Supporting inter-topic entity search for biomedical Linked Data based on heterogeneous relationships

Nansu Zong, Sungin Lee, Jinhyun Ahn, Hong Gee Kim

Research output: Contribution to journalArticlepeer-review


Objective The keyword-based entity search restricts search space based on the preference of search. When given keywords and preferences are not related to the same biomedical topic, existing biomedical Linked Data search engines fail to deliver satisfactory results. This research aims to tackle this issue by supporting an inter-topic search—improving search with inputs, keywords and preferences, under different topics. Methods This study developed an effective algorithm in which the relations between biomedical entities were used in tandem with a keyword-based entity search, Siren. The algorithm, PERank, which is an adaptation of Personalized PageRank (PPR), uses a pair of input: (1) search preferences, and (2) entities from a keyword-based entity search with a keyword query, to formalize the search results on-the-fly based on the index of the precomputed Individual Personalized PageRank Vectors (IPPVs). Results Our experiments were performed over ten linked life datasets for two query sets, one with keyword-preference topic correspondence (intra-topic search), and the other without (inter-topic search). The experiments showed that the proposed method achieved better search results, for example a 14% increase in precision for the inter-topic search than the baseline keyword-based search engine. Conclusion The proposed method improved the keyword-based biomedical entity search by supporting the inter-topic search without affecting the intra-topic search based on the relations between different entities.

Original languageEnglish (US)
Pages (from-to)217-229
Number of pages13
JournalComputers in Biology and Medicine
StatePublished - Aug 1 2017


  • Biomedical Linked Data
  • Inter-topic search
  • Keywords-based entity search
  • Personalized PageRank

ASJC Scopus subject areas

  • Health Informatics
  • Computer Science Applications


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