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2016 ; 939
(ä): 139-166
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Text Mining for Precision Medicine: Bringing Structure to EHRs and Biomedical
Literature to Understand Genes and Health
#MMPMID27807747
Simmons M
; Singhal A
; Lu Z
Adv Exp Med Biol
2016[]; 939
(ä): 139-166
PMID27807747
show ga
The key question of precision medicine is whether it is possible to find
clinically actionable granularity in diagnosing disease and classifying patient
risk. The advent of next-generation sequencing and the widespread adoption of
electronic health records (EHRs) have provided clinicians and researchers a
wealth of data and made possible the precise characterization of individual
patient genotypes and phenotypes. Unstructured text-found in biomedical
publications and clinical notes-is an important component of genotype and
phenotype knowledge. Publications in the biomedical literature provide essential
information for interpreting genetic data. Likewise, clinical notes contain the
richest source of phenotype information in EHRs. Text mining can render these
texts computationally accessible and support information extraction and
hypothesis generation. This chapter reviews the mechanics of text mining in
precision medicine and discusses several specific use cases, including database
curation for personalized cancer medicine, patient outcome prediction from
EHR-derived cohorts, and pharmacogenomic research. Taken as a whole, these use
cases demonstrate how text mining enables effective utilization of existing
knowledge sources and thus promotes increased value for patients and healthcare
systems. Text mining is an indispensable tool for translating genotype-phenotype
data into effective clinical care that will undoubtedly play an important role in
the eventual realization of precision medicine.
|*Precision Medicine
[MESH]
|Data Mining/*statistics & numerical data
[MESH]
|Databases, Factual
[MESH]
|Electronic Health Records/*statistics & numerical data
[MESH]