Table 2

External databases successfully imported into cPath.

Database Name

Database Type

URL

Release Date Tested

Data Format used for cPath Import

Database Stats


Cancer Cell Map

Signaling Pathways

http://cancer.cellmap.org webcite

April, 2006

BioPAX, Level 2

Pathways: 10

Interactions: 2,104

Physical Entities: 899

Database of Interacting Proteins (DIP) [54, 55]

Protein-Protein Interactions

http://dip.doe-mbi.ucla.edu/ webcite

April, 2006

PSI-MI, Level 1

Interactions: 54,511

Physical Entities: 19,003

Ecocyc [56]

Metabolic and Signaling Pathways

http://ecocyc.org/ webcite Registration required to download data

March, 2006

BioPAX, Level 1

Pathways: 224

Interactions: 4,644

Physical Entities: 3,511

Human Protein Reference Database (HPRD) [57]

Protein-Protein Interactions

http://hprd.org/ webcite Registration required to download data

Sept, 2005

PSI-MI, Level 1

Interactions: 4,450

Physical Entities: 12,226

IntAct [46]

Protein-Protein Interactions

http://www.ebi.ac.uk/intact webcite

May, 2006

PSI-MI, Level 1

Interactions: 67,816

Physical Entities: 28,006

KEGG [58, 59]

Metabolic Pathways

ftp://ftp.genome.jp/pub/db/community/biopax/ webcite

July, 2006

BioPAX, Level 2

Human Data Only Pathways: 108

Interactions: 3,285

Physical Entities: 2,018

Molecular Interaction Database (MINT) [45]

Protein-Protein Interactions

http://mint.bio.uniroma2.it/mint/ webcite

May, 2005

PSI-MI, Level 1

Interactions: 44,904

Physical Entities: 16,325

Reactome [47]

Metabolic and Signaling Pathways

http://reactome.org/ webcite

May, 2006

BioPAX, Level 2

Human Data Only Pathways: 775

Interactions: 2,962

Physical Entities: 3,197


Cerami et al. BMC Bioinformatics 2006 7:497   doi:10.1186/1471-2105-7-497

Open Data