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.
As a greater volume of information becomes increasingly available across all disciplines, many approaches, such as document clustering and information visualization, have been proposed to help users manage information easily. However, most of these methods do not directly extract key concepts and their semantic relationships from document corpora, which could help better illuminate the conceptual structures within given information. To address this issue, we propose an approach called "Clonto" to process a document corpus, identify the key concepts, and automatically generate ontologies based on these concepts for the purpose of conceptualization. For a given document corpus, Clonto applies latent semantic analysis to identify key concepts, allocates documents based on these concepts, and utilizes WordNet to automatically generate a corpus-related ontology. The documents are linked to the ontology through the key concepts. Based on two test collections, the experimental results show that Clonto is able to identify key concepts, and outperforms four other clustering algorithms. Moreover, the ontologies generated by Clonto show significant informative conceptual structures.
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