Small Molecule Pathway Database
The Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing more than 30,000 small molecule pathways found in humans. SMPDB provides detailed pathway diagrams for metabolic pathways, metabolic disease pathways, metabolite signaling pathways, and drug-action pathways. All pathways include information on relevant organs, subcellular compartments, cofactors, protein locations, metabolite locations, chemical structures, and protein quaternary structures. Each small molecule is hyperlinked to HMDB or DrugBank and each protein is hyperlinked to UniProt.
[{"category": "Individual", "contact_details": [{"contact_type": "email", "value": "david.wishart@ualberta.ca"}], "label": "David Wishart", "orcid": "0000-0002-3207-2434"}, {"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://smpdb.ca/"}], "label": "The Metabolomics Innovation Centre (TMIC)"}]
[{"category": "GraphProduct", "description": "Neo4j database dump of the Clinical Knowledge Graph and additional relationships", "dump_format": "neo4j", "edge_count": 220000000, "format": "mixed", "id": "clinicalkg.graph", "name": "CKG Graph Dump", "node_count": 16000000, "original_source": ["uniprot", "tissues", "string", "stitch", "smpdb", "signor", "sider", "refseq", "reactome", "phosphositeplus", "pfam", "oncokb", "mutationds", "intact", "hpa", "hmdb", "hgnc", "gwascatalog", "foodb", "drugbank", "disgenet", "diseases", "dgidb", "corum", "cancer-genome-interpreter", "doid", "bto", "efo", "go", "hp", "snomedct", "mod", "mi", "ms", "uo"], "product_url": "https://data.mendeley.com/datasets/mrcf7f4tc2/1"}, {"category": "GraphProduct", "description": "Neo4j database dump of the Clinical Knowledge Graph and additional relationships", "dump_format": "neo4j", "edge_count": 220000000, "format": "mixed", "id": "cancer-genome-interpreter.clinicalkg.graph", "name": "CKG Graph Dump", "node_count": 16000000, "original_source": ["uniprot", "tissues", "string", "stitch", "smpdb", "signor", "sider", "refseq", "reactome", "phosphositeplus", "pfam", "oncokb", "mutationds", "intact", "hpa", "hmdb", "hgnc", "gwascatalog", "foodb", "drugbank", "disgenet", "diseases", "dgidb", "corum", "cancer-genome-interpreter", "doid", "bto", "efo", "go", "hp", "snomedct", "mod", "mi", "ms", "uo"], "product_url": "https://data.mendeley.com/datasets/mrcf7f4tc2/1"}, {"category": "GraphProduct", "description": "Core UniBioMap graph edges file.", "format": "csv", "id": "unibiomap.links", "name": "UniBioMap Graph Links", "original_source": ["unibiomap", "hpa", "go", "bindingdb", "foodb", "tcdb", "biogrid", "ctd", "chebi", "stitch", "tcm-bank", "intact", "uniprot", "unichem", "pubchem", "batman", "string", "ncbigene", "drugbank", "kegg", "sider", "compath", "phosphositeplus", "hp", "chembl", "reactome", "smpdb", "bioblinker", "hijazi20", "uberon", "hmdb", "medgen", "umls", "mesh", "inchikey", "uci", "omim"], "product_file_size": 1406201678, "product_url": "https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv"}, {"category": "GraphProduct", "description": "Auxiliary UniBioMap graph annotations and metadata.", "format": "tsv", "id": "unibiomap.auxs", "name": "UniBioMap Graph Auxiliaries", "original_source": ["unibiomap", "hpa", "go", "bindingdb", "foodb", "tcdb", "biogrid", "ctd", "chebi", "stitch", "tcm-bank", "intact", "uniprot", "unichem", "pubchem", "batman", "string", "ncbigene", "drugbank", "kegg", "sider", "compath", "phosphositeplus", "hp", "chembl", "reactome", "smpdb", "bioblinker", "hijazi20", "uberon", "hmdb", "medgen", "umls", "mesh", "inchikey", "uci", "omim"], "product_file_size": 