Four different CV term search strategies are supported in the OLS Dialog: (i) Term Name Search, locates a CV term by a (partial) match to a search term; (ii) Term ID Search, locates a CV term by its CV term accession number; (iii) PSI-MOD Mass Search, finds the CV term for a modification in the PSI-MOD ontology [5] using the mass of the modification; and (iv) Browse Ontology, browses the ontology as a tree structure and allows the user to locate the desired term. Furthermore, OLS Dialog also provides a Term Hierarchy Graph view that can be used to locate or verify a CV term by inspecting the term hierarchy. Note that the Term Name Search supports both fuzzy/partial searches ('oxid' locates all partially matching CV terms, e.g., 'oxidation' and 'L-cystine S-oxide') and synonym searches (MOD:00045 can be found by searching for 'pros-phosphohistidine', 'phosphorylation', 'Npi-phosphorylated L-histidine', etc).
The main interface of the OLS Dialog is split into three main parts. At the top, the desired ontology is selected. At the time of writing more than 70 different biomedical ontologies are supported in the OLS, including over 900 000 CV terms. A full list of the supported ontologies can be found at http://www.ebi.ac.uk/ols. These ontologies are constantly updated and maintained by specialists in the various fields [6–8], and new changes will be automatically picked up daily by the OLS. It is important to note that the OLS Dialog does not store the ontologies locally but accesses the OLS web service whenever a search is performed. This ensures that the latest versions of the ontologies are always used.
In addition to searching a specific ontology it is also possible to search in all ontologies at once by selecting 'Search In All Ontologies' at the top of the list. This makes it possible to locate a CV term for which the ontology is unknown. Searching in all ontologies slows down the search however, and is not the recommended standard search option.
Below the ontology selection there are four tabs, one for each search option. Although each tab provides a search-specific interface, the overall structure stays the same. The search parameters are inserted or selected at the top of the tab, and the results of the search, i.e., the matching CV terms, are inserted into the 'Search Results' table. By selecting a CV term in the results table the term's associated details will be presented in the 'Term Details' table. The Browse Ontology tab is slightly different, as it replaces the 'Search Results' table with a tree structure of all terms in the currently selected ontology. It is also possible to view the term hierarchy as a graph by clicking the 'View Term Hierarchy' link at the top of the 'Term Details' text area. When a CV term is selected in the table (or in the tree) clicking the 'Use Selected Term' sends the selected term to the parent frame or dialog.
For examples of how the OLS Dialog can be used, see Figure 1, 2 and 3. In Figure 1 Term Name Search is used to find the possible CV terms for the search term 'Oxidation', while in Figure 2 the same term is found using PSI-MOD Mass Search. Figure 3 shows how the Browse Ontology feature can be used to locate the term 'GO:001250'.
To display how the OLS Dialog can be used in other projects we have implemented a simple application, OLS_Example, located in the no.uib.olsdialog.example package. To run the example, download and unzip the OLS Dialog and double click the jar file (or run from the command line using 'java-jar ols-dialog-X.Y.Z', where X.Y.Z represents the version number of the software). More details can be found at the OLS Dialog web page: http://ols-dialog.googlecode.com.
