Evidence Extraction Systems for the Molecular Interaction Literature

伯恩斯，Gully A。 摘要 在主要的研究文章中，科学家根据实验证据提出主张，并报告两者 论文结果部分的声明和支持证据。然而，生物医学数据库- 详细记录科学家提出的主张，但很少提供任何支持证据的描述， 咨询科学家可以用来理解为什么会有这样的说法。目前， 将证据输入数据库需要人工操作，既耗时又昂贵;因此，证据记录在文件中，但 通常在数据库系统中捕获。例如，欧洲生物信息学研究所的INTACT数据库 详细描述了不同分子如何在生物化学上相互作用。他们的特点是- 说谎实验提供了证据，只有两个层次的变量的相互作用：一个代码表示 用于检测分子相互作用的方法，另一个代码表示用于检测每个分子相互作用的方法。 分子。事实上，INTACT描述了94种不同类型的交互检测方法，可用于 与其他实验方法过程相结合，可以以各种不同的方式使用， 揭示了相互作用的不同细节。这一重要信息没有被数据库记录下来。虽然 实验证据是复杂的，它符合实验设计的某些原则：实验研究- 研究一种现象通常涉及测量精心选择的因变量，同时改变 同样精心挑选的独立变量。利用这些原则，我们可以设计一个初步的， 强大的，通用的实验证据表示。在这个项目中，我们将使用这种表示法， 描述与支持分子生物学解释性断言的证据有关的方法和数据， 由INTACT描述的交互。我们项目的一个关键贡献是，我们将开发提取这种物质的方法， 自动从科学论文中提取证据（A）通过对特定子类型的图形进行图像处理， 常见于分子生物学论文和（B）通过使用自然语言处理从 科学家用来描述他们的结果的文本。我们将为INTACT存储库开发这些工具，但包 因此，它们也可以用于与生物医学研究的其他领域有关的证据。

Burns, Gully A. Abstract In primary research articles, scientists make claims based on evidence from experiments, and report both the claims and the supporting evidence in the results section of papers. However, biomedical databases de- scribe the claims made by scientists in detail, but rarely provide descriptions of any supporting evidence that a consulting scientist could use to understand why the claims are being made. Currently, the process of curating evidence into databases is manual, time-consuming and expensive; thus, evidence is recorded in papers but not generally captured in database systems. For example, the European Bioinformatics Institute's INTACT database describes how different molecules biochemically interact with each other in detail. They characterize the under- lying experiment providing the evidence of that interaction with only two hierarchical variables: a code denoting the method used to detect the molecular interaction and another code denoting the method used to detect each molecule. In fact, INTACT describes 94 different types of interaction detection method that could be used in conjunction with other experimental methodological processes that can be used in a variety of different ways to reveal different details about the interaction. This crucial information is not being captured in databases. Although experimental evidence is complex, it conforms to certain principles of experimental design: experimentally study- ing a phenomenon typically involves measuring well-chosen dependent variables whilst altering the values of equally well-chosen independent variables. Exploiting these principles has permitted us to devise a preliminary, robust, general-purpose representation for experimental evidence. In this project, We will use this representation to describe the methods and data pertaining to evidence underpinning the interpretive assertions about molecular interactions described by INTACT. A key contribution of our project is that we will develop methods to extract this evidence from scientific papers automatically (A) by using image processing on a specific subtype of figure that is common in molecular biology papers and (B) by using natural language processing to read information from the text used by scientists to describe their results. We will develop these tools for the INTACT repository but package them so that they may then also be used for evidence pertaining to other areas of research in biomedicine.