Kinase pathway database: an integrated protein-kinase and NLP-based protein-interaction resource.
Protein kinases play a crucial role in the regulation of cellular functions. Various kinds of information about these molecules are important for understanding signaling pathways and organism characteristics. We have developed the Kinase Pathway Database, an integrated database involving major completely sequenced eukaryotes. It contains the classification of protein kinases and their functional conservation, ortholog tables among species, protein-protein, protein-gene, and protein-compound interaction data, domain information, and structural information. It also provides an automatic pathway graphic image interface. The protein, gene, and compound interactions are automatically extracted from abstracts for all genes and proteins by natural-language processing (NLP). The method of automatic extraction uses phrase patterns and the GENA protein, gene, and compound name dictionary, which was developed by our group. With this database, pathways are easily compared among species using data with more than 47,000 protein interactions and protein kinase ortholog tables. The database is available for querying and browsing at http://kinasedb.ontology.ims.u-tokyo.ac.jp/.
Koike
Asako
A
Human Genome Center, Institute of Medical Science, University of Tokyo, Shirokane-dai, Minato-Ku, Tokyo 108-8639, Japan.
Kobayashi
Yoshiyuki
Y
Takagi
Toshihisa
T
D000818:Animals; D017173:Caenorhabditis elegans / Q000145:classification / Q000201:enzymology; D029742:Caenorhabditis elegans Proteins / Q000145:classification; D030541:Databases, Genetic / Q000145:classification*; D029721:Drosophila Proteins / Q000145:classification; D004331:Drosophila melanogaster / Q000145:classification / Q000201:enzymology; D006801:Humans; D020407:Internet; D051379:Mice; D009323:Natural Language Processing; D010770:Phosphotransferases / Q000145:classification* / Q000378:metabolism*; D025941:Protein Interaction Mapping / Q000145:classification*; D011494:Protein Kinases / Q000145:classification* / Q000378:metabolism*; D051381:Rats; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000201:enzymology; D029701:Saccharomyces cerevisiae Proteins / Q000145:classification
D029742:Caenorhabditis elegans Proteins; D029721:Drosophila Proteins; D029701:Saccharomyces cerevisiae Proteins; D010770:Phosphotransferases; D011494:Protein Kinases