Abstract
In the creation of diagnostic decision support systems (DDSS) it is crucial to have validated and precise knowledge in order to create accurate systems. Typically, medical experts are the source of this knowledge, but it is not always possible to obtain all the desired information from them. Another valuable source could be medical books or articles describing the diagnosis of diseases managed by the DDSS, but again, it is not easy to extract this information. In this paper we present the results of our research, in which we have used Web scraping and a combination of natural language processing techniques to extract diagnostic criteria from MedlinePlus articles about infectious diseases.
The erratum of this chapter can be found under DOI 10.1007/978-3-319-19776-0_16
An erratum to this chapter can be found at http://dx.doi.org/10.1007/978-3-319-19776-0_16
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Notes
- 1.
- 2.
- 3.
- 4.
- 5.
- 6.
- 7.
- 8.
- 9.
- 10.
References
Tsumoto, S.: Automated extraction of medical expert system rules from clinical databases based on rough set theory. Inf. Sci. 12(1–4), 67–84 (1998)
Tan, K.C., Yu, Q., Heng, C.M., Lee, T.H.: Evolutionary computing for knowledge discovery in medical diagnosis. Artif. Intell. Med. 27, 129–154 (2003)
Hahn, U., Romacker, M., Schulz, S.: medSynDiKATe—a natural language system for the extraction of medical information from findings reports. Int. J. Med. Inf. 67(1–3), 63–74 (2002)
Amaral, M.B., Roberts, A., Rector, A.L.: NLP techniques associated with the OpenGALEN ontology for semi-automatic textual extraction of medical knowledge: abstracting and mapping equivalent linguistic and logical constructs. In: Proceedings if the AMIA Annual Symposium, pp. 76–80 (2000)
Aronson, A.R.: Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. In: Proceedings of the AMIA Annual Symposium, pp. 17–21 (2001)
Hamosh, A., Scott, A.F., Amberger, J.S., Bocchini, C.A., McKusick, V.A.: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33(1), 514–517 (2005)
Köhler, S., et al.: The human phenotype ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 42(D1), 966–974 (2014)
Bodenreider, O.: The unified medical language system (UMLS): integrating biomedical terminology. Nucleic Acids Res. 32(1), 267–270 (2004)
Okumura, T., Aramaki, E., Tateisi, Y.: Clinical vocabulary and clinical finding concepts in medical literature. In: Proceedings of the International Joint Conference on Natural Language Processing Workshop on Natural Language Processing for Medical and Healthcare Fields, pp. 7–13 (2013)
Okumura, T., Tateisi, Y.: A lightweight approach for extracting disease-symptom relation with MetaMap toward automated generation of Disease Knowledge Base. Health Inf. Sci. 164–172 (2012)
Wu, Y., Denny, J.C., Rosenbloom, S.T., Miller, R.A., Giuse, D.A., Xu, H.A.: comparative study of current clinical natural language processing systems on handling abbreviations in discharge summaries. In: Proceedings of the AMIA Annual Symposium, pp. 997–1003 (2012)
Denecke, K.: Extracting medical Concepts from medical social media with clinical NLP tools: a qualitative study. In: Proceedings of the Fourth Workshop on Building and Evaluation Resources for Health and Biomedical Text Processing (2014)
Rodríguez-González, A., Martinez-Romero, M., Egaña-Aranguren, M., Wilkinson, M.D.: Nanopublishing clinical diagnoses: tracking diagnostic knowledge base content and utilization. In: IEEE 27th International Symposium on Computer-Based Medical Systems (CBMS), pp. 335–340 (2014)
Zhou, X.Z., Menche, J., Barabási, A.-L., Sharma, A.: Human symptoms–disease network. Nat. Commun. 5 (2013)
Acknowledgments
Alejandro Rodríguez González’s and Mark Wilkinson’s work is supported by Isaac Peral Programme of the UPM. Marcos Martínez-Romero work has been supported by a Postdoc Fellowship from the Xunta de Galicia, Spain (ref. POS-A/2013/197).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Rodríguez-González, A., Martínez-Romero, M., Costumero, R., Wilkinson, M.D., Menasalvas-Ruiz, E. (2015). Diagnostic Knowledge Extraction from MedlinePlus: An Application for Infectious Diseases. In: Overbeek, R., Rocha, M., Fdez-Riverola, F., De Paz, J. (eds) 9th International Conference on Practical Applications of Computational Biology and Bioinformatics. Advances in Intelligent Systems and Computing, vol 375. Springer, Cham. https://doi.org/10.1007/978-3-319-19776-0_9
Download citation
DOI: https://doi.org/10.1007/978-3-319-19776-0_9
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-19775-3
Online ISBN: 978-3-319-19776-0
eBook Packages: EngineeringEngineering (R0)