About This Portal
This portal is a user-friendly search tool which reads and dynamically re-presents summary data about targeted and trapped mouse knockout availability and structure from a number distinct BioMarts. These BioMarts currently contain:
- Gene information from MGI
- Knockout information from KOMP, EUCOMM, NorCOMM, Regeneron and TIGM
- Gene expression information from Eurexpress
- Phenotyping data from Europhenome
- Mouse distribution information from EMMA
And shall soon also include (when these datasets become publicly available):
- Gene expression information from GXD
Our motivation arises from our belief that BioMarts are an excellent tool for allowing large datasets to be presented and accessed by computers and expert users. However, BioMarts need more friendly user search mechanisms and interfaces for casual users: this portal is one attempt to provide such an interface. In the process, we believe we have created a portal for the mouse community that can be easily extended to present summarised data as it arises, without extensive re-development.
How This Portal Works
This portal is powered by software called MartSearch, a server-side client written in Ruby used to pull together data from distributed data sources (housed in BioMarts) into a single unified view.
MartSearchr works by first building a search engine (using Apache Solr) looking at all of the available search terms in the cloud of BioMarts and tying/grouping them to an MGI gene locus. Here are some diagrams explaining how this linking is done and the relationships between the data:
When a user performs a search, the query is first run against the search engine which returns a paginated list of MGI gene loci and associated meta data, this meta data is then used to retrieve the information from the cloud of BioMarts (data sources) available to the search interface.