TY - JOUR
T1 - OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript
AU - Adamusiak, Tomasz
AU - Burdett, Tony
AU - Kurbatova, Natalja
AU - van der Velde, K. Joeri
AU - Abeygunawardena, Niran
AU - Antonakaki, Despoina
AU - Kapushesky, Misha
AU - Parkinson, Helen
AU - Swertz, Morris A.
PY - 2011/5/29
Y1 - 2011/5/29
N2 - Background: Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups.Results: OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application.Conclusions: OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases.Availability: http://www.ontocat.org
AB - Background: Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups.Results: OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application.Conclusions: OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases.Availability: http://www.ontocat.org
KW - CONTROLLED VOCABULARY QUERIES
KW - GENE-EXPRESSION
KW - LOOKUP SERVICE
KW - BIOINFORMATICS
KW - PLATFORM
KW - BIOLOGY
KW - ATLAS
KW - MODEL
U2 - 10.1186/1471-2105-12-218
DO - 10.1186/1471-2105-12-218
M3 - Article
SN - 1471-2105
VL - 12
JO - Bmc Bioinformatics
JF - Bmc Bioinformatics
M1 - 218
ER -