LexGrid: A Framework for Representing, Storing, and Querying Biomedical Terminologies from Simple to Sublime

Jyotishman Pathak, Harold R. Solbrig, James D. Buntrock, Thomas M. Johnson, Christopher G. Chute

Research output: Contribution to journalArticle

Abstract

Many biomedical terminologies, classifications, and ontological resources such as the NCI Thesaurus (NCIT), International Classification of Diseases (ICD), Systematized Nomenclature of Medicine (SNOMED), Current Procedural Terminology (CPT), and Gene Ontology (GO) have been developed and used to build a variety of IT applications in biology, biomedicine, and health care settings. However, virtually all these resources involve incompatible formats, are based on different modeling languages, and lack appropriate tooling and programming interfaces (APIs) that hinder their wide-scale adoption and usage in a variety of application contexts. The Lexical Grid (LexGrid) project introduced in this paper is an ongoing community-driven initiative, coordinated by the Mayo Clinic Division of Biomedical Statistics and Informatics, designed to bridge this gap using a common terminology model called the LexGrid model. The key aspect of the model is to accommodate multiple vocabulary and ontology distribution formats and support of multiple data stores for federated vocabulary distribution. The model provides a foundation for building consistent and standardized APIs to access multiple vocabularies that support lexical search queries, hierarchy navigation, and a rich set of features such as recursive subsumption (e.g., get all the children of the concept penicillin). Existing LexGrid implementations include the LexBIG API as well as a reference implementation of the HL7 Common Terminology Services (CTS) specification providing programmatic access via Java, Web, and Grid services.

Original languageEnglish (US)
Pages (from-to)305-315
Number of pages11
JournalJournal of the American Medical Informatics Association
Volume16
Issue number3
DOIs
StatePublished - May 1 2009
Externally publishedYes

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ASJC Scopus subject areas

  • Health Informatics

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