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.

译文

背景:许多农业物种及其病原体均已测序基因组,并且仍在进行中。农业物种提供食物,纤维,异种移植组织,生物药物和生物医学模型。此外,许多农业微生物是人畜共患病。但是,由于功能基因组学数据的系统生物学在农业物种中受到了阻碍,因为与许多模型生物群落相比,农业基因组序列的结构和功能注释相对较差,并且农业研究界的规模较小,资金有限。
描述:为了促进这些传统农业物种中的系统生物学,我们建立了“ AgBase”,这是一个经过整理的,可通过网络访问的公共资源,网址为http://www.agbase.msstate.edu,用于农业基因组的结构和功能注释。 AgBase数据库包括一套使用GO批注的计算工具。我们遵循人类基因组组织基因命名准则使用标准化的命名法,目前正在使用基因本体论(GO)在功能上注释鸡,牛和绵羊的基因产品。我们开发的计算工具可以接受和批处理来自不同公共数据库(具有不同的登录代码)的数据,返回所有现有的GO批注,提供没有GO批注的产品列表,识别潜在的直系同源物,使用GO建模功能基因组学数据并提供帮助EST和EST组装的蛋白质组学分析。我们的日志数据库有助于防止多余的手动GO管理。我们鼓励并公开认可研究人员的GO注释,并为对GO和功能基因组数据分析感兴趣的研究人员提供服务。
结论:AgBase数据库是第一个专门用于对农业重要物种及其病原体进行功能基因组学和系统生物学分析的数据库。我们使用实验数据来改善基因组的结构注释并在功能上表征基因产物。 AgBase还与农业生产,癌症生物学,生物制药,人类健康和进化生物学等领域的研究人员直接相关。此外,我们提供的实验方法和生物信息学工具可广泛应用于包括模型生物在内的许多其他物种。

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