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2016 ; 68
(ä): 47-57
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A method for the development of disease-specific reference standards vocabularies
from textual biomedical literature resources
#MMPMID26971304
Wang L
; Bray BE
; Shi J
; Del Fiol G
; Haug PJ
Artif Intell Med
2016[Mar]; 68
(ä): 47-57
PMID26971304
show ga
OBJECTIVE: Disease-specific vocabularies are fundamental to many knowledge-based
intelligent systems and applications like text annotation, cohort selection,
disease diagnostic modeling, and therapy recommendation. Reference standards are
critical in the development and validation of automated methods for
disease-specific vocabularies. The goal of the present study is to design and
test a generalizable method for the development of vocabulary reference standards
from expert-curated, disease-specific biomedical literature resources. METHODS:
We formed disease-specific corpora from literature resources like textbooks,
evidence-based synthesized online sources, clinical practice guidelines, and
journal articles. Medical experts annotated and adjudicated disease-specific
terms in four classes (i.e., causes or risk factors, signs or symptoms,
diagnostic tests or results, and treatment). Annotations were mapped to UMLS
concepts. We assessed source variation, the contribution of each source to build
disease-specific vocabularies, the saturation of the vocabularies with respect to
the number of used sources, and the generalizability of the method with different
diseases. RESULTS: The study resulted in 2588 string-unique annotations for heart
failure in four classes, and 193 and 425 respectively for pulmonary embolism and
rheumatoid arthritis in treatment class. Approximately 80% of the annotations
were mapped to UMLS concepts. The agreement among heart failure sources ranged
between 0.28 and 0.46. The contribution of these sources to the final vocabulary
ranged between 18% and 49%. With the sources explored, the heart failure
vocabulary reached near saturation in all four classes with the inclusion of
minimal six sources (or between four to seven sources if only counting terms
occurred in two or more sources). It took fewer sources to reach near saturation
for the other two diseases in terms of the treatment class. CONCLUSIONS: We
developed a method for the development of disease-specific reference
vocabularies. Expert-curated biomedical literature resources are substantial for
acquiring disease-specific medical knowledge. It is feasible to reach near
saturation in a disease-specific vocabulary using a relatively small number of
literature sources.