OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript

Autor: K. Joeri van der Velde, Despoina Antonakaki, Morris A. Swertz, Helen Parkinson, Niran Abeygunawardena, Tomasz Adamusiak, Tony Burdett, Misha Kapushesky, Natalja Kurbatova
Přispěvatelé: Life Course Epidemiology (LCE)
Jazyk: angličtina
Rok vydání: 2011
Předmět:
Ontology Inference Layer
020205 medical informatics
Databases
Factual
Computer science
Process ontology
BIOLOGY
02 engineering and technology
Ontology (information science)
lcsh:Computer applications to medicine. Medical informatics
computer.software_genre
Biochemistry
Vocabulary
World Wide Web
Open Biomedical Ontologies
03 medical and health sciences
User-Computer Interface
Structural Biology
0202 electrical engineering
electronic engineering
information engineering
Upper ontology
Humans
lcsh:QH301-705.5
Molecular Biology
LOOKUP SERVICE
030304 developmental biology
GENE-EXPRESSION
0303 health sciences
Database
Applied Mathematics
Ontology-based data integration
CONTROLLED VOCABULARY QUERIES
BIOINFORMATICS
Suggested Upper Merged Ontology
Computational Biology
PLATFORM
ATLAS
Computer Science Applications
MODEL
lcsh:Biology (General)
Vocabulary
Controlled
Ontology
lcsh:R858-859.7
Programming Languages
Ontology alignment
computer
Software
Zdroj: BMC Bioinformatics
Bmc Bioinformatics, 12:218. BioMed Central Ltd.
BMC Bioinformatics, Vol 12, Iss 1, p 218 (2011)
ISSN: 1471-2105
Popis: 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
Databáze: OpenAIRE
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