AgBase: A functional genomics resource for agriculture

Fiona M McCarthy, Nan Wang, G. Bryce Magee, Bindu Nanduri, Mark L. Lawrence, Evelyn B. Camon, Daniel G. Barrell, David P. Hill, Mary E. Dolan, W. Paul Williams, Dawn S. Luthe, Susan M. Bridges, Shane C Burgess

Research output: Contribution to journalArticle

191 Citations (Scopus)

Abstract

Background: Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. Description: To facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource http://www.agbase.msstate.edu for structural and functional annotation of agricultural genomes. The AgBase database includes a suite of computational tools to use GO annotations. We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO). The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes), return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. Our journal database helps prevent redundant manual GO curation. We encourage and publicly acknowledge GO annotations from researchers and provide a service for researchers interested in GO and analysis of functional genomics data. Conclusion: The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. We use experimental data to improve structural annotation of genomes and to functionally characterize gene products. AgBase is also directly relevant for researchers in fields as diverse as agricultural production, cancer biology, biopharmaceuticals, human health and evolutionary biology. Moreover, the experimental methods and bioinformatics tools we provide are widely applicable to many other species including model organisms.

Original languageEnglish (US)
Article number229
JournalBMC Genomics
Volume7
DOIs
StatePublished - Sep 8 2006
Externally publishedYes

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Gene Ontology
Genomics
Agriculture
Molecular Sequence Annotation
Systems Biology
Databases
Genome
Expressed Sequence Tags
Research Personnel
Terminology
Genes
Zoonoses
Computational Biology
Proteomics
Chickens
Sheep
Guidelines
Food
Health
Research

ASJC Scopus subject areas

  • Medicine(all)

Cite this

AgBase : A functional genomics resource for agriculture. / McCarthy, Fiona M; Wang, Nan; Magee, G. Bryce; Nanduri, Bindu; Lawrence, Mark L.; Camon, Evelyn B.; Barrell, Daniel G.; Hill, David P.; Dolan, Mary E.; Williams, W. Paul; Luthe, Dawn S.; Bridges, Susan M.; Burgess, Shane C.

In: BMC Genomics, Vol. 7, 229, 08.09.2006.

Research output: Contribution to journalArticle

McCarthy, FM, Wang, N, Magee, GB, Nanduri, B, Lawrence, ML, Camon, EB, Barrell, DG, Hill, DP, Dolan, ME, Williams, WP, Luthe, DS, Bridges, SM & Burgess, SC 2006, 'AgBase: A functional genomics resource for agriculture', BMC Genomics, vol. 7, 229. https://doi.org/10.1186/1471-2164-7-229
McCarthy FM, Wang N, Magee GB, Nanduri B, Lawrence ML, Camon EB et al. AgBase: A functional genomics resource for agriculture. BMC Genomics. 2006 Sep 8;7. 229. https://doi.org/10.1186/1471-2164-7-229
McCarthy, Fiona M ; Wang, Nan ; Magee, G. Bryce ; Nanduri, Bindu ; Lawrence, Mark L. ; Camon, Evelyn B. ; Barrell, Daniel G. ; Hill, David P. ; Dolan, Mary E. ; Williams, W. Paul ; Luthe, Dawn S. ; Bridges, Susan M. ; Burgess, Shane C. / AgBase : A functional genomics resource for agriculture. In: BMC Genomics. 2006 ; Vol. 7.
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