is an Aggregator.
The Human Metabolome Database (HMDB) is a comprehensive curated knowledgebase of small molecule metabolites found in the human body, integrating chemical, clinical, biochemical, spectral, and physiological data along with associated enzyme, transporter, and disease information to support metabolomics, biomarker discovery, systems biology, and precision medicine research.
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infores:hmdb
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| hmdb.portal | HMDB Web Portal | www.hmdb.ca | GraphicalInterface | http | Web portal providing integrated searc... |
| hmdb.fasta.enzymes ⚠ | HMDB Enzyme Protein Sequences (FASTA) | downloads#protein-gene-sequences | Product | fasta | All metabolite metabolizing enzyme pr... |
| hmdb.fasta.genes ⚠ | HMDB Gene Sequences (FASTA) | downloads#protein-gene-sequences | Product | fasta | All metabolite metabolizing enzyme ge... |
| hmdb.structures.sdf ⚠ | HMDB Metabolite Structures (SDF) | downloads#structures | Product | sdf | All metabolite structures (SDF) |
| hmdb.xml.metabolites | HMDB All Metabolites (XML) | downloads#metabolite-protein-xml | Product | xml | All metabolites dataset (XML) |
| hmdb.xml.proteins | HMDB All Proteins (XML) | downloads#metabolite-protein-xml | Product | xml | All proteins dataset (XML) |
| hmdb.xml.metabolites.urine | HMDB Urine Metabolites (XML) | downloads#metabolite-protein-xml | Product | xml | Urine metabolites subset (XML) |
| hmdb.xml.metabolites.serum | HMDB Serum Metabolites (XML) | downloads#metabolite-protein-xml | Product | xml | Serum metabolites subset (XML) |
| hmdb.xml.metabolites.csf | HMDB CSF Metabolites (XML) | downloads#metabolite-protein-xml | Product | xml | Cerebrospinal fluid (CSF) metabolites... |
| hmdb.xml.metabolites.saliva | HMDB Saliva Metabolites (XML) | downloads#metabolite-protein-xml | Product | xml | Saliva metabolites subset (XML) |
| hmdb.xml.metabolites.feces | HMDB Feces Metabolites (XML) | downloads#metabolite-protein-xml | Product | xml | Feces metabolites subset (XML) |
| hmdb.xml.metabolites.sweat | HMDB Sweat Metabolites (XML) | downloads#metabolite-protein-xml | Product | xml | Sweat metabolites subset (XML) |
| hmdb.spectra.mass.images | HMDB Mass Spectra Images | downloads#spectra | Product | ❔ | Mass spectra image files archive |
| hmdb.spectra.nmr.fid | HMDB NMR Spectra FID Files | downloads#spectra | Product | ❔ | NMR spectra FID files archive |
| hmdb.spectra.nmr.peaklist | HMDB NMR Peaklists (TXT) | downloads#spectra | Product | txt | Raw NMR peaklist text files archive |
| hmdb.spectra.gc.predicted.txt | HMDB GC-MS Predicted Peaklists (TXT) | downloads#spectra | Product | txt | Predicted GC-MS spectra peaklist text... |
| hmdb.spectra.msms.predicted.txt | HMDB MS-MS Predicted Peaklists (TXT) | downloads#spectra | Product | txt | Predicted MS-MS spectra peaklist text... |
| hmdb.spectra.msms.experimental.txt | HMDB MS-MS Experimental Peaklists (TXT) | downloads#spectra | Product | txt | Experimental MS-MS spectra peaklist t... |
| hmdb.spectra.all.peaklists | HMDB All Raw Spectra Peaklists (TXT) | downloads#spectra | Product | txt | All raw spectra peaklists (aggregated... |
| hmdb.spectra.nmr.xml | HMDB NMR Spectra (XML) | downloads#spectra | Product | xml | NMR spectra collection (XML) |
| hmdb.spectra.gc.predicted.xml | HMDB GC-MS Predicted Spectra (XML) | downloads#spectra | Product | xml | Predicted GC-MS spectra collection (XML) |
| hmdb.spectra.gc.experimental.xml | HMDB GC-MS Experimental Spectra (XML) | downloads#spectra | Product | xml | Experimental GC-MS spectra collection... |
| hmdb.spectra.msms.predicted.xml | HMDB MS-MS Predicted Spectra (XML) | downloads#spectra | Product | xml | Predicted MS-MS spectra collection (XML) |
| hmdb.spectra.msms.experimental.xml | HMDB MS-MS Experimental Spectra (XML) | downloads#spectra | Product | xml | Experimental MS-MS spectra collection... |
| hmdb.spectra.all.xml | HMDB All Spectra (XML) | downloads#spectra | Product | xml | All spectra files aggregate (XML) |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| clinicalkg.graph | CKG Graph Dump | 1 | GraphProduct | mixed | had primary source | Neo4j database dump of the Clinical K... |
| automat.hmdb | hmdb_automat | 6715124699b6dbf0 | GraphProduct | kgx-jsonl | had primary source | HMDB Automat |
| cancer-genome-interpreter.clinicalkg.graph | CKG Graph Dump | 1 | GraphProduct | mixed | had primary source | Neo4j database dump of the Clinical K... |
| icees-kg.graph | KGX distribution of the ICEES Exposures KP | 1.5.0 | GraphProduct | kgx-jsonl | had primary source | KGX distribution of the ICEES Exposur... |
| icees-kg.trapi | ICEES KG TRAPI API | icees-kg-trapi | ProgrammingInterface | http | had primary source | Translator Reasoner API (TRAPI) endpo... |
