Metabolomics Workbench
The Metabolomics Workbench is a public repository for metabolomics data and metadata, serving as the National Metabolomics Data Repository (NMDR). It provides tools, protocols, training, and access to over 2,000 metabolomics studies containing data from more than 75,000 samples and 32,000 known metabolites. Funded by the NIH Common Fund from 2012-2022.
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{"activity_status": "active", "category": "DataSource", "contacts": [{"category": "Person", "contact_details": [{"contact_type": "email", "value": "fiehn@ucdavis.edu"}], "label": "Oliver Fiehn"}, {"category": "Person", "contact_details": [{"contact_type": "email", "value": "shankar@sdsc.edu"}], "label": "Shankar Subramaniam"}], "description": "The Metabolomics Workbench is a public repository for metabolomics data and metadata, serving as the National Metabolomics Data Repository (NMDR). It provides tools, protocols, training, and access to over 2,000 metabolomics studies containing data from more than 75,000 samples and 32,000 known metabolites. Funded by the NIH Common Fund from 2012-2022.", "domains": [], "homepage_url": "https://www.metabolomicsworkbench.org/", "id": "mw", "last_modified_date": "2025-11-26T00:00:00Z", "layout": "resource_detail", "name": "Metabolomics Workbench", "products": [{"category": "GraphProduct", "description": "Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access.", "dump_format": "neo4j", "id": "ubkg.neo4j", "name": "UBKG Neo4j Docker Distribution", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}, {"category": "GraphProduct", "description": "Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access.", "format": "csv", "id": "ubkg.csv", "name": "UBKG Ontology CSV Files", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}], "publications": [{"id": "https://doi.org/10.1038/s41592-019-0694-2", "journal": "Nature Methods", "title": "The Metabolomics program", "year": "2020"}], "synonyms": ["MW", "NMDR", "National Metabolomics Data Repository"], "warnings": ["This is an automatically generated stub page. Please replace with accurate information about this resource."]}