Skip to main content

MeKG: Building a Medical Knowledge Graph by Data Mining from MEDLINE

  • Conference paper
  • First Online:
Brain Informatics (BI 2019)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 11976))

Included in the following conference series:

Abstract

Mining data on a knowledge level can help to achieve a higher performance of a decision support system. This study built a knowledge graph based on MEDLINE that has a large number of articles in the medical domain. MEDLINE uses Medical Subject Headings (MeSH) for document index. Based on MeSH, articles are extracted from the MEDLINE correspondent to medical subjects. Using the MeSH as the backbone of knowledge base, the MEDLINE articles were used to generate instances which helped to populate the knowledge base. This approach facilitated the creation of a knowledge graph that was capable of discovering the hidden knowledge among concepts of MeSH. The knowledge graph had a significant effect on improving the quality of healthcare. The contribution of the research is on a framework for building knowledge bases. Moreover, the approach provided an essential source at the knowledge level for researchers in healthcare.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Banuqitah, H., Eassa, F., Jambi, K., Abulkhair, M.: Two level self-supervised relation extraction from MEDLINE using UMLS. Int. J. Data Min. Knowl. Manag. Process 6(3), 11–23 (2016)

    Article  Google Scholar 

  2. Bordes, A., Weston, J., Collobert, R., Bengio, Y.: Learning structured embeddings of knowledge bases. In: Twenty-Fifth AAAI Conference on Artificial Intelligence (2011)

    Google Scholar 

  3. Costa, J.P., et al.: Mining MEDLINE for the visualisation of a global perspective on biomedical knowledge. In: KDD 2018 (24th ACM SIGKDD Conference on Knowledge Discovery and Data Mining) (2018)

    Google Scholar 

  4. Ganguly, D., Roy, D., Mitra, M., Jones, G.J.: Word embedding based generalized language model for information retrieval. In: Proceedings of the 38th International ACM SIGIR Conference on Research and Development in Information Retrieval, pp. 795–798. ACM (2015)

    Google Scholar 

  5. Goh, W.P., Tao, X., Zhang, J., Yong, J.: Decision support systems for adoption in dental clinics: a survey. Knowl.-Based Syst. 104, 195–206 (2016)

    Article  Google Scholar 

  6. Mikolov, T., Sutskever, I., Chen, K., Corrado, G.S., Dean, J.: Distributed representations of words and phrases and their compositionality. In: Advances in Neural Information Processing Systems, pp. 3111–3119 (2013)

    Google Scholar 

  7. Nguyen, G.-H., Tamine, L., Soulier, L., Souf, N.: Learning concept-driven document embeddings for medical information search. In: ten Teije, A., Popow, C., Holmes, J.H., Sacchi, L. (eds.) AIME 2017. LNCS (LNAI), vol. 10259, pp. 160–170. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-59758-4_17

    Chapter  Google Scholar 

  8. Pham, T., Tao, X., Zhanag, J., Yong, J., Zhang, W., Cai, Y.: Mining heterogeneous information graph for health status classification. In: 2018 5th International Conference on Behavioral, Economic, and Socio-Cultural Computing (BESC), pp. 73–78. IEEE (2018)

    Google Scholar 

  9. Shi, L., Li, S., Yang, X., Qi, J., Pan, G., Zhou, B.: Semantic health knowledge graph: semantic integration of heterogeneous medical knowledge and services. BioMed Res. Int. 2017, 12 (2017)

    Google Scholar 

  10. Voskarides, N., Meij, E., Tsagkias, M., De Rijke, M., Weerkamp, W.: Learning to explain entity relationships in knowledge graphs. In: Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing (Volume 1: Long Papers), pp. 564–574 (2015)

    Google Scholar 

  11. Wang, H., Zhang, Q., Yuan, J.: Semantically enhanced medical information retrieval system: a tensor factorization based approach. IEEE Access 5, 7584–7593 (2017)

    Article  Google Scholar 

  12. Xu, C., et al.: RC-NET: a general framework for incorporating knowledge into word representations. In: Proceedings of the 23rd ACM International Conference on Information and Knowledge Management, pp. 1219–1228. ACM (2014)

    Google Scholar 

  13. Xu, R., Wang, Q.: Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing. BMC Bioinform. 14(1), 181 (2013)

    Article  MathSciNet  Google Scholar 

  14. Zheng, G., Callan, J.: Learning to reweight terms with distributed representations. In: Proceedings of the 38th International ACM SIGIR Conference on Research and Development in Information Retrieval, pp. 575–584. ACM (2015)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Thuan Pham .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Pham, T., Tao, X., Zhang, J., Yong, J., Zhou, X., Gururajan, R. (2019). MeKG: Building a Medical Knowledge Graph by Data Mining from MEDLINE. In: Liang, P., Goel, V., Shan, C. (eds) Brain Informatics. BI 2019. Lecture Notes in Computer Science(), vol 11976. Springer, Cham. https://doi.org/10.1007/978-3-030-37078-7_16

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-37078-7_16

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-37077-0

  • Online ISBN: 978-3-030-37078-7

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics