Analysis and comparison of metabolic pathway databases.
Analysis and comparison of metabolic pathway databases.
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DOI：
10.1093/bib/2.2.126
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发表时间：
2001-05-01
影响因子：
9.5
通讯作者：
De Beuckelaer, A
中科院分区：
文献类型：
--
作者：
Wittig, U;De Beuckelaer, A
基因组测序项目和新的实验方法产生了大量的数据。在这一庞大的基因组数据中，在生物体中发现的基因中，有30%-40%的生物功能仍然未知。由于缺乏信息，在特定生物体中发生的所有生物功能的总体模式不能被适当地表现出来。为了了解基因组数据的功能特性，必须收集更多的实验数据。途径数据库是处理生化途径的当前知识的努力，此外还可用于序列数据的解释。一些现有的途径数据库可以被解释为基因组的详细功能注释，因为它们与基因组信息紧密结合。然而，这些数据库中往往缺乏实验数据。本文概述了途径数据库及其相应的一些生物数据库，并从生物学的角度重点介绍了这些数据库的内容和结构、数据的组织和存储信息的可靠性。此外，还给出了有关路径数据的表示和处理数据的工具的信息。指出了所分析的数据库的优缺点，并对生物科学家如何使用这些途径数据库进行了概述。
Enormous amounts of data result from genome sequencing projects and new experimental methods. Within this tremendous amount of genomic data 30-40 per cent of the genes being identified in an organism remain unknown in terms of their biological function. As a consequence of this lack of information the overall schema of all the biological functions occurring in a specific organism cannot be properly represented. To understand the functional properties of the genomic data more experimental data must be collected. A pathway database is an effort to handle the current knowledge of biochemical pathways and in addition can be used for interpretation of sequence data. Some of the existing pathway databases can be interpreted as detailed functional annotations of genomes because they are tightly integrated with genomic information. However, experimental data are often lacking in these databases. This paper summarises a list of pathway databases and some of their corresponding biological databases, and also focuses on information about the content and the structure of these databases, the organisation of the data and the reliability of stored information from a biological point of view. Moreover, information about the representation of the pathway data and tools to work with the data are given. Advantages and disadvantages of the analysed databases are pointed out, and an overview to biological scientists on how to use these pathway databases is given.