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2012 Citations
- Dönitz, Jürgen, and Edgar Wingender. "The ontology-based answers (OBA) service: A connector for embedded usage of ontologies in applications." Frontiers in Genetics 3: 197.
http://www.frontiersin.org/bioinformatics_and_computational_biology/10.3389/fgene.2012.00197/abstract - Kapushesky, Misha, et al. "Gene Expression Atlas update—a value-added database of microarray and sequencing-based functional genomics experiments." Nucleic acids research 40.D1 (2012): D1077-D1081.
http://nar.oxfordjournals.org/content/40/D1/D1077.short - Travillian, Ravensara S., et al. "Anatomy ontologies and potential users: bridging the gap." Journal of biomedical semantics 2.Suppl 4 (2011): S3.
http://www.biomedcentral.com/content/pdf/2041-1480-2-S4-S3.pdf - Tumu, Sudheer, et al. "The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four-and five-codon combinations present in Saccharomyces cerevisiae genes." Database: the journal of biological databases and curation 2012 (2012).
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3275765/ - Segagni, Daniele, et al. "An ICT infrastructure to integrate clinical and molecular data in oncology research." BMC bioinformatics 13.Suppl 4 (2012): S5.
http://www.biomedcentral.com/1471-2105/13/S4/S5/ - Klingström, Tomas, et al. "Workshop on Laboratory Protocol Standards for the Molecular Methods Database." New Biotechnology (2012).
http://www.sciencedirect.com/science/article/pii/S1871678412001215 - Xue, Vincent, et al. "MageComet—web application for harmonizing existing large-scale experiment descriptions." Bioinformatics 28.10 (2012): 1402-1403.
http://bioinformatics.oxfordjournals.org/content/28/10/1402.short - Jalali, Adrin, et al. "Cytometry-Ontology Framework."
http://ontology.buffalo.edu/pro/CytometryOntologyFramework.pdf - Viljanen, Kim, et al. "Normalized Access to Ontology Repositories."
http://www.seco.tkk.fi/publications/2012/viljanen-et-al-nor-2012.pdf - Zhukova, Anna, et al. "LibKiSAO: a Java Library for Querying KiSAO." BMC Research Notes 5.1 (2012): 520.
http://www.biomedcentral.com/content/pdf/1756-0500-5-520.pdf
0.9.9 release
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/
Highly accessed
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:
0.9.8 release
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
OntoCAT paper has now been published by BMC Bioinformatics.
0.9.7 release
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/
0.0.1 release of ontoCAT R package
The ontoCAT R — is an R package that provides a simple interface to ontologies described in two widely used formats: OBO (Open Biomedical Ontology format) and OWL (Web Ontology Language format). Supporting these two formats the ontoCAT package gives unified, format-independent access to ontology terms and the ontology hierarchy in the R environment.
0.9.6 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):
0.9.5 release
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/
New website
Dear OntoCAT friends. We have instantiated a new website to enable all interested to collaborate even more on ontology hacking. This site enables you, our beloved users, to add more examples or tickets for new requests seamlessly. Best wishes, the OntoCAT team.
