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UBERT: A Novel Language Model for Synonymy Prediction at Scale in the UMLS Metathesaurus ...
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Evaluating Biomedical BERT Models for Vocabulary Alignment at Scale in the UMLS Metathesaurus ...
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Assessing the enrichment of dietary supplement coverage in the Unified Medical Language System
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In: J Am Med Inform Assoc (2020)
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Abstract:
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.
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Keyword:
Research and Applications
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URL: http://www.ncbi.nlm.nih.gov/pubmed/32940692 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7566420/ https://doi.org/10.1093/jamia/ocaa128
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IMIA LaMB WG publications: Medical Concept Representation ‐ the Years Beyond 2000 ...
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IMIA LaMB WG publications: Medical Concept Representation ‐ the Years Beyond 2000 ...
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IMIA LaMB WG publications: 'Biomedical Semantics in the Big Data Era' - conference paper introducing the related workshop, MEDINFO, 2015 ...
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IMIA LaMB WG publications: 'Biomedical Semantics in the Big Data Era' - conference paper introducing the related workshop, MEDINFO, 2015 ...
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Auditing SNOMED CT Hierarchical Relations Based on Lexical Features of Concepts in Non-Lattice Subgraphs
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In: Computer Science Faculty Publications (2018)
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Interoperability of Medication Classification Systems: Lessons Learned Mapping Established Pharmacologic Classes (EPCs) to SNOMED CT
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Auditing SNOMED CT hierarchical relations based on lexical features of concepts in non-lattice subgraphs
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“Hybrid Topics” -- Facilitating the Interpretation of Topics Through the Addition of MeSH Descriptors to Bags of Words
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Mining Non-Lattice Subgraphs for Detecting Missing Hierarchical Relations and Concepts in SNOMED CT
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In: Computer Science Faculty Publications (2017)
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Context-Driven Automatic Subgraph Creation for Literature-Based Discovery
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In: Kno.e.sis Publications (2015)
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iExplore: Interactive Browsing and Exploring Biomedical Knowledge
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In: Amit P. Sheth (2014)
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A Graph-Based Recovery and Decomposition of Swanson’s Hypothesis using Semantic Predications
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In: Krishnaprasad Thirunarayan (2014)
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Context-Driven Automatic Subgraph Creation for Literature-Based Discovery
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In: Amit P. Sheth (2014)
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Context-Driven Automatic Subgraph Creation for Literature-Based Discovery
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In: Krishnaprasad Thirunarayan (2014)
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A Graph-Based Recovery and Decomposition of Swanson’s Hypothesis using Semantic Predications
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In: Amit P. Sheth (2014)
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iExplore: Interactive Browsing and Exploring Biomedical Knowledge
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In: Krishnaprasad Thirunarayan (2014)
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A Graph-Based Recovery and Decomposition of Swanson’s Hypothesis using Semantic Predications
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In: Kno.e.sis Publications (2013)
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