Data Query
One of the main goals of the Mouse BIRN collaboration is to make querying and accessing multiple data types and sources within the context of a digital atlas easy and intuitive. To achieve these goals, there are two new query options available. These new options provide all the features of previous versions of MBAT with the added utility of providing an interface that simplifies the query process for the user. In addition, the newly designed interface will enable the easy extension to other data types.
New Features
Concept-based Queries:
The query interface allows the use to search data by date type, subject, and experiment related terms. A query may return multiple types of data most of which can be viewed within MBAT. For those that cannot, a link to an external website may be provided.
Spatial-based Queries:
Spatial-based queries allow the user to search data based on a region of interest in the atlas. This query system has been built suing functionality developed for UCSD's SmartAtlas. The system access 2D images that have been registered using tools developed by the UCSD group.
Both of the query tools have been integrated in to MBAT to allow the user to visualize and download any publicly available data.
Data Source Access
- GeneNetwork
- BIRN Microarray Database
- Cell Centered Database (CCDB)
- BIRN Mediator Microarray Databases
New Data Sources
- SmartAtlas and ArcIMS (spatially registered histologic images)
- Allen Brain Atlas data (with assistance from NeuroCommons)
- GENSAT (with assistance from Stott Parker)
Access to Additional Information Sources
MBAT has the ability to access additional information from web resources and display it in a user-friendly format. These information sources include Bonfire (the BIRN CC ontology tool) and the Brain Architecture Management System (BAMS) at USC.
Original Features
EM/Cell Queries
High resolution cell fills and brain maps spatially linked to the MBAT atlases can be located, viewed, and downloaded. This query tool accesses the database at http://ccdb.ucsd.edu/CCDBWebSite/index.html.
Expression Queries
Expression queries allow the user to search for microarray gene expression data from different databases. This includes the GeneNetwork database http://www.genenetwork.org and the BIRN Microarray database http://www.nbirn.net/bdr/databasing.shtm.
