@article{36624ddef94644d7ab223409c9fc8fd6,
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.",
author = "McCarthy, {Fiona M.} and Gresham, {Cathy R.} and Buza, {Teresia J.} and Philippe Chouvarine and Pillai, {Lakshmi R.} and Ranjit Kumar and Seval Ozkan and Hui Wang and Prashanti Manda and Tony Arick and Bridges, {Susan M.} and Burgess, {Shane C.}",
note = "Funding Information: Mississippi State University—Office of Research (to AgBase); Division of Agriculture and Forestry, College of Veterinary Medicine; Bagley College of Engineering; Life Sciences and Biotechnology Institute and Mississippi Agriculture and Forestry Experiment Station; National Science Foundation project (EPS-0903787 to S.M.B., partial); National Research Initiative of the US Department of Agriculture Cooperative State Research, Education and Extension Service (grant number MISV- 329140); National Institutes of Health National Institute of General Medical Sciences (NIGMS) (project 07111084); US Department of Agriculture, Agricultural Research Service (cooperative agreement number 6402-21000-033-01S); US Department of Agriculture National Institute of Food and Agriculture (grant numbers MIS-069270 and MIS-241080). Approved for publication as Journal Article No J11926 of the Mississippi Agricultural and Forestry Experiment Station, Mississippi State University. Funding for open access charge: US Department of Agriculture Cooperative State Research, Education and Extension Service (grant number MISV-329140, in part). Funding Information: (i) annotations for gene products not supported by the European Bioinformatics Institute GOA (EBI GOA) Project (e.g. transcripts and Genbank {\textquoteleft}predicted{\textquoteright} proteins);",
year = "2011",
month = jan,
doi = "10.1093/nar/gkq1115",
language = "English (US)",
volume = "39",
pages = "D497--D506",
journal = "Nucleic acids research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "SUPPL. 1",
}