Enrichment of French Biomedical Ontologies with UMLS Concepts and Semantic Types for Biomedical Named Entity Recognition Though Ontological Semantic Annotation

Andon Tchechmedjiev 1, 2 Clement Jonquet 1, 3
1 SMILE - Système Multi-agent, Interaction, Langage, Evolution
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
2 ADVANSE - ADVanced Analytics for data SciencE
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : Medical terminologies and ontologies are a crucial resource for semantic annotation of biomedical text. In French, there are considerably less resources and tools to use them than in English. Some terminologies from the Unified Medical Language System have been translated but often the identifiers used in the UMLS Metathesaurus, that make its huge integrated value, have been lost during the process. In this work, we present our method and results in enriching seven French versions of UMLS sources with UMLS Concept Unique Identifiers and Semantic Types based on information extracted from class labels, multilingual translation mappings and codes. We then measure the impact of the enrichment through the application of the SIFR Annotator, a service to identify ontology concepts in free text deployed within the SIFR BioPortal, a repository for French biomedical ontologies and terminologies. We use the Quaero Corpus to evaluate.
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https://hal-lirmm.ccsd.cnrs.fr/lirmm-01605517
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Andon Tchechmedjiev, Clement Jonquet. Enrichment of French Biomedical Ontologies with UMLS Concepts and Semantic Types for Biomedical Named Entity Recognition Though Ontological Semantic Annotation. LOTKS: Language, Ontology, Terminology and Knowledge Structures, Sep 2017, Montpellier, France. ⟨lirmm-01605517v2⟩

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