The MetaCyc & BioCyc Pathway/Genome Databases (SRI Proposal ECU 14-630)

 描述（由申请人提供）：该项目的目标是开发一个生物信息学基础，用于破译和建模具有完全测序基因组的生物体的代谢网络，以支持药物发现，代谢工程，系统生物学和基础科学。我们的方法是基于黄金标准的代谢数据库，MetaCyc，这是由博士策划-水平的生物学家，从实验文献。第二个目标是进一步开发BioCyc，这是一个不断发展的5，000 - 10，000个测序原核基因组的途径/基因组数据库集合。BioCyc是一个主要的原核基因组门户网站，因为它计划全面覆盖原核基因组;它整合了多种信息源;它强大而用户友好的生物信息学搜索，可视化和分析工具;以及它通过多种访问渠道分发数据。 我们有四个具体目标。(1)为了扩展MetaCyc，一个高度策划的代谢途径和酶的多生物体数据库，作为代谢信息的植物参考。MetaCyc可用于从其测序的基因组预测生物体的代谢途径补体。关于实验确定的代谢途径和酶的信息将从生物医学文献中整理到MetaCyc中，重点是原核途径。(2)为了计算生成扩展版本的BioCyc，生物体特异性途径/基因组数据库的集合，用于完全测序的原核生物和模型生物，包括预测的代谢途径，预测的代谢途径孔填充物和预测的操纵子。(3)增强支持MetaCyc和BioCyc数据查询、可视化和分析的PTools软件，以包括代谢组学数据分析操作，包括多生物体代谢计算器和预测观察到的代谢物的代谢来源的工具。(4)通过门户网站和可下载的数据文件和软件向科学界提供MetaCyc和BioCyc。

 DESCRIPTION (provided by applicant): The project objective is to develop a bioinformatics foundation for deciphering and modeling the metabolic networks of organisms with fully sequenced genomes, in support of drug discovery, metabolic engineering, systems biology, and basic science. Our approach is based on a gold-standard metabolic DB, MetaCyc, which is curated by Ph.D.-level biologists, from the experimental literature. A second objective is to further develop BioCyc, an evolving collection of Pathway/Genome Databases for 5,000-10,000 sequenced prokaryotic genomes. BioCyc is a premier prokaryotic genome web portal because of its planned comprehensive coverage of prokaryotic genomes; its integration of multiple information sources; its powerful and user-friendly bioinformatics search, visualization, and analysis tools; and its distribution of data via multiple access channels. We have four specific aims. (1) To expand MetaCyc, a highly curated multi-organism database of metabolic pathways and enzymes that serves as an encyclopedic reference of metabolic information. MetaCyc can be used to predict the metabolic pathway complement of an organism from its sequenced genome. Information about experimentally determined metabolic pathways and enzymes will be curated into MetaCyc from the biomedical literature, with a focus on prokaryotic pathways. (2) To computationally generate extended versions of BioCyc, a collection of organism-specific Pathway/Genome Databases for completely sequenced prokaryotes and model organisms that includes predicted metabolic pathways, predicted metabolic pathway hole fillers, and predicted operons. (3) To enhance the PTools software that supports the querying, visualization, and analysis of MetaCyc and BioCyc data to include operations for analysis of metabolomics data, including a multi-organism metabolic calculator, and a tool for predicting the metabolic origin of observed metabolites. (4) To make MetaCyc and BioCyc available to the scientific community through a web portal and via downloadable data files and software.