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

描述(由申请人提供)：我们提出了一个有两个相互关联的基本目标的研究计划：(1)开发和评估用于使用现有的开放式生物医学本体(OBO)从临床文本语料库中提取信息的软件和(2)开发和评估用于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，我们将提供本体开发和信息提取工具包(ODIE)-一套集成了GATE、PROT和LexGrid的软件组件，将帮助研究人员和本体开发人员执行这些任务。作为我们工作的试验台，我们将主要关注国家癌症研究所主题词表-一个现有的OBO本体，但将开发我们的许多组件以适用于其他OBO本体。我们选择血液病理学领域作为测试案例，是因为我们有丰富多样的临床文献来源，而且我们的软件有潜力推进这一领域的翻译生物医学研究。然而，我们开发的大多数组件将是领域中立的，并将推广到肿瘤学内外的其他领域。我们提出的工作具有重要的三点贡献。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，并对这些备选方法的性能进行评估。其次，我们将开发和传播用于执行这些任务的通用软件资源，这些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。这项工作的结果将从根本上使用OBO本体论来推进生物医学。这项拨款建议开发一套计算机工具，以帮助研究人员(1)提取含义并对医学文档进行编码，以及(2)从这些文档中构建知识的正式表示。这项工作将提高确定特定医学文件中的信息的速度和效率，并允许自动处理大量文件，从而使普通公众受益。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对医学研究和病人护理都有好处。

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.