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[bioontology-support] [bioportal-announce] NCBO BioPortal 4.0 Released

Ray Fergerson ray.fergerson at
Wed Sep 25 19:49:50 PDT 2013

We are very happy to finally announce, after a year of planning and
development work, the release of the reengineering of BioPortal. Because
this is a huge change we care labeling this release BioPortal 4.0.

The primary distinguishing feature of this release is the replacement of
several backend storage and caching mechanisms with a single triple-store
based backend built with on the open source 4store platform.  In addition
we are simultaneously releasing a new version of the BioPortal REST API.
This API is also built on top of the triple store. It provides a much more
uniform and REST-full interface to the underlying BioPortal data than our
previous REST API.

The old API will continue to function through the end of 2013. This API
will only be able to access “old content” (that is, ontologies submitted
or updated before today).  We encourage API users to transition as quickly
as possible to the new API. The new API is the only way to access both new
content (submitted after today) and old content. The reports from beta
users of the new API have been uniformly positive.  Draft documentation
for the new API is available at

BioPortal users will note a few changes from the previous version. Some of
these changes are temporary (we didn’t quite get everything done
) while
others are permanent. There are also a number of minor and cosmetic
changes. The list of the more important changes is available below.

With a release of this size, it is inevitable that some bugs have crept
in. Please report any that you run across to the support at
mailing list. Have confidence that we will be working diligently to
prioritize and fix the problems that arise.

The NCBO Team


Temporary Changes

-          All handling of obsolete classes in UI and API is not supported
yet. Obsolete classes are currently indistinguishable from normal classes.

-          “Slices” and ontology sets (user defined lists of ontologies of
interest) are not supported yet

-          The tree browse UI does not yet distinguish between is-a and
part-of relations for OBO ontologies. Previously (and probably in the
future) icons next to the class name indicated the relationship type.

-          We do not yet have a VM version for this release. We expect to
produce a new VM version by the end of the year. This VM will include the
triple-store based storage mechanism. In addition VM users will be able to
query the VM triple-store directly with SPARQL.

-          Parsing of new ontologies and new versions remains disabled for
the next few days. We will re-enable parsing by early next week.

Permanent Additions

-          New ontologies and new versions of ontologies will be typically
available for text annotation the next day after submission. Previously
the process took several weeks to several months.

-          We now have the latest versions UMLS ontologies. Previously we
updated UMLS ontologies on request only, which left us with some very old
versions. Going forward we will try to update our set of UMLS ontologies
within a month of the UMLS release.

Permanent Subtractions

-          Programmatic and browse access to classes in non-current
versions of ontologies is removed. We still retain metadata about older
versions of ontologies and we still allow you to download the source files
for old versions.

-          We no longer support Protégé Frames format ontologies. Owners
of these ontologies will need to convert them to OWL or OBO to load them.

-          We now use the owlAPI ( to load
OWL and OBO ontologies. This API supports OWL version 2.0. For almost all
features, OWL 2.0 is a superset of OWL 1.0. There are some edge cases
though where ontologies that marginally parsed with an OWL 1.0 parser will
not parse at all with the OWL 2.0 parser. We leave it to OWL ontology
owners to provide valid OWL 2.0 ontologies.

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