- From: Ray Fergerson <ray.fergerson@stanford.edu>
- Date: Thu, 11 Sep 2014 13:46:49 -0700 (PDT)
- To: <bioportal-announce@lists.stanford.edu>
- Message-ID: <81057f9e.00002638.0000000e@BMIR-WIN8L-RF1.stanford.edu>
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
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Received on Thursday, 11 September 2014 20:47:28 UTC