Open-Source Toolkit for Knowledge-Based Querying of Time-Oriented Data

用于基于知识的时间数据查询的开源工具包

基本信息

批准号：
7849699
负责人：
AMARENDRA K. DAS
金额：
$ 80.91万
依托单位：
STANFORD UNIVERSITY
依托单位国家：
美国
项目类别：
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/7849699
关键词：
Address Architecture Area Biological Biological Markers Biomedical Research Clinical Clinical Trials Collaborations Communities Complex Computer software Custom Data Databases Development Disease Progression Documentation Drug Combinations Drug resistance Ensure Environment Evaluation Event Face Foundations Gene Expression Genotype Goals HIV HIV drug resistance Healthcare Immune System Diseases Institutes Internet Intervention Investigation Knowledge Language Maps Methods Mutation Online Systems Ontology Outcome Pathway interactions Patients Pattern Performance Pharmaceutical Preparations Process Research Research Personnel Retrieval Semantics Solutions Specific qualifier value Structure Technology Terminology Testing Time Treatment outcome Viral Load result Viral load measurement Work abstracting base computer based Semantic Analysis data integration distributed data knowledge base novel open source post-market programs public health relevance relational database response time use tool treatment response web site

项目摘要

DESCRIPTION (provided by applicant): In research involving biological pathways, disease progression, and treatment outcomes, investigators face particular difficulties in identifying important relationships among the temporal information they collect. Currently, investigators have limited abilities to discover relevant temporal patterns among volumes of observational and experimental data based, because of the lack of widely available, ready-to-use tools that incorporate temporal and domain knowledge. To address these challenges, we propose a novel method for querying and abstracting temporal patterns that integrates data, ontologies, rules, and formal temporal semantics. Our approach, called Semantic Query-enhanced Web Rule Language (SQWRL), is an extension to W3C standards for the Semantic Web and to the Protigi environment-the mostly widely used, freely available, open-source software for specifying ontologies and knowledge bases. The proposed querying toolkit, called SQWRL-TK, will provide investigators an integrated, scalable framework for domain-driven investigation of temporal phenomena. The goal of our efforts is to develop a set of open-source tools that flexibly integrates knowledge-based methods for the transformation, retrieval, and abstraction of temporal data. Our specific aims are (1) to implement a scalable, reusable software architecture for the querying and abstraction of temporal patterns using ontologies and rules; (2) to develop a data-mapping tool that can map time-oriented data stored in existing relational databases into a temporal ontology suitable for knowledge- based querying; and (3) to create a query-elicitation tool that can allow investigators to formulate domain- relevant temporal patterns for data extraction and inspect the results of those queries. We will develop and evaluate the use of these tools in ongoing collaborations with investigative teams who have well-developed data repositories in the areas of HIV drug resistance research and immune disorder trial management. We plan to undertake a reiterative process of software testing and optimization to ensure accuracy and performance. We will create a website to disseminate these tools (as open-source plug ins to Protigi). The widespread use of such general methods among investigators may greatly enable the discovery of scientifically relevant associations and patterns hidden among time-oriented data within biomedical databases.

描述（由申请人提供）：在涉及生物学途径，疾病进展和治疗结果的研究中，研究人员在识别其收集的时间信息之间的重要关系方面面临特殊困难。目前，由于缺乏可获得的时间和域知识，研究人员在观察和实验数据之间发现相关的时间模式的能力有限。为了应对这些挑战，我们提出了一种新颖的方法，用于查询和抽象的时间模式，以整合数据，本体，规则和正式的时间语义。我们的方法称为语义查询增强的Web规则语言（SQWRL），是Sligantic Web和Protigi环境的W3C标准的扩展，该标准是大多数使用，可自由使用的，可自由使用的开源软件，用于指定本体和知识库。所提出的称为SQWRL-TK的查询工具包将为研究人员提供一个综合，可扩展的框架，用于域驱动的时间现象研究。我们努力的目的是开发一套开源工具，这些工具灵活地集成了基于知识的方法，以转换，检索和抽象的时间数据。我们的具体目的是（1）使用本体和规则实施可重复使用的软件体系结构，以查询和抽象的时间模式；（2）开发一个数据映射工具，该工具可以将存储在现有关系数据库中的时间定向数据映射到适合基于知识的查询的时间本体中；（3）创建一个查询引诱工具，该工具可以允许研究人员制定与数据提取的域相关的时间模式，并检查这些查询的结果。我们将开发和评估这些工具在与在HIV耐药性研究和免疫障碍试验管理领域中发达的数据存储库的调查团队进行的持续合作中的使用。我们计划进行软件测试和优化的重申过程，以确保准确性和性能。我们将创建一个网站来传播这些工具（作为Protigi的开源插头INS）。研究人员之间这种一般方法的广泛使用可能会极大地导致在生物医学数据库中隐藏的科学相关关联和模式。