A literature-driven method to calculate similarities among diseases

Hyunjin Kim, Youngmi Yoon, Jaegyoon Ahn, Sanghyun Park

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)


Background: "Our lives are connected by a thousand invisible threads and along these sympathetic fibers, our actions run as causes and return to us as results". It is Herman Melville's famous quote describing connections among human lives. To paraphrase the Melville's quote, diseases are connected by many functional threads and along these sympathetic fibers, diseases run as causes and return as results. The Melville's quote explains the reason for researching disease-disease similarity and disease network. Measuring similarities between diseases and constructing disease network can play an important role in disease function research and in disease treatment. To estimate disease-disease similarities, we proposed a novel literature-based method. Methods and results: The proposed method extracted disease-gene relations and disease-drug relations from literature and used the frequencies of occurrence of the relations as features to calculate similarities among diseases. We also constructed disease network with top-ranking disease pairs from our method. The proposed method discovered a larger number of answer disease pairs than other comparable methods and showed the lowest p-value. Conclusions: We presume that our method showed good results because of using literature data, using all possible gene symbols and drug names for features of a disease, and determining feature values of diseases with the frequencies of co-occurrence of two entities. The disease-disease similarities from the proposed method can be used in computational biology researches which use similarities among diseases.

Original languageEnglish
Pages (from-to)108-122
Number of pages15
JournalComputer Methods and Programs in Biomedicine
Issue number2
Publication statusPublished - 2015 Nov

Bibliographical note

Funding Information:
This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIP) ( NRF-2015R1A2A1A05001845 ). We also appreciate Mr. Junsik Kim's proofreading efforts.

Publisher Copyright:
© 2015 Elsevier Ireland Ltd.

All Science Journal Classification (ASJC) codes

  • Software
  • Computer Science Applications
  • Health Informatics


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