AgBase: a unified resource for functional analysis in agriculture.

@article{McCarthy2007, 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.}, author = {Mccarthy, Fiona M. and Bridges, Susan M. and Wang, Nan and Magee, Bryce G. and Williams, Paul W. and Luthe, Dawn S. and Burgess, Shane C. }, citeulike-article-id = {2053695}, doi = {10.1093/nar/gkl936}, journal = {Nucleic Acids Res}, keywords = {agriculture, animal, article-pka-pkg, crops, database, domestic, genetics, genomics, integration, interface, internet, protein, proteomics, system, user-computer}, month = {Jan}, number = {Database issue}, pages = {D599--D603}, posted-at = {2007-12-04 01:53:38}, priority = {2}, title = {Ag{B}ase: a unified resource for functional analysis in agriculture.}, volume = {35}, year = {2007} }

TY - JOUR ID - McCarthy2007 L3 - citeulike-article-id:2053695 N2 - 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. IS - Database issue JF - Nucleic Acids Res EP - D603 TI - Ag{B}ase: a unified resource for functional analysis in agriculture. VL - 35 SP - D599 KW - agriculture KW - animal KW - article-pka-pkg KW - crops KW - database KW - domestic KW - genetics KW - genomics KW - integration KW - interface KW - internet KW - protein KW - proteomics KW - system KW - user-computer AU - Mccarthy, Fiona AU - Bridges, Susan AU - Wang, Nan AU - Magee, Bryce AU - Williams, Paul AU - Luthe, Dawn AU - Burgess, Shane PY - 2007/Jan// ER -