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Spanish Named Entity Recognition in the Biomedical Domain

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Information Management and Big Data (SIMBig 2018)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 898))

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Abstract

Named Entity Recognition in the clinical domain and in languages different from English has the difficulty of the absence of complete dictionaries, the informality of texts, the polysemy of terms, the lack of accordance in the boundaries of an entity, the scarcity of corpora and of other resources available. We present a Named Entity Recognition method for poorly resourced languages. The method was tested with Spanish radiology reports and compared with a conditional random fields system.

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Notes

  1. 1.

    Bio-NER refers to biomedical named entity recognition systems.

  2. 2.

    CRF, are defined in Sect. 3.3.

  3. 3.

    Negex is the most popular system for detecting negations and their scope.

  4. 4.

    https://mmtx.nlm.nih.gov/MMTx/.

  5. 5.

    https://www.snomed.org/snomed-ct.

  6. 6.

    https://www.rsna.org/RadLex.aspx.

  7. 7.

    The Message Understanding Conference Scoring Software User’s Manual. https://www-nlpir.nist.gov/related_projects/muc/muc_sw/muc_sw_manual.html, accessed June 2017.

  8. 8.

    We consider that AE and FIs in the French dataset are anatomy and disorders hierarchies of UMLS. In the case of for German, what we consider AEs corresponds to organs and what we consider FI corresponds to symptoms, diagnoses and observations.

  9. 9.

    The paper is not available online. Results were discussed in a personal communication.

  10. 10.

    In Spanish they usually occur before the terms of interest.

  11. 11.

    Acronyms and abbreviations provided by the National Academy of Medicine of Colombia http://dic.idiomamedico.net/Siglas_y_abreviaturas and by the Spanish Ministry of Health http://www.redsamid.net/archivos/201612/diccionario-de-siglas-medicas.pdf?0.

  12. 12.

    in |in the |from.

  13. 13.

    Written as a regular expression.

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Author information

Authors and Affiliations

  1. Department of Computer Science, FCEyN, Universidad de Buenos Aires, Buenos Aires, Argentina

    Viviana Cotik

  2. Polytechnical University of Catalonia, Barcelona, Spain

    Horacio Rodríguez

  3. Universitat Pompeu Fabra, Barcelona, Spain

    Jorge Vivaldi

Authors
  1. Viviana Cotik
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  2. Horacio Rodríguez
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  3. Jorge Vivaldi
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Correspondence to Viviana Cotik .

Editor information

Editors and Affiliations

  1. Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, USA

    Juan Antonio Lossio-Ventura

  2. Fondazione Bruno Kessler, Trento, Italy

    Denisse Muñante

  3. Facultad de Ingeniería, University of the Pacific, Jesús María, Lima, Peru

    Hugo Alatrista-Salas

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Cotik, V., Rodríguez, H., Vivaldi, J. (2019). Spanish Named Entity Recognition in the Biomedical Domain. In: Lossio-Ventura, J., Muñante, D., Alatrista-Salas, H. (eds) Information Management and Big Data. SIMBig 2018. Communications in Computer and Information Science, vol 898. Springer, Cham. https://doi.org/10.1007/978-3-030-11680-4_23

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  • DOI: https://doi.org/10.1007/978-3-030-11680-4_23

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  • Online ISBN: 978-3-030-11680-4

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