The Transporter Classification Database (TCDB)

描述(申请人提供)：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怎么强调都不为过：(1)它们为致病细菌、真菌和原生动物以及肿瘤细胞的多重耐药性提供了基础；(2)它们在许多人类遗传性疾病中存在缺陷；(3)它们是几乎所有病原体毒素分泌系统的基本元件。我们开发了一种运输蛋白分类系统，称为转运蛋白分类(TC)系统。TC系统是一种功能/系统发育系统，用于对地球上活的生物体中发现的所有跨膜运输蛋白进行分类。它与几十年前由国际生物化学和分子生物学联合会(IUBMB)的酶委员会开发的严格功能的EC系统相似但不同，用于酶的分类。TC系统最近被IUBMB采用为国际公认的运输者分类系统。Tcdb是一个精选的事实信息储存库，从10,000多篇参考文献中汇编而成，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，分为大约400个家族。这项建议的主要目标是促进更新、扩大和改进Tcdb，供国际科学界使用。我们的主要目标是，第一，使文本分类和信息提取软件自动化，以便随着新发布的关于转运体的信息可用(具体目标1-3)，促进TcdB的持续更新；第二，设计用于半自动预测假定转运体的运输功能的软件，这些假定转运体有完整的序列数据，但很少或没有实验数据(特定目标4-6)。我们的具体目标是：(1)将一个文本分类系统纳入Tcdb，用于自动识别描述新特征的运输系统或先前特征的系统的已出版文献，在这些系统中，提供了新的信息或更正了旧数据。(2)设计信息提取软件，用于将特定目的#1中确定的出版物的相关信息纳入Tcdb。(3)自动链接到提取特定目标2中的信息的主要文献，以及链接到蛋白质和操纵子分析工具。(4)整合软件，以便能够识别TcdB及其同系物中蛋白质的基序、特征序列、蛋白质结构域、系统发育关系和结构特征，以进行功能预测。(5)采用有助于提取操纵子分析数据的软件，这些数据同样可用于功能预测。(6)制定办法，使具体目标4和5所揭示的不同职能信息能够结合起来。

DESCRIPTION (provided by applicant): 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.