Development and Maintenance of PANTHER Software

PANTHER软件的开发和维护

• 批准号: 7591614
• 负责人: Paul D. Thomas
• 金额: $ 67.95万
• 依托单位: SRI INTERNATIONAL
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-04-01 至 2010-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7591614
• 关键词: Amino Acid Sequence Homology; Animal Model; Biochemical Reaction; Biological; Caenorhabditis elegans; Communities; Computer software; Computers; Data; Data Sources; Databases; Deposition; Development; Drosophila genus; Ensure; Environment; Escherichia coli; Family; Feedback; Funding; Gene Proteins; Genes; Goals; Hereditary Disease; Homologous Gene; Homologous Protein; Human; Human Biology; Inherited; Knowledge; Link; Literature; Maintenance; Medical; Methodology; Mus; Ontology; Organism; Paper; Pathway interactions; Phylogenetic Analysis; Protein Family; Proteins; Publishing; Reading; Relative (related person); Research Infrastructure; Research Personnel; Research Project Grants; Resources; Source; Structure; Testing; Trees; Visual; Writing; Yeasts; base; cost; data exchange; formycin triphosphate; gene function; interoperability; model organisms databases; open source; protein function; public health relevance; repository; software development; tool; web site; web-accessible

DESCRIPTION: Protein sequence homology (i.e., descent from a common ancestral sequence) is perhaps the most widely used tool for annotating the putative functions of genes. Homologous proteins often share functions inherited from the common ancestor, so if the function of one protein has been experimentally determined, the function of its homologues can often, but not always, be inferred to be the same. Homology-based inference allows functional data from experimentally tractable model organisms (such as E. coli, yeast, Drosophila, C. elegans and the mouse) to be applied to other organisms, most notably humans. The past several years have seen a dramatic increase in the amount of structured, computationally accessible data available on the functions of proteins and the genes that encode them, primarily using the Gene Ontology (GO). The most useful of these data have been manually entered (}curated}) by a biologist after reading papers in the scientific literature. The goal of this proposal is to leverage these literature-derived ontology annotations by using them, in a carefully curated and structured manner, as the basis for inferred annotations in other organisms. We will utilize and extend existing software developed in our groups to develop a web-accessible environment for curation of GO terms in the context of evolutionary relationships, and link the data to biological pathway data and data standards. We will integrate the software into current GO term annotation projects, and support a broad data ex- change and dissemination plan across GO and pathway ontology curation efforts and the communities of bio- medical researchers they serve. PUBLIC HEALTH RELEVANCE: The current research project provides a cost-effective, accurate methodology for taking experimentally based information about genes in a wide range of well-studied species, and applying this information to understanding human biology, genetics and disease. The results from this methodology will be made broadly available to both researchers and the public, in formats accessible to both people and computers.

描述：蛋白质序列同源性（即源自共同祖先序列）可能是注释基因推定功能的最广泛使用的工具。同源蛋白质通常共享从共同祖先继承的功能，因此，如果一种蛋白质的功能已通过实验确定，则通常（但并非总是）可以推断其同源物的功能是相同的。基于同源性的推理允许来自实验上可处理的模型生物（例如大肠杆菌、酵母、果蝇、线虫和小鼠）的功能数据应用于其他生物，尤其是人类。在过去的几年里，关于蛋白质功能和编码它们的基因的结构化、可计算访问的数据量急剧增加，主要是使用基因本体论（GO）。这些数据中最有用的数据是由生物学家在阅读科学文献中的论文后手动输入（}整理）的。该提案的目标是以精心策划和结构化的方式利用这些源自文献的本体注释，作为其他生物体中推断注释的基础。我们将利用和扩展我们团队开发的现有软件，开发一个可通过网络访问的环境，用于在进化关系的背景下管理 GO 术语，并将数据与生物途径数据和数据标准联系起来。我们将将该软件集成到当前的 GO 术语注释项目中，并支持跨 GO 和路径本体管理工作及其所服务的生物医学研究人员社区的广泛数据交换和传播计划。公共健康相关性：当前的研究项目提供了一种经济高效、准确的方法，用于获取大量经过充分研究的物种中的基因实验信息，并将这些信息应用于理解人类生物学、遗传学和疾病。这种方法的结果将以人和计算机均可访问的格式广泛提供给研究人员和公众。