OAMiner: Integrative Knowledge Anchored Hypothesis Discovery

OMiner：综合知识锚定假设发现

• 批准号: 7828221
• 负责人: Metin Nafi Gurcan
• 金额: $ 58.42万
• 依托单位: OHIO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-07-01 至 2011-12-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7828221
• 关键词: Acute; Address; Area; Atlases; Biochemical Genetics; Biology; Characteristics; Clinical; Data; Data Set; Data Sources; Databases; Degenerative polyarthritis; Development; Environment; Evaluation; Expert Systems; Genome; Goals; Human; Image; Image Analysis; Imaging Techniques; Incidence; Intervention; Knee Osteoarthritis; Knowledge; Literature; Longitudinal Studies; Malignant Neoplasms; Measures; Medical; Medicine; Molecular; Ontology; Performance; Public Health; Publishing; Quality of life; Research; Research Project Grants; Source; Technology; Testing; Text; Training; Translational Research; Unified Medical Language System; United States National Library of Medicine; base; biomedical informatics; cancer genome; computerized; design; novel; psychologic; public health relevance; quadriceps muscle; repository; text searching; tool; translational study; tumor; verification and validation

DESCRIPTION (provided by applicant):The objective of this proposal, which is designed to address the ever increasing need for integrated knowledge discovery in biology and medicine, is to enable the discovery, verification, and validation of hypotheses concerning interrelationships between image-based, phenotypic, and bio-molecular features in heterogeneous data sets by leveraging multiple conceptual knowledge sources - ultimately supporting "high throughput" knowledge-driven translational science. To provide for a manageable project scope, Osteoarthritis Initiative (OAI) data sets will be used as a primary, motivating use case for the development and evaluation of the projected research products. This project necessarily involves analysis of initial hypotheses by subject matter experts (SMEs) for system training and verification. However, the ultimate goal of our proposed approach is to minimize the need for human intervention to identify or validate knowledge-anchored hypotheses. In order to generate such hypotheses, four interrelated knowledge sources are used: 1) full-text published bio-medical literature accessed by both conventional text mining and NLP analyses of articles as found in the Medline database and associated full text repositories; 2) publically available ontologies included in the National Library of Medicine's Unified Medical Language System (UMLS); 3) one or more databases containing phenotypic and functional (e.g. quality of life, psychological, strength and performance measures) data; and 4) computerized-image analysis derived features (e.g. cross-sectional area of the quadriceps).

描述（由申请人提供）：本提案旨在解决生物学和医学中日益增长的综合知识发现需求，旨在通过利用多个概念性知识源，发现、验证和确认关于异构数据集中基于图像、表型和生物分子特征之间相互关系的假设-最终支持“高通量”知识驱动的转化科学。为了提供可管理的项目范围，骨关节炎倡议（OAI）数据集将被用作开发和评估预计研究产品的主要激励用例。该项目必然涉及由主题专家（SME）进行系统培训和验证的初步假设分析。然而，我们提出的方法的最终目标是最大限度地减少人类干预的需要，以确定或验证知识锚定的假设。为了生成这样的假设，使用四个相互关联的知识源：1）全文发表的生物医学文献，其通过对Medline数据库和相关全文存储库中的文章进行传统文本挖掘和NLP分析来访问; 2）包括在国家医学图书馆的统一医学语言系统（UMLS）中的可检索的本体; 3）包含表型和功能（例如生活质量、心理、力量和性能测量）数据的一个或多个数据库;以及4）计算机化图像分析导出的特征（例如四头肌的横截面积）。

项目成果

Applying knowledge-anchored hypothesis discovery methods to advance clinical and translational research: the OAMiner project.

应用知识锚定的假设发现方法来推进临床和转化研究：OAMiner 项目。

• DOI: 10.1136/amiajnl-2011-000736
• 发表时间: 2012
• 期刊: Journal of the American Medical Informatics Association : JAMIA
• 作者: Payne,PhilipRO;Jackson,RebeccaD;Best,ThomasM;Borlawsky,TaraB;Lai,AlbertM;James,Stephen;Gurcan,MetinN
• 通讯作者: Gurcan,MetinN