A) Keyword and B) Query builder search interface to INDIGO.
The keyword search interface shows an example of the search for “benzoate degradation”. Results are categorized on the left side of the resulting page, showing the number of hits found for genes, domains, pathways, etc. These results are further categorized into hits per genome for different organisms. Clicking on any of these categories shows filtered results. The query builder interface has an option to include or constrains an annotation class attribute, e.g. pathway name is constrained for “benzoate degradation”, while the organism attribute ‘short name’ is constrained to “SSPSH”. The annotation feature class attributes to be included in the result list here are gene db identifier, symbol, organism’s short name and pathway name. User can select any of the available annotation class attributes making it possible to integrate annotation from several different sources. Results of constrained query builder search are shown as a list. There are summary and filter options on the list page that allow a user to further analyze these results.