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posted on 2024-02-13, 13:42 authored by Fiona McCarthy, Shane Burgess, Cathy Gresham, Jinhui Zhang, Mike Rice, Mais Ammari

AgBase Version 2.0 is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products including gene ontology annotations. Its long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. AgBase uses controlled vocabularies developed by the Gene Ontology (GO) Consortium to describe molecular function, biological process, and cellular component for genes and gene products in agricultural species. For more information about the AgBase database visit the Educational Resources page or refer to the AgBase publications.

AgBase will also accept annotations from any interested party in the research communities. AgBase develops freely available tools for functional analysis, including tools for using GO.

AgBase 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 provides Text, BLAST, Taxonomy, and Gene Ontology search functions, and dedicated pages for Animals (channel catfish, cat, chick, bovine, daphnia, dog, horse, pig, salmon, sheep, trout, turkey), Plants (cotton, maize, Miscanthus, pine, poplar, rice, soybean), Microbes (26 taxa), and Parasites (10 taxa). AgBase currently provides 2,069,320 Gene Ontology (GO) annotations to 394,599 gene products in 534 different taxons, 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 AgBase provides comprehensive, species-specific GO annotation files for a variety of animal and plant organisms. AgBase hosts several associated databases and provide genome browsers for agricultural pathogens. Comprehensive training resources (including worked examples and tutorials) are available via links to Educational Resources at the AgBase website.

Resources in this dataset:

  • Resource Title: Website Pointer to AgBase [Version 2.0].

    File Name: Web Page, url:

    Provides agricultural plant and animal Gene Ontology (GO) annotation search options, related tools, and genome browsers.


Mississippi State University

USDA: 2011-67015-30332

USDA: 2007-35205-17941

USDA: MISV-329140

USDA-ARS: 6402-21000-033-01S

USDA-NIFA: MIS-069270 and MIS-241080

National Institutes of Health: NIGMS project 07111084

National Science Foundation: EPSCoR award number EPS 0903787


Data contact name

McCarthy, Fiona

Data contact email


University of Arizona; Mississippi State University

Intended use

To serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models.


  • Not specified

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

crops; animals; genes; gene ontology; agricultural research; researchers; models; databases; educational resources; computer software; genomics; parasites; Internet; taxonomy; chicks; cattle; Daphnia; dogs; horses; sheep; trout; cotton; corn; Miscanthus; rice; soybeans; microorganisms; microarray technology; hosts; pathogens; Felis catus; Gallus gallus; Bos taurus; Canis lupus familiaris; Equus caballus; Sus scrofa; Salmo salar; Ovis aries; Oncorhynchus mykiss; Meleagris gallopavo; Gossypium; Zea mays; Miscanthus gigenteus; Miscanthus sinensis; Pinus; Populus; Oryza; Glycine max; viruses; bacteria; Anaplasma marginale; Babesia bovis; Dendroctonus frontalis; Eimeria tenella; Fasciola hepatica; Haemonchus contortus; Ichthyophthirius multifiliis; Lepeophtheirus salmonis; Theileria annulata; Theileria parva; animal models; laboratory animals; biomedical research

Primary article PubAg Handle

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

McCarthy, Fiona; Burgess, Shane; Gresham, Cathy; Zhang, Jinhui; Rice, Mike; Ammari, Mais (2019). AgBase. University of Arizona; Mississippi State University.

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