The Transporter Classification Database (TCDB)

描述（由申请人提供）：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无论怎样强调都不过分，因为（1）它们为致病细菌、真菌和原生动物以及肿瘤细胞的多药耐药性提供了基础，（2）它们在许多人类遗传疾病中是有缺陷的，以及（3）它们是几乎所有致病生物体的毒素分泌系统的基本要素。我们已经开发了一种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，用于对地球上生物体中发现的所有跨膜转运蛋白进行分类。它与严格的功能EC系统相似但不同，后者是几十年前由国际生物化学和分子生物学联合会（IUBMB）的酶委员会开发的酶分类。国际生物多样性和海洋生物多样性联合会最近采用了TC系统，作为国际公认的运输者分类系统。TCDB是一个精选的事实信息库，收集了10，000多篇参考文献，包括大约3，000种代表性的转运蛋白和推定的转运蛋白，分为大约400个家族。本提案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，首先，自动化文本分类和信息提取软件，以促进TCDB的不断更新，因为新发布的有关运输商的信息变得可用（具体目标1-3），第二，设计用于半自动预测推定转运蛋白转运功能的软件，对于这些转运蛋白，完整的序列数据但很少或没有实验数据可用（具体目标4-6）。我们的具体目标是：（1）在TCDB中纳入文本分类系统，以自动识别描述新特征的运输系统或先前特征的系统的已发表文献，其中提供了新信息或纠正了旧数据。(2)设计信息提取软件，将具体目标1中确定的出版物中的相关信息纳入TCDB。(3)自动链接到主要文献，从中提取特定目标#2中的信息，以及链接到蛋白质和操纵子分析工具。(4)纳入软件，以便识别TCDB中蛋白质及其同源物的基序、特征序列、蛋白质结构域、系统发育关系和结构特征，以便进行功能预测。(5)纳入软件，这将有助于提取操纵子分析数据，可以类似地用于功能预测。(6)制定方法，以便整合具体目标4和5中所揭示的不同功能信息。

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.