FHIRCat: Enabling the Semantics of FHIR and Terminologies for Clinical and Translational Research

项目摘要 HL7快速医疗互操作性资源(FHIR)是新兴的下一代标准框架 电子医疗信息的交换。杉木令人兴奋的方面之一是它是 第一个纳入Tim Berners-Lee在《语义网》中描述的“语义网”愿景的临床数据标准 2001年。在这篇文章中，他断言语义网是下一个“杀手级应用程序”，并概述了成功的秘诀：1) 以单一、通用格式表示信息和意义--资源描述框架(RDF)；2) 创建URI目录，这些URI在给定的使用环境中用作RDF表示的共享标识符； 3)创建工具，将现有数据和知识资源转换为RDF的通用语言 还有URI。这允许来自不同来源和结构的信息被组合成单个， “链接开放数据”的联合集合。此链接数据模型允许将临床数据与 环境、遗传、地理和任何其他相关数据，并作为一个整体进行分析。 今天，最新的FHIR版本1)可以用RDF表示临床信息，2)提供了一个共享目录 医疗保健的标准化RDF标识符。目前已有工具可以将XML、电子表格、 数据库等转换成RDF。然而，仍然缺少的是将共享的 标准FHIR目录识别符及其在其他临床信息模型中的等价物。我们之前已经 展示了RDF、OWL语义和形状表达式(ShEx)模式的组合 语言可以成为将不同的数据模型和范例集成到单一、 面向资源的接口集合，使实现Berners-Lee的医疗保健愿景成为可能 这反过来为临床数据集成和基于标准的发现创造了新的机会 临床和转化性研究的分析。该项目的目标是设计、开发和 评估利用语义网技术的名为FHIRCat的新型信息平台 模型和配置文件，以及基于标准的有效数据集成本体，以实现高质量 可重复的临床和转译研究。我们的具体目标是：1)发展FHIR ShEx/RDF FHIR数据验证规范和工具；2)基于RDF的数据转换的标准化和部署 在外部模型和FHIR之间建立了一个基于本体的数据访问系统OBDA 临床数据库。该项目的成果使伯纳斯-李的愿景成为可能 医疗保健在不久的将来，进而为推进杉木自动化创造新的机遇- 基于临床数据的集成和共享，并加快基于标准的数据发现和分析 临床和转化性研究。 1

Project Summary HL7 Fast Healthcare Interoperability Resources (FHIR) is an emerging next generation standard framework for the exchange of electronic healthcare information. One of the exciting aspects of FHIR is that it is one of the first clinical data standards to incorporate the vision of the “Semantic Web” described by Tim Berners-Lee in 2001. In it, he asserts that the Semantic Web is the next "killer app" and outlines a formula for success: 1) represent information and meaning in a single, universal format - Resource Description Framework (RDF); 2) Create a catalog of URIs that serve as shared identifiers for the RDF representation in a given context of use; and 3) Create tools for transforming existing data and knowledge resources into the universal language of RDF and URIs. This allows information from disparate sources and structures to be combined into a single, federated collection of “linked open data”. This linked data model allows clinical data to be combined with environmental, genetic, geographic, and any other relevant data and to be analyzed as an integrated whole. Today, the latest FHIR release 1) can represent clinical information in RDF and 2) provides a catalog of shared standardized RDF identifiers for healthcare. Tools exist today that can transform XML, spreadsheets, databases etc. into RDF. What is still missing, however, are mechanisms that convert to and from the shared standard FHIR catalog identifiers and their equivalent in other clinical information models. We have previously demonstrated that the combination of RDF, OWL semantics and the Shape Expressions (ShEx) schema language could be an ideal platform for integrating disparate data models and paradigms under a single, resource oriented collection of interfaces, making it possible to complete Berners-Lee's vision for healthcare which, in turn, creates new opportunities for the clinical data integration and standards-based discovery and analytics for clinical and translational research. The objective of the this project is to design, develop and evaluate a novel informatics platform known as FHIRCat that leverages Semantic Web technologies, FHIR models and profiles, and ontologies for effective standards-based data integration for enabling high-quality reproducible clinical and translational research. Our specific aims are: 1) Develop FHIR ShEx/RDF specification and tools for FHIR data validation; 2) Standardize and deploy the RDF-based data transformation between external models and FHIR; and 3) Build a FHIR ontology-based data access (OBDA) system for clinical data repositories. The outcome of the project makes it possible to realize Berners-Lee's vision for healthcare in the very near future, in turn creating new opportunities for advancing the automation of FHIR- based clinical data integration and sharing, and accelerating standards-based data discovery and analytics in clinical and translational research. 1