The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries

BMC Bioinformatics
Richard CôtéHenning Hermjakob

Abstract

With the vast amounts of biomedical data being generated by high-throughput analysis methods, controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform controlled vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries. The Ontology Lookup Service (OLS) was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A samp...Continue Reading

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Citations

Aug 14, 2009·Molecular & Cellular Proteomics : MCP·David E GloriamHenning Hermjakob
Jul 16, 2008·Briefings in Bioinformatics·Heinz StockingerNazim Rahman
Jun 10, 2010·Bioinformatics·Thomas Wächter, Michael Schroeder
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Methods Mentioned

BETA
two hybrid

Software Mentioned

MOBY
Apache
AJAX
Java Servlet
PRIDE
Ontology Lookup Service ( OLS
Apache AXIS
IntAct
Apache Lucene
Struts

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