Skip to main content

An Efficient Tool for Semantic Biomedical Document Analysis

  • Conference paper
  • First Online:
Advances in Intelligent Information Hiding and Multimedia Signal Processing

Abstract

With the rapid growth of biomedical documents, finding out interested documents efficiently becomes a challenging for researchers. To improve the efficiency and display biomedical information in a more direct way, a medical knowledge graph-based semantic text analysis tool is developed. This tool is based on improved bag-of-words and ontology-based semantic text mining algorithms, supporting visualized biomedical conception and documents analysis. The testing results show that proposed models perform well on medical documents clustering, accuracy in different dataset is above 82% and the best one reaches 96%.

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 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover 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

Similar content being viewed by others

References

  1. Stanford CoreNLP 4.0.0: https://corenlp.run/. Last accessed 2020-04-16

  2. NLPIR: https://github.com/NLPIR-team/NLPIR. Last accessed 2020-04-28

  3. Word2Vec: https://radimrehurek.com/gensim/models/word2vec.html. Last accessed 2020-04-28

  4. Zhang, Y., Jia, Y., Fu, L., Wang, X.: AceMap academic map and AceKG academic knowledge graph for academic data visualization. J. Shanghai Jiaotong Univ. (Sci.) 52(10), 1357–1362 (2018)

    Google Scholar 

  5. Singhal, A.: Introducing the knowledge graph: things, not strings. https://goo-gleblog.blogspot.com/2012/05/introduc-ing-knowledge-graph-things-not.html. Last accessed 2020-05-05

  6. NCBI MESH: https://www.ncbi.nlm.nih.gov/mesh. Last accessed 2020-07-01

  7. Yu, G.: Using meshes for MeSH term enrichment and semantic analyses. Bioinformatics 21(21) (2018)

    Google Scholar 

  8. Resnik, O.: Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity and natural language. J. Artif. Intell. Res. 19, 95–1130 (1999)

    Article  Google Scholar 

  9. Lin, D.: Principle-based parsing without overgeneration. In: Proceedings of 31st Annual Meeting on Association for Computational Linguistics (ACL’93), Association for Computational Linguistics, Stroudsburg, PA, USA, pp. 112–120 (1993)

    Google Scholar 

  10. Lord, P., Stevens, R., Brass, A., Goble, C.: Investigating semantic similarity measures across the gene ontology: the relationship between sequence and annotation. Bioinformatics 19(10), 1275–1283 (2003)

    Article  Google Scholar 

  11. Jiang, J., Conrath, D.: Semantic similarity based on corpus statistics and lexical taxonomy. Proceedings of the International Conference on Research in Computational Linguistics (1997)

    Google Scholar 

  12. Luo, Z., Shi, M.-W., Yang, Z., Zhang, H.-Y., Chen, Z.: pyMeSHSim: an integrative python package to realize biomedical named entity recognition, normalization and comparison. https://doi.org/10.1101/459172 (2018)

  13. Zhou, J., Shui, Y., Peng, S., Li, X., Mamitsuka, H., Zhu, S.: MeSHSim: an R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents. J. Bioinform. Comput. Biol. 13(06), 1542002 (2015)

    Article  Google Scholar 

  14. Leacock, C., Chodorow, M.: Filling in a sparse training space for word sense identification. ms (1994)  

    Google Scholar 

  15. Wu, Y., Zhao, S., Li, C., et al.: Text classification method based on TF-IDF and cosine similarity. J. Chin. Inf. Process. 31(05), 138–145 (2017)

    Google Scholar 

  16. PubMed: https://pubmed.ncbi.nlm.nih.gov/. Last accessed 2020-03-01

  17. Python.Scrapy 2.1 documentation. https://scrapy.org. Last accessed 2020-04-28

  18. UMLS: https://umls.nlm.nih.gov/. Last accessed 2020-04-28

  19. MetaMap Document: https://metamap.nlm.nih.gov/Docs/. Last accessed 2020-04-28

  20. MacKay, D.: An example inference task: clustering. In: Information Theory, Inference and Learning Algorithms, pp. 284–292, Cambridge University Press, Cambridge (2003)

    Google Scholar 

  21. Zare, H., Shooshtari, P., Gupta, A., Brinkman, R.: Data reduction for spectral clustering to analyze high throughput flow cytometry data. BMC Bioinformatics 11(1) (2010)

    Google Scholar 

  22. Spring Boot: https://spring.io/projects/spring-boot. Last accessed 2020-04-28

  23. Hersh, W., Cohen, A., Yang, J., Bhupatiraju, R.T., Roberts, P., Hearst, M.: Trec 2005 genomics track overview. In: TREC 2005 Notebook, pp. 14–25 (2005)

    Google Scholar 

  24. Evaluation of clustering. https://nlp.stanford.edu/IR-book/html/htmledition/evaluation-of-clustering-1.html. Last accessed 2020-04-28

Download references

Acknowledgements

This research was supported by the National Natural Science Foundation of China (Grant No. 61702324 and Grant No. 61911540482) in People’s Republic of China, and by the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT and Future Planning (NRF-2019K2A9A2A06020672).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Keun Ho Ryu .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Li, M., Hu, J., Ryu, K.H. (2021). An Efficient Tool for Semantic Biomedical Document Analysis. In: Pan, JS., Li, J., Ryu, K.H., Meng, Z., Klasnja-Milicevic, A. (eds) Advances in Intelligent Information Hiding and Multimedia Signal Processing. Smart Innovation, Systems and Technologies, vol 212. Springer, Singapore. https://doi.org/10.1007/978-981-33-6757-9_63

Download citation

Publish with us

Policies and ethics