The ODIE Toolkit - Software for Information Extraction and Biomedical Ontology De

描述（由申请人提供）：我们提出了一个具有两个相互关联的基础目标的研究项目：(1)开发和评估使用现有开放生物医学本体（OBO）从临床文本语料库中提取信息的软件；(2)开发和评估从临床文本语料库中丰富现有生物医学本体的软件。作为我们工作的结果，我们将交付本体开发和信息提取工具包（ODIE）——一组与GATE、Prot和LexGrid集成的软件组件，这将帮助研究人员和本体开发人员执行这些任务。作为我们工作的测试平台，我们将主要关注国家癌症研究所同义词典——一个现有的OBO本体，但我们将开发许多组件以推广到其他OBO本体。我们之所以选择血液病领域作为测试案例，是因为临床文件来源丰富多样，而且我们的软件有潜力推动该领域的转化生物医学研究。然而，我们开发的大部分组件将是领域中立的，并将推广到肿瘤学内外的其他领域。我们提出的工作有三个重要贡献。首先，我们将开发新的方法或修改现有的方法来完成信息提取和本体丰富，我们将评估这些替代方案的性能。其次，我们将开发和传播执行这些任务的通用软件资源，利用国家生物医学本体中心支持的工具。第三，我们将为现有OBO本体的发展做出贡献。这项工作的结果将在基础上使用OBO本体来推进生物医学。该基金建议开发一套计算机工具，以帮助研究人员(1)提取医学文件的含义和编纂，以及(2)从这些文件中建立知识的正式表示。这项工作将提高确定特定医疗文档中包含哪些信息的速度和效率，并允许对大量文档进行自动化处理，从而使公众受益。此外，该项目将通过帮助研究人员构建更全面的本体，为开发其他应用程序的软件做出贡献。这项工作的结果可能有利于医学研究和病人护理。

DESCRIPTION (provided by applicant): We propose a program of research with two interlocking, foundational goals: (1) to develop and evaluate software for information extraction from clinical text corpora using existing Open Biomedical Ontologies (OBO) and (2) to develop and evaluate software for enrichment of existing biomedical ontologies from clinical text corpora. As a result of our work we will deliver the Ontology Development and Information Extraction Toolkit (ODIE) - a set of software components integrated with GATE, Prot¿g¿ and LexGrid, that will assist researchers and ontology developers in performing these tasks. As a testbed for our work, we will focus mainly on the National Cancer Institute Thesaurus - an existing OBO ontology, but will develop many of our components to be generalizable to other OBO ontologies. We have chosen the domain of hematopathology as a test case because of the rich and varied source of clinical documents, and the potential for our software to advance translational biomedical research in this area. However the majority of the components that we develop will be domain-neutral and will generalize to other areas within and outside of Oncology. The work we propose is significant for three contributions. First, we will develop novel methods or modify existing methods for accomplishing information extraction and ontology enrichment and we will evaluate the performance of these alternatives. Second, we will develop and disseminate generic software resources for performing these tasks, which leverage the National Center for Biomedical Ontology supported tools. Third, we will contribute to the development of existing OBO ontologies. The results of this work will use OBO ontologies in fundamental ways to advance biomedicine. This grant propose to develop a set of computer tools to assist researchers in (1) extracting meaning and codifying medical documents, and (2) building formal representations of knowledge from those documents. This work would benefit the general public by increasing the speed and efficiency of determining what information is in a particular medical document and allowing automated processing of large numbers of documents. Additionally, the project would contribute to the software for developing other applications by helping researchers build more comprehensive ontologies. The results of this work may benefit both medical research and patient care.