Nansu Zong1, Sungin Lee2, Jinhyun Ahn2, Hong-Gee Kim2. 1. Department of Biomedical Informatics, School of Medicine, University of California, San Diego, USA. Electronic address: nazong@ucsd.edu. 2. Biomedical Knowledge Engineering Laboratory, School of Dentistry, Seoul National University, South Korea.
Abstract
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.
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.
Authors: Simon Jupp; James Malone; Jerven Bolleman; Marco Brandizi; Mark Davies; Leyla Garcia; Anna Gaulton; Sebastien Gehant; Camille Laibe; Nicole Redaschi; Sarala M Wimalaratne; Maria Martin; Nicolas Le Novère; Helen Parkinson; Ewan Birney; Andrew M Jenkinson Journal: Bioinformatics Date: 2014-01-11 Impact factor: 6.937