Control for Mappings – We have implemented
access control to prevent people other than the author from deleting a
mapping. (012)
- 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. (013)
- 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. (014)
- Enabled Upload and Download Large Ontologies – We have
fixed various timeout problems which prevented users from uploading or
downloading large ontologies. (015)
- Fixed Bugs! – Fixed a very large number of bugs, some new
with the new system, and some carried forward from the old system. (016)
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: (017)
http://data.bioontology.org/documentation (018)
Please try out the new features and let us know what you think. (019)
The NCBO BioPortal Team (020)
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