Nucleic Acids Research, 2010, Vol. 38, Web Server issue W157 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. INTERACTIVE USER INTERFACE IMPROVEMENTS Users of the OLS website typically do one of two things: query the database using the auto-suggestion search box or browse an ontology (or a subset thereof). Once a term has been highlighted, either from the search suggestions or from the ontology browser, the user will be shown a table containing all the metadata associated with this term (synonyms, deﬁnitions, comments, cross-references and any other annotations that were captured during the loading process). When using the ontology browser, a graph showing either all the possible paths from the selected term to the root term(s) of the ontology and the relationships between all involved terms (Figure 3) or a local relationship graph with only the direct parent terms and children terms will also be shown. The type of graph to be displayed is conﬁgurable from the ontology browser interface. These graphs are clickable image maps that will zoom and re-root the ontology browser to the selected term. REUSABLE CODE COMPONENTS As mentioned previously, the OLS has always provided a SOAP web service. This service has been used by several large projects, such as PRIDE (4), IntAct (5), CheBI (6) and the Proteomics Standards Initiative (PSI) (7). However, the main drawback to its wider accept- ance and uptake has been the lack of a simple GUI com- ponent that could easily be plugged in to existing code projects. This has now been solved through the release of the open source OLS Dialog GUI component (8) (Figure 4). The OLS Dialog can easily be integrated into existing Java applications and gives access to the full range of query types supported by the OLS. Users can search for terms by name or by identiﬁer, as well as use a graphical ontology browser to navigate an ontology and select a term. It is also possible to query terms from the PSI protein modiﬁcation (PSI-MOD) (9) based on captured annotations from the source ontology. Users can select the type of annotation to query and enter a mass in Daltons and a desired precision and obtain all of the PSI-MOD entries that ﬁt those parameters (e.g. ﬁnd all PSI-MOD entries whose annotated monoisotopic mass is 120 D ± 1 D) The OLS Dialog has been developed as part of the PRIDE Converter toolkit (10), which allows users to convert multiple mass spectroscopy ﬁle formats into