迈向生物信息学中的论证应用：一个基因表达案例研究。

Towards the use of argumentation in bioinformatics: a gene expression case study.

作者信息

McLeod Kenneth, Burger Albert

机构信息

Department of Computer Science, Heriot-Watt University, Edinburgh, UK.

出版信息

Bioinformatics. 2008 Jul 1;24(13):i304-12. doi: 10.1093/bioinformatics/btn157.

DOI:10.1093/bioinformatics/btn157

PMID:18586728

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2718635/

Abstract

MOTIVATION

Due to different experimental setups and various interpretations of results, the data contained in online bioinformatics resources can be inconsistent, therefore, making it more difficult for users of these resources to assess the suitability and correctness of the answers to their queries. This work investigates the role of argumentation systems to help users evaluate such answers. More specifically, it looks closely at a gene expression case study, creating an appropriate representation of the underlying data and series of rules that are used by a third-party argumentation engine to reason over the query results provided by the mouse gene expression database EMAGE.

RESULTS

A prototype using the ASPIC argumentation engine has been implemented and a preliminary evaluation carried out. This evaluation suggested that argumentation can be used to deal with inconsistent data in biological resources.

AVAILABILITY

The ASPIC argumentation engine is available from http://www.argumentation.org. EMAGE gene expression data can be obtained from http://genex.hgu.mrc.ac.uk. The argumentation rules for the gene expression example are available from the lead author upon request.

摘要

动机

由于不同的实验设置以及对结果的各种解读，在线生物信息学资源中包含的数据可能不一致，因此，这些资源的用户更难评估其查询答案的适用性和正确性。这项工作研究了论证系统在帮助用户评估此类答案方面的作用。更具体地说，它仔细研究了一个基因表达案例研究，创建了基础数据的适当表示形式以及一系列规则，第三方论证引擎使用这些规则对小鼠基因表达数据库EMAGE提供的查询结果进行推理。