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KGDDS: A System for Drug-Drug Similarity Measure in Therapeutic Substitution based on Knowledge Graph Curation

Abstract

Measuring drug-drug similarity is important but challenging. Significant progresses have been made in drugs whose labeled training data is sufficient and available. However, handling data skewness and incompleteness with domain-specific knowledge graph, is still a relatively new territory and an under-explored prospect. In this paper, we present a system KGDDS for node-link-based bio-medical Knowledge Graph curation and visualization, aiding Drug-Drug Similarity measure. Specifically, we reuse existing knowledge bases to alleviate the difficulties in building a high-quality knowledge graph, ranging in size up to 7 million edges. Then we design a prediction model to explore the pharmacology features and knowledge graph features. Finally, we propose a user interaction model to allow the user to better understand the drug properties from a drug similarity perspective and gain insights that are not easily observable in individual drugs. Visual result demonstration and experimental results indicate that KGDDS can bridge the user/caregiver gap by facilitating antibiotics prescription knowledge, and has remarkable applicability, outperforming existing state-of-the-art drug similarity measures.

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  1. 1.

    https://ckan.org/

  2. 2.

    http://kw.fudan.edu.cn/apis/cndbpedia/

  3. 3.

    https://www.drugbank.ca/

  4. 4.

    disease-ontology.org/

  5. 5.

    infectiousdiseaseontology.org/

  6. 6.

    https://bioportal.bioontology.org/ontologies/IDODEN

  7. 7.

    https://pypi.python.org/pypi/Owlready

  8. 8.

    https://www.drugbank.ca/

  9. 9.

    sideeffects.embl.de/

  10. 10.

    https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT/

  11. 11.

    https://www.ncbi.nlm.nih.gov/pubmed/

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Acknowledgements

This work was financially supported by the National Natural Science Foundation of China (No.61602013), and the Shenzhen Fundamental Research Project (No. JCYJ20170818091546869, JCYJ20160330095313861). Min Yang was sponsored by CCF-Tencent Open Research Fund.

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Correspondence to Kai Lei.

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Shen, Y., Yuan, K., Dai, J. et al. KGDDS: A System for Drug-Drug Similarity Measure in Therapeutic Substitution based on Knowledge Graph Curation. J Med Syst 43, 92 (2019). https://doi.org/10.1007/s10916-019-1182-z

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Keywords

  • Drug-drug similarity
  • Knowledge graph
  • Therapeutic substitution
  • Medical knowledge curation
  • Visualization