Karp P D, Paley S, Krieger C J, Zhang P
SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
Pac Symp Biocomput. 2004:190-201. doi: 10.1142/9789812704856_0019.
An important emerging need in Model Organism Databases (MODs) and other bioinformatics databases (DBs) is that of capturing the scientific evidence that supports the information within a DB. This need has become particularly acute as more DB content consists of computationally predicted information, such as predicted gene functions, operons, metabolic pathways, and protein properties. This paper presents an ontology for encoding the type of support and the degree of support for DB assertions, and for encoding the literature source in which that support is reported. The ontology includes a hierarchy of 35 evidence codes for modeling different types of wet-lab and computational evidence for the existence of operons and metabolic pathways, and for gene functions. We also describe an implementation of the ontology within the Pathway Tools software environment, which is used to query and update Pathway/Genome DBs such as EcoCyc, MetaCyc, and HumanCyc.
模式生物数据库（MODs）和其他生物信息学数据库（DBs）中一个重要的新需求是捕获支持数据库内信息的科学证据。随着越来越多的数据库内容由计算预测信息组成，如预测的基因功能、操纵子、代谢途径和蛋白质特性，这一需求变得尤为迫切。本文提出了一种本体，用于编码对数据库断言的支持类型和支持程度，以及编码报告该支持的文献来源。该本体包括一个由35个证据代码组成的层次结构，用于对操纵子和代谢途径的存在以及基因功能的不同类型的湿实验室和计算证据进行建模。我们还描述了该本体在Pathway Tools软件环境中的实现，该环境用于查询和更新诸如EcoCyc、MetaCyc和HumanCyc等通路/基因组数据库。
