TY - JOUR
T1 - Assessing the enrichment of dietary supplement coverage in the unified medical language system
AU - Vasilakes, Jake
AU - Bompelli, Anusha
AU - Bishop, Jeffrey R.
AU - Adam, Terrence J.
AU - Bodenreider, Olivier
AU - Zhang, Rui
N1 - Publisher Copyright:
© The Author(s) 2020.
PY - 2020/10/1
Y1 - 2020/10/1
N2 - Objective: We sought to assess the need for additional coverage of dietary supplements (DS) in the Unified Medical Language System (UMLS) by investigating (1) the overlap between the integrated DIetary Supplements Knowledge base (iDISK) DS ingredient terminology and the UMLS and (2) the coverage of iDISK and the UMLS over DS mentions in the biomedical literature. Materials and Methods: We estimated the overlap between iDISK and the UMLS by mapping iDISK to the UMLS using exact and normalized strings. The coverage of iDISK and the UMLS over DS mentions in the biomedical literature was evaluated via a DS named-entity recognition (NER) task within PubMed abstracts. Results: The coverage analysis revealed that only 30% of iDISK terms can be matched to the UMLS, although these cover over 99% of iDISK concepts. A manual review revealed that a majority of the unmatched terms represented new synonyms, rather than lexical variants. For NER, iDISK nearly doubles the precision and achieves a higher F1 score than the UMLS, while maintaining a competitive recall. Discussion: While iDISK has significant concept overlap with the UMLS, it contains many novel synonyms. Furthermore, almost 3000 of these overlapping UMLS concepts are missing a DS designation, which could be provided by iDISK. The NER experiments show that the specialization of iDISK is useful for identifying DS mentions. Conclusions: Our results show that the DS representation in the UMLS could be enriched by adding DS designations to many concepts and by adding new synonyms.
AB - Objective: We sought to assess the need for additional coverage of dietary supplements (DS) in the Unified Medical Language System (UMLS) by investigating (1) the overlap between the integrated DIetary Supplements Knowledge base (iDISK) DS ingredient terminology and the UMLS and (2) the coverage of iDISK and the UMLS over DS mentions in the biomedical literature. Materials and Methods: We estimated the overlap between iDISK and the UMLS by mapping iDISK to the UMLS using exact and normalized strings. The coverage of iDISK and the UMLS over DS mentions in the biomedical literature was evaluated via a DS named-entity recognition (NER) task within PubMed abstracts. Results: The coverage analysis revealed that only 30% of iDISK terms can be matched to the UMLS, although these cover over 99% of iDISK concepts. A manual review revealed that a majority of the unmatched terms represented new synonyms, rather than lexical variants. For NER, iDISK nearly doubles the precision and achieves a higher F1 score than the UMLS, while maintaining a competitive recall. Discussion: While iDISK has significant concept overlap with the UMLS, it contains many novel synonyms. Furthermore, almost 3000 of these overlapping UMLS concepts are missing a DS designation, which could be provided by iDISK. The NER experiments show that the specialization of iDISK is useful for identifying DS mentions. Conclusions: Our results show that the DS representation in the UMLS could be enriched by adding DS designations to many concepts and by adding new synonyms.
KW - Dietary supplements
KW - Named entity recognition
KW - Natural language processing
KW - Terminology
KW - Unified medical language system
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U2 - 10.1093/jamia/ocaa128
DO - 10.1093/jamia/ocaa128
M3 - Article
C2 - 32940692
AN - SCOPUS:85092244779
SN - 1067-5027
VL - 27
SP - 1547
EP - 1555
JO - Journal of the American Medical Informatics Association
JF - Journal of the American Medical Informatics Association
IS - 10
ER -