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

• 批准号: 7654754
• 负责人: AMARENDRA K. DAS
• 金额: $ 80.16万
• 依托单位: STANFORD 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 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7654754
• 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; response; time use; tool; treatment response; web site

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，研究人员在识别他们收集的时间信息之间的重要关系方面面临着特殊的困难。目前，由于缺乏广泛可用的、现成的工具来整合时间和领域知识，研究人员在大量的观察和实验数据基础上发现相关时间模式的能力有限。为了解决这些挑战，我们提出了一种新的方法查询和抽象的时间模式，集成了数据，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W3C标准的语义Web和Protigi环境的扩展，最广泛使用的，免费提供的，开源软件指定的本体和知识库。建议的查询工具包，称为SQWRL-TK，将为调查人员提供一个集成的，可扩展的框架，域驱动的时间现象的调查。我们努力的目标是开发一组开源工具，灵活地集成基于知识的方法，用于时态数据的转换，检索和抽象。我们的具体目标是（1）实现一个可扩展的、可重用的软件体系结构，用于使用本体和规则进行时态模式的查询和抽象：（2）开发一个数据映射工具，可以将存储在现有关系数据库中的面向时间的数据映射到适合于基于知识的查询的时态本体;以及（3）创建查询启发工具，该工具可以允许调查人员制定用于数据提取的领域相关的时间模式，并检查这些查询的结果。我们将与在艾滋病毒耐药性研究和免疫紊乱试验管理领域拥有完善的数据库的调查小组持续合作，开发和评估这些工具的使用。我们计划进行软件测试和优化的迭代过程，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的开源插件）。在研究人员中广泛使用这种通用方法可能会大大有助于发现隐藏在生物医学数据库中面向时间的数据中的科学相关关联和模式。