The Transporter Classification Database (TCDB)

运输系统为所有活细胞提供必要的功能。它们对医学的重要性不能 被过分强调的原因是：(1)它们为病原菌、真菌和 原生动物以及肿瘤细胞，(2)它们在许多人类遗传病中存在缺陷，以及(3) 它们是几乎所有病原生物体毒素分泌系统的基本要素。 我们已经开发了一种称为转运蛋白分类的运输蛋白分类系统 (TC)系统。TC系统是一个功能/系统发育系统，设计用于对所有 在地球上的生物体中发现的跨膜运输蛋白。它既相似又不同于 严格功能的EC系统，几十年前由国际酶委员会开发 生物化学和分子生物学联合会(IUBMB)用于酶的分类。TC系统 最近被IUBMB采纳为国际公认的分类系统 传送者。Tcdb是一个精选的事实信息储存库，从10,000多个 参考文献，包括大约3,000个具有代表性的转运蛋白和假定的转运蛋白， 它们被分成大约400个家庭。这项建议的主要目标是促进更新、扩展 和改进Tcdb，以供国际科学界使用。 我们的主要目标是首先实现文本分类和信息提取软件的自动化，以便 促进Tcdb的持续更新，因为最新公布的关于运输商的信息将成为 可用(具体目标1-3)；第二，设计半自动交通预测软件 假定的转运蛋白的功能，其完整的序列数据但很少或没有实验数据是 可用(具体目标4-6)。 我们的具体目标是：(1)在Tcdb中加入一个文本分类系统，用于自动 识别描述新表征的运输系统或以前的已出版文献 提供新信息或纠正旧数据的特征系统。(2)设计资料 用于从特定目标#1中确定的出版物中纳入相关信息的提取软件 转换成Tcdb。(3)自动链接到主要文献的链接，具体目标2中的信息来自这些文献 以及指向蛋白质和操纵子分析工具的链接。(4)安装将允许 基序、特征序列、蛋白质结构域、系统发育关系和结构的鉴定 用于功能预测的TcdB及其同系物中蛋白质的特征。(5) 结合有助于提取操纵子分析数据的软件，这些数据可以类似地用于 功能预测。(6)开发能够整合不同职能部门的方法 具体目标4和5中披露的信息。

Transport systems provide essential functions for all living cells. Their importance to medicine cannot be overemphasized as (1) they provide a basis for multidrug resistance in pathogenic bacteria, fungi and protozoans as well as in tumor cells, (2) they are defective in numerous human genetic diseases, and (3) they are essential elements of toxin secretion systems by virtually all pathogenic organisms. We have developed a classification system for transport proteins called the Transporter Classification (TC) system. The TC system is a functional/phylogenetic system designed for the classification of all transmembrane transport proteins found in living organisms on Earth. It parallels but differs from the strictly functional EC system, developed decades ago by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology (IUBMB) for the classification of enzymes. The TC system has recently been adopted by the IUBMB as the internationally acclaimed system to the classification of transporters. TCDB is a curated repository for factual information compiled from more than 10,000 references, encompassing approximately 3,000 representative transport proteins and putative transporters, classified into about 400 families. The primary goal of this proposal is to facilitate the updating, expansion and improvement of TCDB for use by the international scientific community. Our primary goals are first, to automate text classification and information extraction software so as to facilitate the continual updating of TCDB as newly published information about transporters becomes available (Specific Aims 1-3), and second, to devise software for the semiautomatic prediction of transport functions for putative transporters for which complete sequence data but little or no experimental data are available (Specific Aims 4-6). Our specific aims are to: (1) Incorporate into TCDB a text classification system for automatically identifying published literature describing newly characterized transport systems or previously characterized systems where new information is provided or old data are corrected. (2) Design information extraction software for incorporation of pertinent information from publications identified in specific aim #1 into TCDB. (3) Automate links to the primary literature from which the information in specific aim #2 was extracted as well as links to protein and operon analysis tools. (4) Incorporate software that will allow identification of motifs, signature sequences, protein domains, phylogenetic relationships and structural features for the proteins in TCDB and their homologues for the purpose of functional prediction. (5) Incorporate software that will facilitate the extraction of operon analysis data that can similarly be used for functional prediction. (6) Develop approaches that will allow integration of the different lines of functional information revealed in specific aims #4 and 5.