The Transporter Classification Database (TCDB)

运输系统为所有活细胞提供基本功能。它们对医学的重要性 （1）它们为致病细菌、真菌和真菌的多药耐药性提供了基础， 原生动物以及肿瘤细胞，（2）它们在许多人类遗传疾病中有缺陷，和（3） 它们是几乎所有病原生物体的毒素分泌系统的基本要素。 我们已经开发了一个转运蛋白的分类系统，称为转运蛋白分类 (TC)系统TC系统是一个功能性/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转运蛋白。它类似于但不同于 严格的功能EC系统，几十年前由国际酶委员会开发 生物化学与分子生物学联合会（IUBMB）对酶的分类。TC系统 最近被IUBMB采用为国际公认的分类系统， 运输机TCDB是一个精选的事实信息库，收集了10，000多个 参考文献，包括大约3，000种代表性的转运蛋白和推定的转运蛋白， 大约有400个家庭。本提案的主要目标是促进更新、扩展 和改进TCDB供国际科学界使用。 我们的主要目标是首先，自动化文本分类和信息提取软件，以便 促进TCDB的不断更新，因为新发布的有关运输商的信息变得 第二，设计用于半自动预测运输的软件 功能的推定转运蛋白，其完整的序列数据，但很少或没有实验数据， （具体目标4-6）。 具体目标是：（1）在TCDB中引入文本自动分类系统， 识别描述新特征的交通系统或以前的已发表文献 提供新信息或纠正旧数据的特征系统。(2)设计信息 用于纳入特定目标1中确定的出版物相关信息的提取软件 到TCDB。(3)自动链接到特定目标#2中的信息所来自的主要文献 提取以及蛋白质和操纵子分析工具的链接。(4)整合软件， 识别基序、特征序列、蛋白质结构域、系统发育关系和结构 TCDB及其同源物中蛋白质的特征，用于功能预测。（五） 整合软件，以便于提取操纵子分析数据，这些数据同样可用于 功能预测(6)制定方法，将允许整合不同的职能线， 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.