Meta-All: a system for managing metabolic pathway information.
Meta-All: a system for managing metabolic pathway information.
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DOI：
10.1186/1471-2105-7-465
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发表时间：
2006-10-23
影响因子：
3
通讯作者：
Junker BH
中科院分区：
文献类型：
--
作者：
Weise S;Grosse I;Klukas C;Koschützki D;Scholz U;Schreiber F;Junker BH
人们正在进行许多尝试，试图在系统层面上理解生物学科。这些方法的一个主要来源是生物学数据库，存储关于DNA、RNA和蛋白质序列的多种信息，包括它们的功能和结构基序、分子标记、mRNA表达水平、代谢物浓度、蛋白质-蛋白质相互作用、表型特征或分类关系。由于这些数据库是为特殊应用领域而设计的，因此缺乏普遍性，这往往妨碍了它们的使用。代谢途径数据库为系统一级的许多生化过程分析提供了越来越重要的基础，也不例外。存储在中央数据库(如KEGG、Brenda或Sabio-RK)中的数据通常仅限于只读访问。如果实验者想要存储他们自己的数据，可能还在调查中，有两种可能性。他们可以开发自己的信息系统来管理自己的数据，这非常耗时和昂贵，或者他们可以尝试将他们的数据存储在现有的系统中，这通常是受限的。因此，需要一个用于管理代谢途径数据的开箱即用的信息系统。我们设计了Meta-All，这是一个信息系统，允许管理代谢途径，包括反应动力学、详细位置、环境因素和分类信息。数据可以与质量标签一起存储，并可以以不同的并行版本存储。Meta-All使用Oracle DBMS和Oracle Application Express。我们提供元信息系统供下载和使用。在本文中，我们描述了数据库结构，并提供了有关提交和访问数据的工具的信息。作为Meta-All的第一个应用，我们展示了如何存储和访问包含在详细动力学模型中的信息。Meta-All是一个用于管理有关代谢途径的信息的系统。它便于处理与途径相关的数据，旨在帮助生物化学家和分子生物学家进行日常研究。它可以在网站上获得，也可以免费下载并在本地安装。
Many attempts are being made to understand biological subjects at a systems level. A major resource for these approaches are biological databases, storing manifold information about DNA, RNA and protein sequences including their functional and structural motifs, molecular markers, mRNA expression levels, metabolite concentrations, protein-protein interactions, phenotypic traits or taxonomic relationships. The use of these databases is often hampered by the fact that they are designed for special application areas and thus lack universality. Databases on metabolic pathways, which provide an increasingly important foundation for many analyses of biochemical processes at a systems level, are no exception from the rule. Data stored in central databases such as KEGG, BRENDA or SABIO-RK is often limited to read-only access. If experimentalists want to store their own data, possibly still under investigation, there are two possibilities. They can either develop their own information system for managing that own data, which is very time-consuming and costly, or they can try to store their data in existing systems, which is often restricted. Hence, an out-of-the-box information system for managing metabolic pathway data is needed. We have designed META-ALL, an information system that allows the management of metabolic pathways, including reaction kinetics, detailed locations, environmental factors and taxonomic information. Data can be stored together with quality tags and in different parallel versions. META-ALL uses Oracle DBMS and Oracle Application Express. We provide the META-ALL information system for download and use. In this paper, we describe the database structure and give information about the tools for submitting and accessing the data. As a first application of META-ALL, we show how the information contained in a detailed kinetic model can be stored and accessed. META-ALL is a system for managing information about metabolic pathways. It facilitates the handling of pathway-related data and is designed to help biochemists and molecular biologists in their daily research. It is available on the Web at and can be downloaded free of charge and installed locally.
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影响因子：
14.9
作者：
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通讯作者：
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