title: Common data model for natural language processing based on two existing standard information models: CDA+GrAF.
abstract: An increasing need for collaboration and resources sharing in the Natural Language Processing (NLP) research and development community motivates efforts to create and share a common data model and a common terminology for all information annotated and extracted from clinical text. We have combined two existing standards: the HL7 Clinical Document Architecture (CDA), and the ISO Graph Annotation Format (GrAF; in development), to develop such a data model entitled "CDA+GrAF". We experimented with several methods to combine these existing standards, and eventually selected a method wrapping separate CDA and GrAF parts in a common standoff annotation (i.e., separate from the annotated text) XML document. Two use cases, clinical document sections, and the 2010 i2b2/VA NLP Challenge (i.e., problems, tests, and treatments, with their assertions and relations), were used to create examples of such standoff annotation documents, and were successfully validated with the XML schemata provided with both standards. We developed a tool to automatically translate annotation documents from the 2010 i2b2/VA NLP Challenge format to GrAF, and automatically generated 50 annotation documents using this tool, all successfully validated. Finally, we adapted the XSL stylesheet provided with HL7 CDA to allow viewing annotation XML documents in a web browser, and plan to adapt existing tools for translating annotation documents between CDA+GrAF and the UIMA and GATE frameworks. This common data model may ease directly comparing NLP tools and applications, combining their output, transforming and "translating" annotations between different NLP applications, and eventually "plug-and-play" of different modules in NLP applications.
authors.affiliation: Department of Biomedical Informatics, University of Utah, School of Medicine, Salt Lake City, UT 84112, USA. stephane.meystre@hsc.utah.edu
authors.forename: Stéphane M
authors.initials: SM
authors.lastname: Meystre
authors.forename: Sanghoon
authors.initials: S
authors.lastname: Lee
authors.forename: Chai Young
authors.initials: CY
authors.lastname: Jung
authors.forename: Raphaël D
authors.initials: RD
authors.lastname: Chevrier
mesh_terms: D004282:Documentation / Q000379:methods; D057286:Electronic Health Records; D008490:Medical Informatics / Q000379:methods*; D008962:Models, Theoretical; D009323:Natural Language Processing; D015203:Reproducibility of Results