Kinase pathway database: An integrated protein-kinase and NLP-based protein-interaction resource
Kinase pathway database: An integrated protein-kinase and NLP-based protein-interaction resource
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DOI：
10.1101/gr.835903
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发表时间：
2003-06-01
期刊：
影响因子：
7
通讯作者：
Takagi, T
中科院分区：
文献类型：
--
作者：
Koike, A;Kobatashi, Y;Takagi, T
蛋白激酶在细胞功能的调节中起着至关重要的作用。关于这些分子的各种信息对于理解信号通路和生物体特征是重要的。我们已经开发了激酶途径数据库，一个包含主要完整测序的真核生物的综合数据库。它包含蛋白激酶的分类和它们的功能保守性，物种间的直系同源表，蛋白质-蛋白质，蛋白质-基因，蛋白质-化合物相互作用数据，结构域信息和结构信息。它还提供了一个自动路径图形图像界面。蛋白质、基因和化合物相互作用通过自然语言处理（NLP）从所有基因和蛋白质的摘要中自动提取。自动抽取的方法使用短语模式和我们小组开发的GENA蛋白质、基因和化合物名称词典。有了这个数据库，物种间的途径很容易比较！使用超过47，000个蛋白质相互作用和蛋白激酶直系同源物表的数据。该数据库可在http://kinasedb.ontology上查询和浏览。ims.u-tokyo.ac.jp/.
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 specie!; 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/.