W158 Nucleic Acids Research, 2010, Vol. 38, Web Server issue 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). PRIDE XML in preparation for submission to the PRIDE database and requires users to annotate their sub- mission ﬁles with terms from speciﬁc ontologies. User feedback has indicated that the PRIDE Converter and OLS Dialog have made submissions to PRIDE much easier and this has been made apparent in the submission ﬁgures to PRIDE (11). DISCUSSION The OLS has matured into a stable system and has proven to be popular beyond our initial expectations. Besides being used as a stand-alone system, its functionality has been incorporated into several independent tools and large-scale projects and is also being used by several