Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows

Journal of Biomedical Semantics
Xiao FuSophia Ananiadou

Abstract

Chronic obstructive pulmonary disease (COPD) is a life-threatening lung disorder whose recent prevalence has led to an increasing burden on public healthcare. Phenotypic information in electronic clinical records is essential in providing suitable personalised treatment to patients with COPD. However, as phenotypes are often "hidden" within free text in clinical records, clinicians could benefit from text mining systems that facilitate their prompt recognition. This paper reports on a semi-automatic methodology for producing a corpus that can ultimately support the development of text mining tools that, in turn, will expedite the process of identifying groups of COPD patients. A corpus of 30 full-text papers was formed based on selection criteria informed by the expertise of COPD specialists. We developed an annotation scheme that is aimed at producing fine-grained, expressive and computable COPD annotations without burdening our curators with a highly complicated task. This was implemented in the Argo platform by means of a semi-automatic annotation workflow that integrates several text mining tools, including a graphical user interface for marking up documents. When evaluated using gold standard (i.e., manually validated) ann...Continue Reading

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Citations

Dec 19, 2015·Journal of Biomedical Semantics·Larisa N SoldatovaNigam H Shah
May 18, 2016·Database : the Journal of Biological Databases and Curation·Riza Batista-NavarroSophia Ananiadou
Sep 4, 2016·Database : the Journal of Biological Databases and Curation·Qinghua WangCecilia N Arighi
Nov 27, 2016·Database : the Journal of Biological Databases and Curation·Piotr PrzybyłaSophia Ananiadou
Dec 24, 2018·Database : the Journal of Biological Databases and Curation·Aurore BritanPascale Gaudet

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Methods Mentioned

BETA
X-ray

Software Mentioned

Argo
Phenoscape
Phenex
Phenotype
GoldenGATE
GENIA Tagger
OpenAccess
BioC
NERsuite
NCBO Annotator

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