BMC Bioinformatics. 2012 Jan 25;13 Suppl 1(Suppl 1):S8. doi: 10.1186/1471-2105-13-S1-S8.
In situ hybridisation gene expression information helps biologists identify where a gene is expressed. However, the databases that republish the experimental information online are often both incomplete and inconsistent. Non-monotonic reasoning can help resolve such difficulties - one such form of reasoning is computational argumentation. Essentially this involves asking a computer to debate (i.e. reason about) the validity of a particular statement. Arguments are produced for both sides - the statement is true and, the statement is false - then the most powerful argument is used. In this work the computer is asked to debate whether or not a gene is expressed in a particular mouse anatomical structure. The information generated during the debate can be passed to the biological end-user, enabling their own decision-making process.
This paper examines the evolution of a system, Argudas, which tests using computational argumentation in an in situ gene hybridisation gene expression use case. Argudas reasons using information extracted from several different online resources that publish gene expression information for the mouse. The development and evaluation of two prototypes is discussed. Throughout a number of issues shall be raised including the appropriateness of computational argumentation in biology and the challenges faced when integrating apparently similar online biological databases.
From the work described in this paper it is clear that for argumentation to be effective in the biological domain the argumentation community need to develop further the tools and resources they provide. Additionally, the biological community must tackle the incongruity between overlapping and adjacent resources, thus facilitating the integration and modelling of biological information. Finally, this work highlights both the importance of, and difficulty in creating, a good model of the domain.
原位杂交基因表达信息帮助生物学家确定基因的表达位置。然而，在线重新发布实验信息的数据库往往既不完整也不一致。非单调推理可以帮助解决这些困难——推理的一种形式是计算论证。本质上，这涉及到要求计算机争论（即推理）特定陈述的有效性。为双方生成论点——陈述为真和陈述为假——然后使用最有力的论点。在这项工作中，计算机被要求争论一个基因是否在特定的小鼠解剖结构中表达。辩论过程中生成的信息可以传递给生物学最终用户，从而使他们能够进行自己的决策过程。
本文研究了一个系统 Argudas 的演变，该系统在原位基因杂交基因表达用例中使用计算论证进行测试。Argudas 使用从几个不同的在线资源中提取的信息进行推理，这些资源发布了用于小鼠的基因表达信息。讨论了两个原型的开发和评估。在整个过程中，将提出许多问题，包括计算论证在生物学中的适当性以及在集成看似相似的在线生物数据库时面临的挑战。
从本文描述的工作中可以清楚地看出，为了使论证在生物学领域有效，论证社区需要进一步开发他们提供的工具和资源。此外，生物学界必须解决重叠和相邻资源之间的不一致性，从而促进生物信息的集成和建模。最后，这项工作强调了创建良好的领域模型的重要性和困难。
