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Examples
Pathway Database Links
| Pathway Database | Full Name | Support Formats | Download URL |
|---|---|---|---|
| Arabidopsis Reactome | A curated knowledgebase of plant biological pathways | BioPAX,SBML | http://www.arabidopsisreactome.org/download/index.html |
| BIND | Biomolecular Interaction Network Database | PSI-MI | http://bond.unleashedinformatics.com/ |
| BioGRID | Biological General Repository for Interaction Datasets | PSI-MI | http://www.thebiogrid.org/downloads.php |
| BioModels | BioModels Database | BioPAX,SBML | http://www.ebi.ac.uk/biomodels-main/news |
| Cancer Cell Map | The Cancer Cell Map | BioPAX | http://cbio.mskcc.org/cell_map/release/ |
| CORUM | Comprehensive resource of mammalian protein complexes | PSI-MI | http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html |
| CPDB | ConsensusPathDB | PSI-MI | http://cpdb.molgen.mpg.de/CPDB/daccess |
| DIP | Database of Interacting Proteins | PSI-MI | http://dip.doe-mbi.ucla.edu/dip/Download.cgi?SM=3 |
| HPRD | Human Protein Reference Database | PSI-MI | http://www.hprd.org/download |
| I2D | Interologous Interaction Database | PSI-MI | http://ophid.utoronto.ca/ophidv2.201/downloads.jsp |
| InnateDB | A Knowledge Resource for Innate Immunity Interactions and Pathways | PSI-MI | http://www.innatedb.ca/download.jsp |
| INOH | Integrating Network Objects with Hierarchies | BioPAX | http://www.inoh.org/download.html#PathwayData |
| IntAct | IntAct | PSI-MI | http://www.ebi.ac.uk/intact/main.xhtml?conversationContext=1 |
| InteroPorc | Automatic molecular interaction predictions | PSI-MI | http://biodev.extra.cea.fr/interoporc/Default.aspx |
| iRefIndex | Interaction Reference Index | PSI-MI | ftp://ftp.no.embnet.org/irefindex/data/ |
| KEGG | Kyoto Encyclopedia of Genes and Genomes | KGML | ftp://ftp.genome.jp/pub/kegg/ |
| MatrixDB | Extracellular matrix interactions database | PSI-MI | http://matrixdb.ibcp.fr/cgi-bin/download |
| MINT | Molecular Interaction Database | PSI-MI | ftp://mint.bio.uniroma2.it/pub/release/psi/current/ |
| MIPS CYGD | MIPS Comprehensive Yeast Genome Database | PSI-MI | ftp://ftpmips.gsf.de/yeast/ |
| MIPS-MPPI | MIPS Mammalian Protein-Protein Interaction Database | PSI-MI | http://mips.helmholtz-muenchen.de/proj/ppi/ |
| NetPath | NetPath | PSI-MI,BioPAX,SBML | http://www.netpath.org/browse |
| PANTHER | Protein ANalysis THrough Evolutionary Relationships | SBML | ftp://ftp.pantherdb.org/pathway/ |
| PC | Pathway Commons | PSI-MI,BioPAX | http://www.pathwaycommons.org/pc-snapshot/ |
| PID | NCI-Nature Pathway Interaction Database | BioPAX | http://pid.nci.nih.gov/download.shtml |
| PIMRider | Protein Interaction Map - Hybrigenics | PSI-MI | http://pimr.hybrigenics.com/PIMRider/PIMRider-Categorie/DATA-DOWNLOAD.html |
| Reactome | Reactome KnowledgeBase | BioPAX,SBML | http://www.reactome.org/download/index.html |
| Rhea | Reaction database | BioPAX | ftp://ftp.ebi.ac.uk/pub/databases/rhea/biopax/ |
| SGD Pathway Tools | Saccharomyces Genome Database Pathway Tools | BioPAX | http://downloads.yeastgenome.org/ |
| SignaLink | SignaLink: a signaling pathway resource | SBML | http://signalink.org/w/download.php |
| SPIKE | Signaling Pathway Integrated Knowledge Engine | BioPAX | http://www.cs.tau.ac.il/~spike/download.html |
| STKE | Signal Transduction Knowledge Environment | SBML | http://stke.sciencemag.org/cm/ |
| SYSTOMONAS | SYSTems biology of pseudOMONAS | SBML | http://www.systomonas.de/download.php |
| Yeast consensus metabolic network | A consensus reconstruction of yeast metabolism | SBML | http://www.comp-sys-bio.org/yeastnet/ |