Abstract

BackgroundMany 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.DescriptionTo facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource 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.ConclusionThe 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.

Highlights

  • Many agricultural species and their pathogens have sequenced genomes and more are in progress

  • To ensure that structural data is based on high quality proteomics identifications, we have developed a method for assigning probabilities to mass spectral identifications during proteogenomic mapping [26]

  • We provide advice on Gene Ontology (GO) annotation and are developing a mechanism for researchers to be publicly acknowledged for GO annotations they submit to AgBase

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Summary

Introduction

Many agricultural species and their pathogens have sequenced genomes and more are in progress. 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. A relatively large proportion of these genes in these species are electronically predicted Another problem is that, compared to human and mouse, the chicken and cow have 10-fold fewer ESTs to aid in structural annotation and functional analysis. These statistics, combined with smaller funding bases and resources for manual genome structural annotation, suggest that the human and mouse paradigm for genome structural annotation is unlikely to be successful for agricultural species [12]

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