A database for post-genome analysis.

By Minoru Kanehisa. 1997

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Citations in the corpus

SWEETLEAD: an In Silico Database of Approved Drugs, Regulated Chemicals, and Herbal Isolates for Computer-Aided Drug Discovery (2013, background): “While several databases are available containing vast amounts of chemical data[22-30], when querying these databases for a given drug conflicting information is occasionally retrieved.”
Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. (2000, background): “…has been fully sequenced and annotated, the entire metabolic map representing all the metabolic reactions taking place in the cell can be constructed, and extensive on-line databases have collected this information for a number of organisms (Kanehisa, 1997; Karp et al., 1998; Selkov et al., 1998).”
Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities (2005, methodology): “We first replicated the result of [21] by directly applying popular the off-the-shelf gene expression tools, CLUSTER and TreeView [52], to perform single-linkage hierarchical clustering on the KEGG vectors from several communities (Figure 1).”
The KEGG databases at GenomeNet (2002, methodology): “The primary resource of the GenomeNet is the Kyoto Encyclopedia of Genes and Genomes (KEGG) ( 2 ).”
Development of a BACarray translational profiling approach for the molecular characterization of CNS cell types (2008, background): “GO terms delineate the known molecular functions, biological processes, and cellular localizations (components) for a particular gene (Ashburner et al., 2000), whereas KEGG pathways summarize known molecular interaction and reaction networks (Kanehisa, 1997).”
Using the KEGG Database Resource (2005, background): “First, it is a comprehensive drug information resource for approved drugs in Japan, U.S.A., and Europe uniﬁed based on the chemical structures and/or chemical components.”
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes (2005, background): “It is important to note that there are large and ongoing efforts that address similar objectives—most notably the KEGG (http://www.genome.jp/kegg/kegg2.html) ( 22 ,23), GO (http://www.geneontology.org/) (5) and MetaCyc (http:// metacyc.org/) (24) projects.”
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema (2004, methodology): “For example, data from the Gene Ontology (GO) (9), Enzyme Commission (http://www.chem.qmul.ac.uk/iubmb/enzyme/), KEGG Pathways ( 10 ,11) and NCBI resources (including LocusLink, OMIM, SNP and BookShelf) (12) are mapped onto structures and loaded into the database.”
Significance analysis of functional categories in gene expression studies: a structured permutation approach (2005, background): “At the other extreme, detailed pathways are being developed for the direct interaction of genes at the translational level ( Kanehisa, 1997 ), based on careful study of model organisms.”
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary (2005, methodology): “Wecalculate similarity using BLASTX for a new DNA sequence and BLASTP for a new proteinsequence(Altschul etal .,1990,1997).”
From genomics to chemical genomics: new developments in KEGG (2005, methodology): “The KEGG database project was initiated in 1995, the last year of the ﬁrst 5-year phase of the Japanese Human Genome Programme (1).”
KOBAS server: a web-based platform for automated annotation and pathway identification (2006, unknown): “Towards this goal, we have previously studied the KEGG Orthology (KO) ( 10 ,11), part of the KEGG suite of resources (12), as an alternative controlled vocabulary (13).”
Bio-PEPA: A framework for the modelling and analysis of biological systems (2009, methodology): “We focus on biochemical networks, such as those collected in the Biomodels Database [48] and KEGG [43].”