1a.Objectives (from AD-416)
ARS and the Cooperator are interested in integrating a bioinformatics tool for gene and pathway discovery (InnateDB) with an expressed sequence data resource for cattle (the Bovine Gene Atlas (BGA) database a compendium of over 7.2 million unique 20 base Illumina DGE tags representing 100 tissue transcriptomes collected primarily from L1 Dominette, the Hereford cow whose genome was sequenced, her father, and male and female offspring). The goal is to further develop the Cooperator's existing computational platform as a tool for cattle functional genomics that will allow a user to search for a particular bovine gene or large set of genes of interest using InnateDB (www.innatedb.com) and then return BGA expression data as part of the functional query. InnateDB would then be tested to extend use of the BGA data to query particular pathways or networks of interest - carry out pathway/ontology analysis etc.

1b.Approach (from AD-416)
The project will be managed jointly between ARS and the Cooperator. The Cooperator will evaluate the integration of InnateDB with the BGA. ARS will provide BGA tag data with gene alignment information. This analysis will aid the Cooperator, but may be altered to be compatible to existing InnateDB schema. Both ARS and the Cooperator will jointly aid development of this resource, and provide some annotation expertise to help prepare the data for publication.

3.Progress Report

This report serves to document research conducted under funding proposal (2008-35205-18846) from the USDA NRI-CGP 43.1 Animal Genome. Award money (~$67,000) is a sub-contract to the Beltsville Area made available in March, 2008 that terminates on Aug. 31, 2010. The objectives of this grant proposal were to: .
1)transfer the Bovine Gene Atlas tag dataset with gene map information to TEAGASC and.
2)test functionality of the integration of InnateDB (a database storing gene interaction information for hypothesis building) with the Bovine Gene Atlas dataset. Objective one was completed after ARS scientists completed additional annotation of bovine gene atlas sequence tags to better assign the tags with gene identification. Objective 2 is in progress. Monitoring activities associated with this project included email correspondence and conference calls. This research continues to support one objective of its related in-house project to develop biological resources and computational tools to enhance characterization of the bovine genome sequence (obj. #1).