The Ontology Lookup Service: bigger and better

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 functionality in external applications.

Figure 1.

Growth chart of the OLS data content. The amount of data loaded into the OLS, based on unique terms, has shown a 7-fold increase since the service went online. The first large increase is due to the incorporation of the NEWT taxonomy and the second large increase is due to the addition of a large number of ontologies at once.

Figure 2.

An example of custom synonyms and annotations. The synonyms in the blue box are uniquely defined in the PSI-MOD ontology. The annotations in the red box are examples of how the OLS can capture user-defined name–value attribute pairs.

Figure 3.

An example term hierarchy graph from the Ontology browser of the OLS. When using the ontology browser, selecting a term will provide a graphical display of all paths from that term to the ontology root term(s). Users can click on the terms to zoom the ontology browser to a particular term. Note the cross-ontology links in this example. The term scan start time from the MS (mass spectrometry) ontology has a relation to the second and minute terms of the unit ontology (UO), which in turn has relations to the PATO (phenotypic quality ontology).

Figure 4.

Two screenshots of the OLS Dialog GUI component. The OLS Dialog allows Java application developers to seamlessly integrate OLS functionality in existing tools. Users can query the OLS by term name or ID. They can also locate terms by browsing an ontology and search the PSI-MOD ontology entries by term annotations specific to the ontology. In the left panel, a search on term names will also include partial matches and synonyms. In both cases, when a term is selected, the relevant associated metadata will be displayed and a graph similar to Figure 3 can be shown (not shown in these examples).