Agbase: a Unified Resource for Functional Analysis in Agriculture.
From: Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, PO Box 6100, Mississippi, MS 39762, USA. fmccarthy@cvm.msstate.edu
Nucleic acids research
- Publish Date: Jan 2007
- ISSN: 1362-4962
- Volume: 35
- Issue: Database issue
- Pages: D599-603
- Medium: Internet
- Language: English
- Citation (JAMA): McCarthy Fiona M, Bridges Susan M, Wang Nan, et al. Agbase: a Unified Resource for Functional Analysis in Agriculture.. Nucleic Acids Res. Jan 2007;35:D599-603
Abstract
Analysis of functional genomics (transcriptomics and proteomics) datasets is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation. To facilitate systems biology in these species we have established the curated, web-accessible, public resource ‘AgBase’ (www.agbase.msstate.edu). We have improved the structural annotation of agriculturally important genomes by experimentally confirming the in vivo expression of electronically predicted proteins and by proteogenomic mapping. Proteogenomic data are available from the AgBase proteogenomics link. We contribute Gene Ontology (GO) annotations and we provide a two tier system of GO annotations for users. The ‘GO Consortium’ gene association file contains the most rigorous GO annotations based solely on experimental data. The ‘Community’ gene association file contains GO annotations based on expert community knowledge (annotations based directly from author statements and submitted annotations from the community) and annotations for predicted proteins. We have developed two tools for proteomics analysis and these are freely available on request. A suite of tools for analyzing functional genomics datasets using the GO is available online at the AgBase site. We encourage and publicly acknowledge GO annotations from researchers and provide an online mechanism for agricultural researchers to submit requests for GO annotations.
Mesh Headings (Keywords): Agriculture, Animals, Animals, Domestic, Crops, Agricultural, Databases, Genetic, Genomics, Internet, Proteins, Proteomics, Systems Integration, User-Computer Interface
Check for Full Text / PubMed Unique Identifier (PMID): 17135208
This abstract is part of PubMed, a service of the U.S. National Library of Medicine. PubMed includes more than 17 million citations from MEDLINE and other life science journals for biomedical articles. See Copyright and Disclaimers.
Linked medical terms appearing on this page are added by Healia to help readers find more information and are not part of the original PubMed document.
The data herein was last updated on July 8th, 2008 and may not reflect the most current and accurate data available from NLM.