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- W2271340329 abstract "The Gene Ontology (GO) is a large public database that not only provides a set of controlled biological and biochemical vocabularies (terms) to describe gene products based upon their functions in the cell, but also contains gene annotation data from heterogeneous data sources. Although the controlled biochemical or biological vocabularies in the GO database address the need for consistent descriptions of genes in different data sources, there is still not an accurate and effective method to quantitatively determine the functional similarities of genes or gene products based on gene annotation information from heterogeneous data sources. To address this critical need, a novel method to decode a GO term's semantics (biological meanings) into a numeric value by aggregating the semantic contributions of its ancestor terms including this term in the GO graph is proposed. In turn, a family of new algorithms for calculating the similarity of GO terms is proposed. Based on the semantic similarities of GO terms used for annotating genes, new algorithms to measure the functional similarities of genes are designed. Our methods, which are capable of finding functionally equivalent or functionally related proteins that are not homologous, are independent of their sequence similarities. The results of using one of these algorithms to measure the functional similarities of genes in pathways retrieved from the Saccharomyces Genome Database (SGD) and the outcomes of clustering these genes based on the similarity values obtained by the algorithm are shown to be consistent with the existing biological experiments. Furthermore, a set of online tools for GO similarity measurement, gene similarity measurement and knowledge discovery have been developed. Formal analysis demonstrate the correctness of algorithms on which these tools base, and experimental studies show the efficiency of these tools. These tools have been widely used by biomedical researchers all over the world." @default.
- W2271340329 created "2016-06-24" @default.
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- W2271340329 date "2008-01-01" @default.
- W2271340329 modified "2023-09-25" @default.
- W2271340329 title "Biomedical knowledge discovery using the gene ontology database" @default.
- W2271340329 hasPublicationYear "2008" @default.
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