591290539, "product_url": "https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv"}, {"category": "GraphProduct", "description": "Predicted UniBioMap graph edges with confidence scores.", "format": "csv", "id": "unibiomap.pred", "name": "UniBioMap Predicted Graph", "original_source": ["unibiomap", "hpa", "go", "bindingdb", "foodb", "tcdb", "biogrid", "ctd", "chebi", "stitch", "tcm-bank", "intact", "uniprot", "unichem", "pubchem", "batman", "string", "ncbigene", "drugbank", "kegg", "sider", "compath", "phosphositeplus", "hp", "chembl", "reactome", "smpdb", "bioblinker", "hijazi20", "uberon", "hmdb", "medgen", "umls", "mesh", "inchikey", "uci", "omim"], "product_file_size": 2484982268, "product_url": "https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv"}, {"category": "GraphProduct", "description": "Full unfiltered UniBioMap predicted graph edges file.", "format": "csv", "id": "unibiomap.pred.full", "name": "UniBioMap Predicted Graph (Full)", "original_source": ["unibiomap", "hpa", "go", "bindingdb", "foodb", "tcdb", "biogrid", "ctd", "chebi", "stitch", "tcm-bank", "intact", "uniprot", "unichem", "pubchem", "batman", "string", "ncbigene", "drugbank", "kegg", "sider", "compath", "phosphositeplus", "hp", "chembl", "reactome", "smpdb", "bioblinker", "hijazi20", "uberon", "hmdb", "medgen", "umls", "mesh", "inchikey", "uci", "omim"], "product_file_size": 6303875907, "product_url": "https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv"}]
{"activity_status": "active", "category": "DataSource", "contacts": [{"category": "Individual", "contact_details": [{"contact_type": "email", "value": "david.wishart@ualberta.ca"}], "label": "David Wishart", "orcid": "0000-0002-3207-2434"}, {"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://smpdb.ca/"}], "label": "The Metabolomics Innovation Centre (TMIC)"}], "creation_date": "2025-12-03T00:00:00Z", "description": "The Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing more than 30,000 small molecule pathways found in humans. SMPDB provides detailed pathway diagrams for metabolic pathways, metabolic disease pathways, metabolite signaling pathways, and drug-action pathways. All pathways include information on relevant organs, subcellular compartments, cofactors, protein locations, metabolite locations, chemical structures, and protein quaternary structures. Each small molecule is hyperlinked to HMDB or DrugBank and each protein is hyperlinked to UniProt.", "domains": ["pathways", "biological systems", "drug discovery", "chemistry and biochemistry"], "homepage_url": "https://smpdb.ca/", "id": "smpdb", "infores_id": "smpdb", "last_modified_date": "2025-12-03T00:00:00Z", "layout": "resource_detail", "name": "Small Molecule Pathway Database", "products": [{"category": "GraphProduct", "description": "Neo4j database dump of the Clinical Knowledge Graph and additional relationships", "dump_format": "neo4j", "edge_count": 220000000, "format": "mixed", "id": "clinicalkg.graph", "name": "CKG Graph Dump", "node_count": 16000000, "original_source": ["uniprot", "tissues", "string", "stitch", "smpdb", "signor", "sider", "refseq", "reactome", "phosphositeplus", "pfam", "oncokb", "mutationds", "intact", "hpa", "hmdb", "hgnc", "gwascatalog", "foodb", "drugbank", "disgenet", "diseases", "dgidb", "corum", "cancer-genome-interpreter", "doid", "bto", "efo", "go", "hp", "snomedct", "mod", "mi", "ms", "uo"], "product_url": "https://data.mendeley.com/datasets/mrcf7f4tc2/1"}, {"category": "GraphProduct", "description": "Neo4j database dump of the Clinical Knowledge Graph and additional relationships", "dump_format": "neo4j", "edge_count": 220000000, "format": "mixed", "id": "cancer-genome-interpreter.clinicalkg.graph", "name": "CKG Graph