MaNER: A MedicAl Named Entity Recogniser

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9103)

Abstract

This paper describes a medicinal products and active ingredients named entity recogniser (MaNER) for Spanish technical documents. This rule-based system uses high quality and low-maintenance lexicons. Our results (F-measure 90 %) proves that dictionary-based approaches, without any deep natural language processing (e.g. POS tagging), can achieve a high performance in this task. Our system obtains better results when compared to similar systems.

Keywords

Named Entity Recognition Lexicon Medicinal product Active ingredient Spanish 

Notes

Acknowledgments

This paper has been partially supported by the Spanish Government (grant no. TIN2012-38536-C03-03 and TIN2012-31224)

References

  1. 1.
  2. 2.
    Cimino, J.J.: Desiderata for controlled medical vocabularies in the twenty-first century. Meth. Inf. Med. - Author manuscript; available in PMC 2012 August 10 37(4—-5), 394–403 (1998)Google Scholar
  3. 3.
    Cruanes Vilas, J.: Una aproximación léxico-semántica para el mapeado automático de medicamentos y su aplicación al enriquecimiento de ontologías farmacoterapéuticas. Ph.D. thesis, Universida de Alicante (2014). http://hdl.handle.net/10045/42146
  4. 4.
    Cunningham, H., Maynard, D., Bontcheva, K., Tablan, V., Aswani, N., Roberts, I., Gorrell, G., Funk, A., Roberts, A., Damljanovic, D., Heitz, T., Greenwood, M., Saggion, H., Petrak, J., Li, Y., Peters, W., Al, E.: Developing Language Processing Components with GATE Version 7 (A User Guide), vol. 8 (2012). http://gate.ac.uk
  5. 5.
    Deléger, L., Grouin, C., Zweigenbaum, P.: Extracting medical information from narrative patient records: the case of medication-related information. J. Am. Med. Inf. Assoc.: JAMIA 17(5), 555–558 (2010). doi: 10.1136/jamia.2010.003962 CrossRefGoogle Scholar
  6. 6.
    Doan, S., Bastarache, L., Klimkowski, S., Denny, J.C., Xu, H.: Integrating existing natural language processing tools for medication extraction from discharge summaries. J. Am. Med. Inf. Assoc. 17(5), 528–531 (2010). doi: 10.1136/jamia.2010.003855 CrossRefGoogle Scholar
  7. 7.
    Feldman, R., Sanger, J.: The Text Mining Handbook: Advanced Approaches in Analyzing Unstructured Data, 2009th edn. Cambridge University Press, New York (2009). doi: 10.1017/CBO9780511546914 Google Scholar
  8. 8.
    Friedman, C., Rindflesch, T.C., Corn, M.: Natural language processing: state of the art and prospects for significant progress, a workshop sponsored by the National Library of Medicine. J. Biomed. Inf. 46(5), 765–773 (2013). doi: 10.1016/j.jbi.2013.06.004 CrossRefGoogle Scholar
  9. 9.
    González-González, A.I., Sánchez Mateos, J., Sanz Cuesta, T., Riesgo Fuertes, R., Escortell Mayor, E., Hernández Fernández, T.: Estudio de las necesidadesde información generadas por los médicos de atención primaria (proyecto ENIGMA)*. Atención primaria 38(4), 219–224 (2006). http://www.sciencedirect.com/science/article/pii/S0212656706704814 CrossRefGoogle Scholar
  10. 10.
    Hamon, T., Grabar, N.: Linguistic approach for identification of medication names and related information in clinical narratives. J. Am. Med. Inf. Assoc. 17(5), 549–554 (2010). doi: 10.1136/jamia.2010.004036 CrossRefGoogle Scholar
  11. 11.
    Meystre, S.M., Thibault, J., Shen, S., Hurdle, J.F., South, B.R.: Textractor: a hybrid system for medications and reason for their prescription extraction from clinical text documents. J. Am. Med. Inf. Assoc. 17(5), 559–562 (2010). doi: 10.1136/jamia.2010.004028 CrossRefGoogle Scholar
  12. 12.
    Moreno, I., Moreda, P., Romá-Ferri, M.: Reconocimiento de entidades nombradas en dominios restringidos. In: Actas del III Workshop en Tecnologías de la Informática, pp. 41–57. Alicante, Spain (2012)Google Scholar
  13. 13.
    Sanchez-Cisneros, D., Aparicio Gali, F.: UEM-UC3M: an ontology-based named entity recognition system for biomedical texts. In: Proceedings of the Seventh International Workshop on Semantic Evaluation (SemEval 2013), vol. 2, pp. 622–627 (2013). http://www.aclweb.org/anthology/S13-2104
  14. 14.
    Segura-Bedmar, I., Martnez, P., Herrero-Zazo, M.: SemEval-2013 task 9: extraction of drug-drug interactions from biomedical texts (DDIExtraction 2013). In: Proceedings of the Seventh International Workshop on Semantic Evaluation (SemEval 2013), vol. 2011 (2013). www.aclweb.org/anthology/S13-2056
  15. 15.
    Segura-Bedmar, I., Revert, R., Martínez, P.: Detecting drugs and adverse events from spanish health social media streams. In: Proceedings of the 5th International Workshop on Health Text Mining and Information Analysis (Louhi) @ EACL 2014, pp. 106–115 (2014). https://www.aclweb.org/anthology/W/W14/W14-1117.pdf
  16. 16.
    Tikk, D., Solt, I.: Improving textual medication extraction using combined conditional random fields and rule-based systems. J. Am. Med. Inf. Assoc. 17(5), 540–544 (2010). doi: 10.1136/jamia.2010.004119 CrossRefGoogle Scholar
  17. 17.
    Uzuner, O., Solti, I., Cadag, E.: Extracting medication information from clinical text. J. Am. Med. Inf. Assoc. 17(5), 514–518 (2010). doi: 10.1136/jamia.2010.003947 CrossRefGoogle Scholar
  18. 18.
    WHO collaborating center for drug statistics methodology: guidelines for ATC classification and DDD assignment (2015). http://www.whocc.no/atc_ddd_publications/guidelines/
  19. 19.
    Yang, H.: Automatic extraction of medication information from medical discharge summaries. J. Am. Med. Inf. Assoc. 17(5), 545–548 (2010). doi: 10.1136/jamia.2010.003863 CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Isabel Moreno
    • 1
  • Paloma Moreda
    • 1
  • M. T. Romá-Ferri
    • 2
  1. 1.Department of Software and Computing SystemsUniversity of AlicanteAlicanteSpain
  2. 2.Department of NursingUniversity of AlicanteAlicanteSpain

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