title: AgBase: supporting functional modeling in agricultural organisms.
abstract: AgBase (http://www.agbase.msstate.edu/) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. The website is redesigned to improve accessibility and ease of use, including improved search capabilities. Expanded capabilities include new dedicated pages for horse, cat, dog, cotton, rice and soybean. We currently provide 590 240 Gene Ontology (GO) annotations to 105 454 gene products in 64 different species, including GO annotations linked to transcripts represented on agricultural microarrays. For many of these arrays, this provides the only functional annotation available. GO annotations are available for download and we provide comprehensive, species-specific GO annotation files for 18 different organisms. The tools available at AgBase have been expanded and several existing tools improved based upon user feedback. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. We host several associated databases and provide genome browsers for three agricultural pathogens. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website.
authors.affiliation: Department of Basic Sciences, College of Veterinary Medicine, PO Box 6100, Mississippi State University, MS 39762, USA. fmccarthy@cvm.msstate.edu
authors.forename: Fiona M
authors.initials: FM
authors.lastname: McCarthy
authors.forename: Cathy R
authors.initials: CR
authors.lastname: Gresham
authors.forename: Teresia J
authors.initials: TJ
authors.lastname: Buza
authors.forename: Philippe
authors.initials: P
authors.lastname: Chouvarine
authors.forename: Lakshmi R
authors.initials: LR
authors.lastname: Pillai
authors.forename: Ranjit
authors.initials: R
authors.lastname: Kumar
authors.forename: Seval
authors.initials: S
authors.lastname: Ozkan
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
authors.forename: Prashanti
authors.initials: P
authors.lastname: Manda
authors.forename: Tony
authors.initials: T
authors.lastname: Arick
authors.forename: Susan M
authors.initials: SM
authors.lastname: Bridges
authors.forename: Shane C
authors.initials: SC
authors.lastname: Burgess
mesh_terms: D000383:Agriculture; D000818:Animals; D000829:Animals, Domestic / Q000235:genetics; D002415:Cats; D018556:Crops, Agricultural / Q000235:genetics; D030541:Databases, Genetic; D004285:Dogs; D020869:Gene Expression Profiling; D023281:Genomics; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D014584:User-Computer Interface