Limits...
KEGG for linking genomes to life and the environment.

Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y - Nucleic Acids Res. (2007)

Bottom Line: KEGG BRITE is an ontology database representing functional hierarchies of various biological objects, including molecules, cells, organisms, diseases and drugs, as well as relationships among them.The KEGG resource is being expanded to suit the needs for practical applications.KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.

ABSTRACT
KEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking genomes to life through the process of PATHWAY mapping, which is to map, for example, a genomic or transcriptomic content of genes to KEGG reference pathways to infer systemic behaviors of the cell or the organism. In addition, KEGG provides a reference knowledge base for linking genomes to the environment, such as for the analysis of drug-target relationships, through the process of BRITE mapping. KEGG BRITE is an ontology database representing functional hierarchies of various biological objects, including molecules, cells, organisms, diseases and drugs, as well as relationships among them. KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps. In addition, smaller pathway modules are defined and stored in KEGG MODULE that also contains other functional units and complexes. The KEGG resource is being expanded to suit the needs for practical applications. KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers.

Show MeSH

Related in: MedlinePlus

The new KEGG metabolism map created as an SVG file.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2238879&req=5

Figure 1: The new KEGG metabolism map created as an SVG file.

Mentions: KEGG PATHWAY has been significantly expanded over the last 2 years with the addition of about 50 new pathway maps, mostly for signal transduction, cellular processes and human diseases. However, the traditional KEGG metabolic pathway maps are still most widely used including the KGML (KEGG XML) version. They are now supplemented with two new features introduced as a response to user feedback. The first feature is a global map shown in Figure 1, which is created as an SVG file by manually combining about 120 existing maps. Each node (circle) is a chemical compound and each line (curved or straight) connecting two nodes is a series of reactions (one to several reactions), which is also manually defined as a segment lacking branches. The new KEGG metabolism map allows the user to view and compare the entire metabolism, such as by mapping metagenomics data or microarray data. KGML users should also find the new KEGG metabolism map much easier to manipulate.Figure 1.


KEGG for linking genomes to life and the environment.

Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y - Nucleic Acids Res. (2007)

The new KEGG metabolism map created as an SVG file.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238879&req=5

Figure 1: The new KEGG metabolism map created as an SVG file.
Mentions: KEGG PATHWAY has been significantly expanded over the last 2 years with the addition of about 50 new pathway maps, mostly for signal transduction, cellular processes and human diseases. However, the traditional KEGG metabolic pathway maps are still most widely used including the KGML (KEGG XML) version. They are now supplemented with two new features introduced as a response to user feedback. The first feature is a global map shown in Figure 1, which is created as an SVG file by manually combining about 120 existing maps. Each node (circle) is a chemical compound and each line (curved or straight) connecting two nodes is a series of reactions (one to several reactions), which is also manually defined as a segment lacking branches. The new KEGG metabolism map allows the user to view and compare the entire metabolism, such as by mapping metagenomics data or microarray data. KGML users should also find the new KEGG metabolism map much easier to manipulate.Figure 1.

Bottom Line: KEGG BRITE is an ontology database representing functional hierarchies of various biological objects, including molecules, cells, organisms, diseases and drugs, as well as relationships among them.The KEGG resource is being expanded to suit the needs for practical applications.KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.

ABSTRACT
KEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking genomes to life through the process of PATHWAY mapping, which is to map, for example, a genomic or transcriptomic content of genes to KEGG reference pathways to infer systemic behaviors of the cell or the organism. In addition, KEGG provides a reference knowledge base for linking genomes to the environment, such as for the analysis of drug-target relationships, through the process of BRITE mapping. KEGG BRITE is an ontology database representing functional hierarchies of various biological objects, including molecules, cells, organisms, diseases and drugs, as well as relationships among them. KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps. In addition, smaller pathway modules are defined and stored in KEGG MODULE that also contains other functional units and complexes. The KEGG resource is being expanded to suit the needs for practical applications. KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers.

Show MeSH
Related in: MedlinePlus