This release includes some minor fixes (see release notes), updates to latest BioPortal REST signatures, and adds a new method - OntologyTerm.getURI() to retrieve term's URI.

You can download the latest release from:  https://sourceforge.net/projects/ontocat/files/ontoCAT/release/

Our recent  OntoCAT paper has just reached the list of top 10 most most viewed articles in BMC Bioinformatics this month:

 http://www.biomedcentral.com/bmcbioinformatics/mostviewed

Yay!

And a screenshot of the page for posterity:

This release includes a number of minor fixes since the last major release (see release notes) and the two following major changes:

The addition of apikey to BioPortal queries. All NCBO Web services are required to contain the parameter "apikey=YourApiKey" starting June 2011. OntoCAT's default apikey is now added to all BioPortal REST queries (note that you can also use your private apikey by supplying it in the alternative BioportalOntologyService constructor)

As per  OBO Foundry policy OBO accessions are now translated by OWL API into URIs. This results in colons (!:) being replaced with underscores (_) in term accessions. In line with this policy OntoCAT leaves the accessions as is, however it it still possible to use OBO accessions in getTerm(), e.g. GO:0000003, but the accession on the retrieved OntologyTerm will be modified, i.e., GO_0000003.

You can download the latest release from:  https://sourceforge.net/projects/ontocat/files/ontoCAT/release/

 OntoCAT paper has now been published by BMC Bioinformatics.

In this release:

• OWL Reasoner support via ReasonedFileOntologyService (see example 15)
• Similarity sorting of the search result list
• More robust XML parsing of the BioPortal REST signatures
• A number of minor fixes

Download from:  https://sourceforge.net/projects/ontocat/files/ontoCAT/release/

In this release:

Updated OWL API dependence to 3.1

On creation of FileOntologyService you can specify a user-defined ontology accession

New utils package containing convenience methods for the R ontocat package

BioportalOntologyService .getOntologies() now includes the ontology views

FIX: Unnecessary warnings when searching OLS

FIX: Occasional incorrect parsing of ontology accessions when searching OLS

FIX: FileOntologyService throwing an exception if there were classes with no properties

The latest distribution can be downloaded from (under release):

 https://sourceforge.net/projects/ontocat/files/

In this release:

• Added support for labels being part of the class URI
• FIX: removed unnecessary eager fetching on some of the methods in BioportalOntologyService (e.g. getParents, getChildren where the return list was post-processed on individual term basis)
• FIX: updated to the latest BioPortal service signature, i.e. instances XML
• Less warnings on using unoptimised getAllParents and getAllChildren

Download from:  https://sourceforge.net/projects/ontocat/files/