Development and Maintenance of PANTHER Software

描述：蛋白质序列同源性(即共同祖先序列的后代)可能是解释基因假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经通过实验确定，则其同源蛋白的功能通常但不总是可以推断是相同的。基于同源性的推理允许来自实验上容易处理的模型生物(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，最明显的是人类。在过去的几年里，主要使用基因本体论(GO)，关于蛋白质及其编码基因的功能的结构化、可通过计算获得的数据的数量急剧增加。其中最有用的数据是生物学家在阅读了科学文献中的论文后手动输入的。这项提议的目标是通过以精心策划和结构化的方式使用这些文献派生的本体注释来利用它们，作为在其他生物体中推断注释的基础。我们将利用和扩展我们小组开发的现有软件，以开发一个可在网络上访问的环境，用于在进化关系的背景下管理围棋术语，并将数据与生物途径数据和数据标准联系起来。我们将把该软件集成到当前的围棋术语注释项目中，并支持在围棋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之间进行广泛的数据交换和传播计划。与公共健康相关：目前的研究项目提供了一种成本效益高、准确的方法，用于获取关于广泛研究过的物种中的基因的实验信息，并将这些信息应用于了解人类生物学、遗传学和疾病。这一方法的结果将以人和计算机都能获得的格式向研究人员和公众广泛提供。

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.