[bioportal-announce] NCBO BioPortal 4.10 Released

We are happy to announce the release of BioPortal 4.10. We have had a
number of "silent releases" since the 4.6 release in late April. We are
pleased to announce the latest BioPortal release and fill you in on
features that have been released silently in the interim:

 

.         Reengineered the entire Resource Index to achieve better and
more consistent performance and to align the Resource Index with the new
BioPortal backend (released last year). In addition to allowing us to
support additional resources, this revision removes a number of
inconsistencies that resulted from the Resource Index using the old
BioPortal backend.

.         Upgraded the OWL and OBO parser to the latest version and
reparsed all OBO and OWL ontologies. This reprocessing fixed a large
number of problems with ontologies that either did not parse or that
failed  search indexing or metrics calculations. 

.         We now create and make available for download a comma-separated
value (CSV) file for most ontologies. These files have one row/class and a
standard set of properties in the columns. We cannot make these files
available for ontologies if the license for the ontology does not permit
it (e.g. SNOMED-CT and MedDRA).

.         Fixed PURLS for all ontologies. There were a large number of
ontologies for which the PURLs we created, in the old system or the new
one, no longer worked correctly.

.         Reworked the entire mappings system so that mappings will be
always up-to-date with the latest version of the ontologies.

.         Created a web page
(http://bioportal.bioontology.org/validate_ontology_file) so that users
can validate that their ontologies parse correctly with the latest version
of the OWL/OBO parser.

.         Removed a number of bogus ontologies and spam notes.

.         Fixed implementation of "longest only" parameter in Annotator.

.         We now reparse and reindex an ontology if the administrator of
the ontology changes the metadata for the ontology. The reparse  is
necessary because the metadata contains information, such as the
properties that contain synonyms or definitions, that influence the
parsing and indexing.

.         Recalculated metrics for all ontologies. This process filled in
metrics for many ontologies that lacked them, and corrected the
calculations of some metrics in other ontologies.

.         We now allow the download of RDF (Turtle) files for UMLS
ontologies whose license allows users to download them.

.         Reindexing ontologies for search no longer interferes with the
use of search on those ontologies. Previously search for an ontology was
either broken or incomplete for an ontology that was being indexed.

.         Added an ontology properties endpoint to the REST API. This
endpoint allows a user to query for the properties used by an ontology.

 

As previously noted, we have permanently retired the old NCBO BioPortal
API. New API documentation is available at 

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

 

Ray