Table 1.

Pathway databases.

PDB Name	Pathway focus	URL	Y.O.R.	Standard formats
EcoCyc	M,S	biocyc.org	1995	SBML, BioPAX
KEGG	M,S,D	kegg.jp	1996	BioPAX
RegulonDB	GR	regulondb.ccg.unam.mx	1997	BioPAX
MetaCyc	M	metacyc.org	1999	SBML, BioPAX
STRINGDB	PPI	string-db.org	2000	PSI-MI
PANTHER	S,D,PS	pantherdb.org	2004	SBML, SBGN, BioPAX
Gene Ontology	PPI,M,S	geneontology.org	2000
REACTOME	M,S,D	reactome.org	2005	SBML, SBGN, BioPAX, PSI-MI
MSigDb	M,S,GR	broadinstitute.org/gsea/msigdb	2005
Ingenuity Knowledge Base*	PPI,PCI,M,S,GR,D	ingenuity.com	2005
NCI PID	S,D	pid.nci.nih.gov	2006	BioPAX
WikiPathways	M,S,D	wikipathways.org	2008	BioPAX
Small Molecule Pathway DB	M,S	smpdb.ca	2009	SBML, BioPAX
ConsensusPathDB	PPI,PCI,M,S,GR	consensuspathdb.org	2009	BioPAX, PSI-MI
Pathway Commons	PPI,PCI,M,S	pathwaycommons.org	2010	BioPAX

A brief example of the diversity of available PDBs found online. The second column shows the kind of biological focus pursued by each database: (PPI, protein-protein intereactions; PCI, protein-compound interactions; M, metabolic; S, signaling; GR, gene regulation; D, diagrams; PS, protein sequence). The last column addresses the standard pathway languages adopted to provide data. Additionally, in the third column the links to web sites are supplied. YOR, Year of release.

^*Commercial database.