Skip to main content

An Efficient Semantic Document Similarity Calculation Method Based on Double-Relations in Gene Ontology

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

Part of the book series: Smart Innovation, Systems and Technologies ((SIST,volume 157))

  • 631 Accesses

Abstract

Semantic text mining is a challenging research topic in recent years. Many types of research focus on measuring the similarity of two documents with ontologies such as Medical Subject Headings (Mesh) and Gene Ontology (GO). However, most of the researches considered the single relationship in an ontology. To represent the document comprehensively, a semantic document similarity calculation method is proposed, based on utilizing Average Maximum Match algorithm with double-relations in GO. In the experiment, the results show that the double-relations based similarity calculation method is better than traditional semantic similarity measurements.

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

References

  1. Danushka, B., Georgios, K., Sophia, A.: A cross-lingual similarity measure for detecting biomedical term translations. PLoS One 10(6), 7–15 (2015)

    Google Scholar 

  2. Spasić, I., Ananiadou, S.: A flexible measure of contextual similarity for biomedical terms. In: Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing, pp. 197–208 (2005)

    Google Scholar 

  3. Rey-Long, L.: Passage-based bibliographic coupling: an inter-article similarity measure for biomedical articles. PLoS One 10(10), 6–10 (2015)

    Google Scholar 

  4. Chen, C., Hsieh, S., Weng, Y.: Semantic similarity measure in biomedical domain leverage Web Search Engine. In: 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology (2010)

    Google Scholar 

  5. Wu, Z., Palmer, M.: Verbs semantics and lexical selection. In: Proceedings of the 32nd Annual Meeting of the Associations for Computational Linguistics (ACL’94), pp. 133–138 (1994)

    Google Scholar 

  6. Leacock, C., Chodorow, M.: Filling in a sparse training space for word sense identification. In: Proceedings of the 32nd Annual Meeting of the Associations for Computational Linguistics (ACL94), pp. 248–256 (1994)

    Google Scholar 

  7. Li, Y., Bandar, Z., McLean, D.: An approach for measuring semantic similarity between words using multiple information sources. IEEE Trans. Knowl. Data Eng. Bioinform. 15(4), 871–882 (2003)

    Article  Google Scholar 

  8. Choudhury, J., Kimtani, D.K., Chakrabarty, A.: Text clustering using a word net-based knowledge-base and the Lesk algorithm. Int. J. Comput. Appl. 48(21), 20–24 (2012)

    Google Scholar 

  9. 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 

  10. 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. Bibliometr. 19(11), 95–130 (1999)

    Article  Google Scholar 

  11. Lin, D.: Principle-based parsing without overgeneration. In: 31st Annual Meeting of the Association for Computational Linguistics, pp. 112–120. Association for Computational Linguistics, USA (1993)

    Google Scholar 

  12. Zhang, X., Jing, L., Hu, X., et al.: A comparative study of ontology based term similarity measures on PubMed document clustering. In: International Conference on Database Systems, pp. 115–126. Springer, Berlin, Heidelberg (2007)

    Google Scholar 

  13. Jing, Z., Yuxuan, S., Shengwen, P., Xuhui, L., Hiroshi, M., Shanfeng, Z.: MeSHSim: an R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents. J. Bioinform. Comput. (2015) (BioMed Central)

    Google Scholar 

  14. Logeswari, S., Kandhasamy, P.: Designing a semantic similarity measure for biomedical document clustering. J. Med. Imaging Health Inform. 5(6), 1163–1170 (2015)

    Article  Google Scholar 

  15. The Gene Ontology Resource Home. http://geneontology.org/. Accessed 27 Feb 2019

  16. Wang, J.Z., Du, Z., Payattakool, R., Yu, P.S., Chen, C.F.: A new method to measure the semantic similarity of go terms. Bioinformatics 23(10), 1274–1281 (2007)

    Article  Google Scholar 

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

    Google Scholar 

  18. Dongen, V.: A cluster algorithm for graphs. In: Information Systems, pp. 1–40. CWI (2000)

    Google Scholar 

  19. Ester, M., Kriegel, H.-P., Sander, J., Xu, X.: A density-based algorithm for discovering clusters in large spatial databases with noise. In: KDD’96 Proceedings of the Second International Conference on Knowledge Discovery and Data Mining, pp. 226–231 (1996)

    Google Scholar 

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

    Google Scholar 

  21. Robertson, S.: Understanding inverse document frequency: on theoretical arguments for IDF. J. Doc. 60(5), 503–520 (2004)

    Article  Google Scholar 

Download references

Acknowledgements

This study was supported by the National Natural Science Foundation of China (61702324).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Meijing Li .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Singapore Pte Ltd.

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Hu, J., Li, M., Zhang, Z., Li, K. (2020). An Efficient Semantic Document Similarity Calculation Method Based on Double-Relations in Gene Ontology. In: Pan, JS., Li, J., Tsai, PW., Jain, L. (eds) Advances in Intelligent Information Hiding and Multimedia Signal Processing. Smart Innovation, Systems and Technologies, vol 157. Springer, Singapore. https://doi.org/10.1007/978-981-13-9710-3_19

Download citation

Publish with us

Policies and ethics