Dump", "node_count": 16000000, "original_source": ["uniprot", "tissues", "string", "stitch", "smpdb", "signor", "sider", "refseq", "reactome", "phosphositeplus", "pfam", "oncokb", "mutationds", "intact", "hpa", "hmdb", "hgnc", "gwascatalog", "foodb", "drugbank", "disgenet", "diseases", "dgidb", "corum", "cancer-genome-interpreter", "doid", "bto", "efo", "go", "hp", "snomedct", "mod", "mi", "ms", "uo"], "product_url": "https://data.mendeley.com/datasets/mrcf7f4tc2/1"}, {"category": "GraphProduct", "description": "Core UniBioMap graph edges file.", "format": "csv", "id": "unibiomap.links", "name": "UniBioMap Graph Links", "original_source": ["unibiomap", "hpa", "go", "bindingdb", "foodb", "tcdb", "biogrid", "ctd", "chebi", "stitch", "tcm-bank", "intact", "uniprot", "unichem", "pubchem", "batman", "string", "ncbigene", "drugbank", "kegg", "sider", "compath", "phosphositeplus", "hp", "chembl", "reactome", "smpdb", "bioblinker", "hijazi20", "uberon", "hmdb", "medgen", "umls", "mesh", "inchikey", "uci", "omim"], "product_file_size": 1406201678, "product_url": "https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv"}, {"category": "GraphProduct", "description": "Auxiliary UniBioMap graph annotations and metadata.", "format": "tsv", "id": "unibiomap.auxs", "name": "UniBioMap Graph Auxiliaries", "original_source": ["unibiomap", "hpa", "go", "bindingdb", "foodb", "tcdb", "biogrid", "ctd", "chebi", "stitch", "tcm-bank", "intact", "uniprot", "unichem", "pubchem", "batman", "string", "ncbigene", "drugbank", "kegg", "sider", "compath", "phosphositeplus", "hp", "chembl", "reactome", "smpdb", "bioblinker", "hijazi20", "uberon", "hmdb", "medgen", "umls", "mesh", "inchikey", "uci", "omim"], "product_file_size": 591290539, "product_url": "https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv"}, {"category": "GraphProduct", "description": "Predicted UniBioMap graph edges with confidence scores.", "format": "csv", "id": "unibiomap.pred", "name": "UniBioMap Predicted Graph", "original_source": ["unibiomap", "hpa", "go", "bindingdb", "foodb", "tcdb", "biogrid", "ctd", "chebi", "stitch", "tcm-bank", "intact", "uniprot", "unichem", "pubchem", "batman", "string", "ncbigene", "drugbank", "kegg", "sider", "compath", "phosphositeplus", "hp", "chembl", "reactome", "smpdb", "bioblinker", "hijazi20", "uberon", "hmdb", "medgen", "umls", "mesh", "inchikey", "uci", "omim"], "product_file_size": 2484982268, "product_url": "https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv"}, {"category": "GraphProduct", "description": "Full unfiltered UniBioMap predicted graph edges file.", "format": "csv", "id": "unibiomap.pred.full", "name": "UniBioMap Predicted Graph (Full)", "original_source": ["unibiomap", "hpa", "go", "bindingdb", "foodb", "tcdb", "biogrid", "ctd", "chebi", "stitch", "tcm-bank", "intact", "uniprot", "unichem", "pubchem", "batman", "string", "ncbigene", "drugbank", "kegg", "sider", "compath", "phosphositeplus", "hp", "chembl", "reactome", "smpdb", "bioblinker", "hijazi20", "uberon", "hmdb", "medgen", "umls", "mesh", "inchikey", "uci", "omim"], "product_file_size": 6303875907, "product_url": "https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv"}], "publications": [{"authors": ["Wishart DS", "Frolkis A", "Knox C", "et al."], "id": "https://doi.org/10.1093/nar/gkp1002", "preferred": true, "title": "SMPDB: The Small Molecule Pathway Database", "year": "2010"}, {"authors": ["Jewison T", "Su Y", "Disfany FM", "et al."], "id": "https://doi.org/10.1093/nar/gkt1067", "title": "SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database", "year": "2014"}], "synonyms": ["SMPDB"], "taxon": ["NCBITaxon:9606"]}