The current trend towards multi-domain data analysis, compounded with the vast amounts of data being generated by high-throughput methods, presents a significant data management challenge. Controlled vocabularies and ontologies therefore become crucial tools for data annotation and analysis to help provide a stable and consistent context for large data sets.
The Ontology Lookup Service (OLS) was created to provide a simple, centralized, integrated interface to query multiple biomedical ontologies by interactive and programmatic means. Prior to its creation, users wishing to query ontologies had to go to individual websites—when available—and use whatever query interface was made available. Many ontologies were only available in flat-file format and few ontologies could be queried by programmatic means. Querying multiple ontologies was a difficult and time-consuming proposition.
The OLS has been in production since mid-2005 and has proven to be a popular tool with data producers and consumers. The OLS has been previously described and readers are invited to refer to the original publication for in-depth information on the technical architecture and data models (1
The core functionality of the OLS provides users with the means to perform queries on controlled vocabulary and ontology terms and synonyms, as well as navigate the relationships between terms and obtain additional metadata (such as definitions, comments, synonyms or cross-references to other databases) and annotations on selected terms.
Data producers can use the online interface to search for appropriate terms to annotate their submissions in one specific ontology or across all available ontologies served by the OLS. An ontology browser is also available to navigate ontologies and controlled vocabularies to find the appropriate context and level of detail for a given term. Application developers can use the provided web service interface to fully integrate OLS functionality within their applications.
Since its inception, it has become an integral part of many highly accessed databases (2–5
) and has been recommended as a data submission resource by the Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) (6
) and by the International Molecular Interaction Exchange consortium (IMEX) (7
Application developers are making use of the OLS web service interface to enrich their own applications. Examples of this include the Proteome Harvest data submission tool for PRIDE (8
) and the Map2OWL Protégé plug-in (http://map2owl.sourceforge.net/
This article describes the new data available in the OLS as well as the many improvements to both the online and the programmatic interfaces through which this data can be browsed and queried.