Semantic Modeling for Exposomics with Exploratory Evaluation in Clinical Context

Jung Wei Fan, Jianrong Li, Yves A. Lussier

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Exposome is a critical dimension in the precision medicine paradigm. Effective representation of exposomics knowledge is instrumental to melding nongenetic factors into data analytics for clinical research. There is still limited work in (1) modeling exposome entities and relations with proper integration to mainstream ontologies and (2) systematically studying their presence in clinical context. Through selected ontological relations, we developed a template-driven approach to identifying exposome concepts from the Unified Medical Language System (UMLS). The derived concepts were evaluated in terms of literature coverage and the ability to assist in annotating clinical text. The generated semantic model represents rich domain knowledge about exposure events (454 pairs of relations between exposure and outcome). Additionally, a list of 5667 disorder concepts with microbial etiology was created for inferred pathogen exposures. The model consistently covered about 90% of PubMed literature on exposure-induced iatrogenic diseases over 10 years (2001-2010). The model contributed to the efficiency of exposome annotation in clinical text by filtering out 78% of irrelevant machine annotations. Analysis into 50 annotated discharge summaries helped advance our understanding of the exposome information in clinical text. This pilot study demonstrated feasibility of semiautomatically developing a useful semantic resource for exposomics.

Original languageEnglish (US)
Article number3818302
JournalJournal of Healthcare Engineering
Volume2017
DOIs
StatePublished - Jan 1 2017
Externally publishedYes

Fingerprint

Semantics
Microbiological Phenomena
Unified Medical Language System
Iatrogenic Disease
Precision Medicine
PubMed
Pathogens
Medicine
Ontology
Research

ASJC Scopus subject areas

  • Biotechnology
  • Surgery
  • Biomedical Engineering
  • Health Informatics

Cite this

Semantic Modeling for Exposomics with Exploratory Evaluation in Clinical Context. / Fan, Jung Wei; Li, Jianrong; Lussier, Yves A.

In: Journal of Healthcare Engineering, Vol. 2017, 3818302, 01.01.2017.

Research output: Contribution to journalArticle

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