Abstract
BackgroundWith the growing amount of biomedical data available in public databases it has become increasingly important to annotate data in a consistent way in order to allow easy access to this rich source of information. Annotating the data using controlled vocabulary terms and ontologies makes it much easier to compare and analyze data from different sources. However, finding the correct controlled vocabulary terms can sometimes be a difficult task for the end user annotating these data.ResultsIn order to facilitate the location of the correct term in the correct controlled vocabulary or ontology, the Ontology Lookup Service was created. However, using the Ontology Lookup Service as a web service is not always feasible, especially for researchers without bioinformatics support. We have therefore created a Java front end to the Ontology Lookup Service, called the OLS Dialog, which can be plugged into any application requiring the annotation of data using controlled vocabulary terms, making it possible to find and use controlled vocabulary terms without requiring any additional knowledge about web services or ontology formats.ConclusionsAs a user-friendly open source front end to the Ontology Lookup Service, the OLS Dialog makes it straightforward to include controlled vocabulary support in third-party tools, which ultimately makes the data even more valuable to the biomedical community.
Highlights
With the growing amount of biomedical data available in public databases it has become increasingly important to annotate data in a consistent way in order to allow easy access to this rich source of information
Four different controlled vocabularies (CV) term search strategies are supported in the OLS Dialog: (i) Term Name Search, locates a CV term by a 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
At the time of writing more than 70 different biomedical ontologies are supported in the OLS, including over 900 000 CV terms
Summary
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. 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. 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. The OLS Dialog uses PSI-MOD Mass Search to find the possible CV terms for modifications with a mass of 15.994915 Da with an accuracy of 0.1 Da. Browse Ontology feature can be used to locate the term ‘GO:001250’. More details can be found at the OLS Dialog web page: http://ols-dialog.googlecode.com
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