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

Abstract

Background: 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.

Results: 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 sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence.

Conclusion: The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO) format. It can be accessed interactively or programmatically at http://www.ebi.ac.uk/ontology-lookup/.

Figure 1

OLS Architecture. Loaders will connect to a CVS server to retrieve the latest versions of the ontology source files, transform the data into objects of the data model. The query layer is responsible for creating searchable text indexes as well as communicating with the database via the ORM layer. Programmatic access to the query layer is done via a SOAP interface. Interactive access is done via a Struts web application.

Figure 2

AJAX-based auto-completion of a search term. A list of possible suggestions will be updated as users type in a search term. If too many terms match the search keyword, users can select the "... and more" option at the bottom of the suggestion list (not shown in this figure). Users can search all ontologies at once or limit their search to a specific ontology.

Figure 3

Full listing of a search. All the possible matches to a search keyword are listed in this page. Users can click on the term accession to return to the main page, which will display the definition and annotations stored for this term. When available, the user can click on the term name to be directed to term entry at the principal website associated with the selected ontology.

Figure 4

AJAX-based ontology browser. Users can browse a complete ontology or a subset of one by clicking on the ''browse'' button from the search form on the main page. The root term(s) of the ontology or subset are shown. Users can navigate the ontology dynamically by clicking on a term to load its children. Selecting a term will display the term name, accession, definition, synonyms and any annotations. Hovering over a term will display its relationship with its parent.