122 5 Survey of Ontologies in Bioinformatics
signaling, genetic regulatory, and genetic pathways. BioPAX is an OWL on-
tology.
KEGG http://www.genome.ad.jp/kegg
The Kyoto Encyclopedia of Genes and Genomes (Kanehisa and Goto 2000;
Kanehisa et al. 2002) is the primary database resource of the Japanese Genome-
Net service for understanding higher-order functional meanings and utilities
of the cell or the organism from its genome information. KEGG consists of
the PATHWAY database for the computerized knowledge of molecular in-
teraction networks such as pathways and complexes, the GENES database
for information about genes and proteins generated by genome sequencing
projects, and the LIGAND database for information about chemical com-
pounds and chemical reactions that are relevant to cellular processes. In ad-
dition to these three main databases, limited amounts of experimental data
for microarray gene expression profiles and yeast two-hybrid systems are
stored in the EXPRESSION and BRITE databases, respectively. Furthermore,
a new database, named SSDB, is available for exploring the universe of all
protein coding genes in the complete genomes and for identifying functional
links and ortholog groups. The data objects in the KEGG databases are all
represented as graphs and various computational methods are developed to
detect graph features that can be related to biological functions.
The KEGG Markup Language (KGML) is the exchange format of the KEGG
graph objects, especially the KEGG pathway maps that are manually drawn
and updated. KGML enables automatic drawing of KEGG pathways and
provides facilities for computational analysis and modeling of protein net-
works and chemical networks.
EcoCyc ecocyc.org
EcoCyc is an organism-specific pathway database that describes the metabolic
and signal transduction pathways ofE. coliK12 MG1655, its enzymes, and
its transport proteins (Karp et al. 2002c). EcoCyc and MetaCyc are part of the
BioCyc relational database, which is available as a collection of flat files.
MetaCyc metacyc.org/
MetaCyc is a metabolic-pathway database that describes nonredundant, ex-
perimentally elucidated metabolic pathways from more than 240 different
organisms. (Karp et al. 2002c). Applications of MetaCyc include pathway
analysis of genomes, metabolic engineering, and biochemistry education.
MetaCyc and EcoCyc are queried using the Pathway Tools GUI, which pro-
vides a wide variety of query operations and visualization tools (Karp et al.
2002b).