Semantic Approaches to Phenotypic Databases Analyses

表型数据库分析的语义方法

• 批准号: 7217171
• 负责人: Yves A. Lussier
• 金额: $ 15.66万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-05-01 至 2008-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7217171
• 关键词: Internet; automated data processing; cancer information system; computer graphics /printing; computer human interaction; computer simulation; computer system design /evaluation; genetic registry /resource /referral center; molecular biology information system; phenotype; semantics; systematic biology; vocabulary development for information system

The long-term goal of this project is to build innovative informatics tools, capable of automatically querying and organizing phenotypic data (traits, syndromes, etc.) across Phenotype databases, to facilitate phenotypic research that aims to unlock the gene-disease-relationships. While genomic research at the molecular level (genes and proteins) has been intensively pursued, little progress has been made in functional genomics research, especially phenotypic research. However, there will soon be a pressing demand for greater integration of medicine and biology, and for related innovative informatics tools to facilitate research requiring phenotypic data. One limiting factor that significantly hinders the progress of phenotypic research is the lack of timely access to relevant phenotypes across databases. This application proposes to adopt a multidisciplinary approach (informatics, genomics and biomedical research) to explore the value of semantic, probabilistic and terminological technologies in phenotypic data and knowledge processing. The project focuses on the research and development of the Phenotype Organizer System (POS), a system designed to automate the processes of integration, organization and visualization of phenotypic data and knowledge. The hypotheses to be explored in this project are 1) a Phenotype Organizer System can be developed to effectively handle phenotypic data and knowledge from cancer and Model Organism System Databases, and 2) POS, by using the contextual knowledge of term usage (semantic, terminological and probabilistic) can improve the incorporation and organization of phenotypic information from distinct databases. Specific aims to test these hypotheses are: (i) to model and map the terminological components of various phenotypic databases using extended semantic networks; (ii) to create a knowledge base containing the contextual properties of the terminological components; and (iii) to develop the Web-enabled Phenotype Organizer System based on aims (i) and (ii). The proposed research may provide a unique approach to accelerate biomedical research by improving access to phenotypic data and knowledge processing - the Semantic Phenome (phenotypic-genomic relations). Further, results from these studies may yield innovative biomedical informatics tools that could be highly valuable for interdisciplinary mining of genomic, proteomic and clinical databases.

该项目的长期目标是建立创新的信息学工具，能够自动查询和组织表型数据（特征，综合症等）跨表型数据库，以促进旨在释放基因 - 疾病关系的表型研究。尽管在分子水平（基因和蛋白质）的基因组研究得到了强烈的追求，但在功能基因组学研究，尤其是表型研究中几乎没有取得进展。但是，很快将有迫切要求对医学和生物学的更大整合，以及相关的创新信息学工具，以促进需要表型的研究 数据。显着阻碍表型研究进展的一个限制因素是缺乏及时访问数据库中相关表型的限制。该应用程序建议采用多学科方法（信息学，基因组学和生物医学研究）来探索语义，概率和术语技术在表型数据和知识处理中的价值。该项目着重于表型组织者系统（POS）的研究和开发，该系统旨在自动化表型数据和知识的集成，组织和可视化过程。该项目中要探索的假设是1）可以开发出一种表型的组织器系统来有效处理表型 癌症和模型生物系统数据库的数据和知识以及2）POS通过使用术语使用的上下文知识（语义，术语和概率）可以改善来自不同数据库的表型信息的掺入和组织。测试这些假设的具体目的是：（i）使用扩展的语义网络对各种表型数据库的术语组成进行建模和绘制； （ii）创建一个知识库，其中包含术语组成部分的上下文属性； （iii）基于目标（i）和（ii）开发启用网络的表型组织器系统。拟议的研究可能通过改善访问来提供一种独特的方法来加速生物医学研究 表型数据和知识处理 - 语义现象（表型基因组关系）。此外，这些研究的结果可能会产生创新的生物医学信息学工具，这些工具对于基因组，蛋白质组学和临床数据库的跨学科挖掘可能非常有价值。

项目成果

Guideline interaction: a study of interactions among drug-disease contraindication rules.

指南相互作用：药物与疾病禁忌规则之间相互作用的研究。

• 发表时间: 2003
• 期刊: AMIA ... Annual Symposium proceedings. AMIA Symposium
• 作者: Kuo,TeHui;Mendonca,EneidaA;Li,Jianrong;Lussier,YvesA
• 通讯作者: Lussier,YvesA

Partitioning knowledge bases between advanced notification and clinical decision support systems.

在高级通知和临床决策支持系统之间划分知识库。

• 发表时间: 2005
• 期刊: AMIA ... Annual Symposium proceedings. AMIA Symposium
• 作者: Borlawsky,Tara;Li,Jianrong;Jalan,Srikant;Stern,Edie;Williams,Rose;Lussier,YvesA
• 通讯作者: Lussier,YvesA

Word-of-Mouth Innovation: Hypothesis Generation for Supplement Repurposing based on Consumer Reviews.

口碑创新：基于消费者评论的补充剂再利用假设生成。

• 发表时间: 2017
• 期刊: AMIA ... Annual Symposium proceedings. AMIA Symposium
• 作者: Fan,Jung-Wei;Lussier,YvesA
• 通讯作者: Lussier,YvesA

Curation-free biomodules mechanisms in prostate cancer predict recurrent disease.

• DOI: 10.1186/1755-8794-6-s2-s4
• 发表时间: 2013
• 期刊: BMC medical genomics
• 影响因子: 2.7
• 作者: Chen JL;Hsu A;Yang X;Li J;Lee Y;Parinandi G;Li H;Lussier YA
• 通讯作者: Lussier YA

Simulation of ICD-9 to ICD-10-CM Transition for Family Medicine: Simple or Convoluted?

• DOI: 10.3122/jabfm.2016.01.150146
• 发表时间: 2016-01-01
• 期刊: JOURNAL OF THE AMERICAN BOARD OF FAMILY MEDICINE
• 影响因子: 2.9
• 作者: Grief, Samuel N.;Patel, Jesal;Boyd, Andrew D.
• 通讯作者: Boyd, Andrew D.