title: OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.
abstract: 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.
  
  
  BACKGROUND
  http://www.ontocat.org.
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK. tomasz@ebi.ac.uk
authors.forename: Tomasz
authors.initials: T
authors.lastname: Adamusiak
authors.forename: Tony
authors.initials: T
authors.lastname: Burdett
authors.forename: Natalja
authors.initials: N
authors.lastname: Kurbatova
authors.forename: K
authors.initials: K
authors.lastname: Joeri van der Velde
authors.forename: Niran
authors.initials: N
authors.lastname: Abeygunawardena
authors.forename: Despoina
authors.initials: D
authors.lastname: Antonakaki
authors.forename: Misha
authors.initials: M
authors.lastname: Kapushesky
authors.forename: Helen
authors.initials: H
authors.lastname: Parkinson
authors.forename: Morris A
authors.initials: MA
authors.lastname: Swertz
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D006801:Humans; D011381:Programming Languages; D012984:Software; D014584:User-Computer Interface; D014825:Vocabulary; D018875:Vocabulary, Controlled