Published online 11 May 2010 Nucleic Acids Research, 2010, Vol. 38, Web Server issue W155–W160 doi:10.1093/nar/gkq331 The Ontology Lookup Service: bigger and better Richard C oˆte´ 1,*, Florian Reisinger1, Lennart Martens2,3, Harald Barsnes4, Juan Antonio Vizcaino1 and Henning Hermjakob1 1European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK, 2Department of Medical Protein Research, VIB, Ghent, Belgium, 3Department of Biochemistry, Ghent University, Ghent, Belgium and 4Department of Informatics, University of Bergen, Norway Received January 29, 2010; Revised April 4, 2010; Accepted April 17, 2010 ABSTRACT The Ontology Lookup Service (OLS; http://www.ebi .ac.uk/ols) has been providing several means to query, browse and navigate biomedical ontologies and controlled vocabularies since it first went into production 4 years ago, and usage statistics indicate that it has become a heavily accessed service with millions of hits monthly. The volume of data available for querying has increased 7-fold since its inception. OLS functionality has been integrated into several high-usage databases and data entry tools. Improvements in the data model and loaders, as well as interface enhancements have made the OLS easier to use and capture more annotations from the source data. In addition, newly released software packages now provide easy means to fully integrate OLS function- ality in external applications. INTRODUCTION Ontologies and controlled vocabularies (CVs) have more than demonstrated their essential function when dealing with large volumes of complex data currently being generated by high-throughput multi-domain analysis tech- niques (1). They provide a framework around which large data sets can be systematically annotated and queried. For this framework to function eﬃciently, however, the ontologies and CVs must be made available to the user community. The Ontology Lookup Service (OLS) has been in pro- duction since mid-2005 and has quickly become one of the most accessed services in the Proteomics Services team at the EBI, with monthly usage ﬁgures in the millions of hits. This includes both the programmatic as well as the inter- active interfaces that the service oﬀers. The OLS has been previously described and readers are invited to refer to the original publication for in-depth information on the tech- nical architecture and data models (2,3). The core functionality of the OLS has remained largely unchanged since its inception, allowing users to query ontologies and CVs by name or identiﬁer as well as ob- taining metadata, such as synonyms, deﬁnitions, cross ref- erences and other annotations, for a given term. Users can also traverse the relationships between terms. The usabil- ity and volume of data captured, however, has been enhanced and this will be expanded below. The OLS has always been designed to be used in other projects as a means to integrate ontology and CV anno- tation and query functionality. A SOAP web service has been available since the OLS went into production. A full description of the web service has already been published (2,3) and users who wish to make use of it are encouraged to go to the OLS web service developer section for the most up-to-date documentation and code samples (http://www.ebi.ac.uk/ontology-lookup/WSDLDocument ation.do). AVAILABLE DATA The ﬁrst OLS publication described it as containing 42 ontologies, accounting for roughly 135 000 terms. Over a 4-year period, the data loaded into the OLS has been expanded to 79 ontologies, representing over 971 000 unique terms (Figure 1). These cover far-ranging topics such as model organism anatomy and development, physi- ology and disease, instrumentation and methods and many others. In the 2 years since the OLS was previously published in NAR, 25 new ontologies have been added (Table 1). Users are encouraged to go online at http://www.ebi.ac.uk/ontology-lookup/ontologyList.do to access a full listing of currently available ontologies and CVs. The ontologies and CVs loaded in the OLS are main- tained by various external groups that are domain experts in their ﬁelds. To maintain the OLS as up-to-date as possible with the current state of knowledge, the ontology providers are polled on a daily basis and updated ﬁles are downloaded and parsed to update the core OLS database. Currently, the OLS loaders poll six *To whom correspondence should be addressed. Tel: +44 1223 492 610; Fax: +44 1223 494 468; Email: rcote@ebi.ac.uk The Author(s) 2010. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.