GOClonto: An ontological clustering approach for conceptualizing PubMed abstracts

Authors:
Hai-Tao Zheng;Charles Borchert;Hong-Gee Kim
Affiliations:
Biomedical Knowledge Engineering Laboratory, BK21 College of Dentistry, Seoul National University, 28 Yeongeon-dong, Jongro-gu, Seoul 110-749, Republic of Korea and Graduate School at Shenzhen, Ts ...;Biomedical Knowledge Engineering Laboratory, BK21 College of Dentistry, Seoul National University, 28 Yeongeon-dong, Jongro-gu, Seoul 110-749, Republic of Korea;Biomedical Knowledge Engineering Laboratory, BK21 College of Dentistry, Seoul National University, 28 Yeongeon-dong, Jongro-gu, Seoul 110-749, Republic of Korea
Venue:
Journal of Biomedical Informatics
Year:
2010

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Abstract

Concurrent with progress in biomedical sciences, an overwhelming of textual knowledge is accumulating in the biomedical literature. PubMed is the most comprehensive database collecting and managing biomedical literature. To help researchers easily understand collections of PubMed abstracts, numerous clustering methods have been proposed to group similar abstracts based on their shared features. However, most of these methods do not explore the semantic relationships among groupings of documents, which could help better illuminate the groupings of PubMed abstracts. To address this issue, we proposed an ontological clustering method called GOClonto for conceptualizing PubMed abstracts. GOClonto uses latent semantic analysis (LSA) and gene ontology (GO) to identify key gene-related concepts and their relationships as well as allocate PubMed abstracts based on these key gene-related concepts. Based on two PubMed abstract collections, the experimental results show that GOClonto is able to identify key gene-related concepts and outperforms the STC (suffix tree clustering) algorithm, the Lingo algorithm, the Fuzzy Ants algorithm, and the clustering based TRS (tolerance rough set) algorithm. Moreover, the two ontologies generated by GOClonto show significant informative conceptual structures.