| icees-kg.metadata | ICEES KG Metadata | metadata-metadata-get-icees-kg | Product | json | had primary source | Meta knowledge graph and metadata des... |
| rampdb.database | RaMP-DB Integrated Database | rampdb.nih.gov | DatabaseProduct | ❔ | had primary source | Multi-sourced relational database int... |
| unibiomap.links | UniBioMap Graph Links | unibiomap.links.csv (1.3 GB) | GraphProduct | csv | had primary source | Core UniBioMap graph edges file. |
| unibiomap.auxs | UniBioMap Graph Auxiliaries | unibiomap.auxs.tsv (563.9 MB) | GraphProduct | tsv | had primary source | Auxiliary UniBioMap graph annotations... |
| unibiomap.pred | UniBioMap Predicted Graph | unibiomap.pred.csv (2.3 GB) | GraphProduct | csv | had primary source | Predicted UniBioMap graph edges with ... |
| unibiomap.pred.full | UniBioMap Predicted Graph (Full) | unibiomap.pred.full.csv (5.9 GB) | GraphProduct | csv | had primary source | Full unfiltered UniBioMap predicted g... |
| ckg.graph | CKG Graph Database Dump | 1 | GraphProduct | neo4j | had primary source | Graph database dump and additional re... |
| medkb.site | MedKG Site | medkg | GraphicalInterface | ❔ | had primary source | Graphical interface for MedKG |
| rtx-kg2.graph.nodes | RTX-KG2.10.1c KGX JSONL Nodes | kg2c-2.10.1-v1.0-nodes.jsonl.gz (359.1 MB) | GraphProduct | kgx-jsonl | had primary source | Nodes for KGX distribution of the RTX... |
| rtx-kg2.graph.edges | RTX-KG2.10.1c KGX JSONL Edges | kg2c-2.10.1-v1.0-edges.jsonl.gz (1.7 GB) | GraphProduct | kgx-jsonl | had primary source | Edges for KGX distribution of the RTX... |
| rtx-kg2.neo4j | RTX-KG2 Neo4j | arax.ncats.io | ProgrammingInterface | ❔ | had primary source | Neo4j distribution of the RTX-KG2 as ... |
| pharmebinet.json | PharMeBINet JSON Release | content (1.8 GB) | GraphProduct | json | was derived from | PharMeBINet V2 JSON release published... |
| pharmebinet.tsv | PharMeBINet TSV Release | content (1.8 GB) | GraphProduct | tsv | was derived from | PharMeBINet V2 TSV release published ... |
| pharmebinet.graphml | PharMeBINet GraphML Release | content (1.9 GB) | GraphProduct | mixed | was derived from | PharMeBINet V2 GraphML release publis... |
| pharmebinet.neo4j | PharMeBINet Neo4j Database | content (3.6 GB) | GraphProduct | neo4j | was derived from | PharMeBINet V2 Neo4j database release... |
| pharmebinet.neo4j.dump | PharMeBINet Neo4j Dump | content (3.4 GB) | GraphProduct | neo4j | was derived from | PharMeBINet V2 Neo4j dump release pub... |
| markerdb.api | MarkerDB API | markerdb_api | ProgrammingInterface | http | was informed by | MarkerDB API documentation and endpoi... |
| markerdb.chemicals.tsv ⚠ | MarkerDB Chemical Biomarkers TSV | download_all_chemicals?format=tsv | Product | tsv | was informed by | TSV export of MarkerDB chemical bioma... |
| pathwhiz.pathways | PathWhiz Pathway Library | pathways | GraphicalInterface | http | was informed by | Public library of pathway diagrams th... |
| harmonizome.downloads | Harmonizome Downloads | download | Product | mixed | was derived from | Harmonizome 3.0 processed dataset dow... |
| harmonizome.kg-neo4j | Harmonizome Knowledge Graph Neo4j Database | harmonizome-kg.maayanlab.cloud | GraphProduct | neo4j | was derived from | Neo4j knowledge graph serialization o... |
| foodb.web | FooDB Web Interface | foodb.ca | GraphicalInterface | ❔ | was informed by | Web interface that allows searching, ... |
| foodb.data.csv | FooDB CSV Data | foodb_2020_4_7_csv.tar.gz (952.1 MB) | Product | csv | was informed by | Complete FooDB database in CSV format |
| foodb.data.xml | FooDB XML Data | foodb_2020_4_7_xml.tar.gz (6.3 GB) | Product | xml | was informed by | Complete FooDB database in XML format |
| foodb.data.json | FooDB JSON Data | foodb_2020_04_07_json.zip (86.6 MB) | Product | json | was informed by | Complete FooDB database in JSON format |
| foodb.data.mysql | FooDB MySQL Dump | foodb_2020_4_7_mysql.tar.gz (172.5 MB) | Product | ❔ | was informed by | Complete FooDB database as MySQL dump |
| biobtree.api | BioBTree REST API | api | ProgrammingInterface | http | had primary source | REST API for searching identifiers an... |
HMDB integrates chemical, clinical, biochemical, and spectral information for more than 200,000 human metabolites, linking each to rich metadata (biofluid concentrations, pathways, spectra, disease associations, enzymes, and transporters). Download packages provide structured XML, spectral collections, and sequence datasets. Use of large portions of HMDB requires proper citation and (for commercial reuse) permission.
Please cite the core HMDB publications (HMDB 1.0–5.0) as listed on the website; for current analyses, the HMDB 5.0 paper (Nucleic Acids Research 2022, D622–D631) is recommended.
HMDB data are freely available for academic/non-commercial research with appropriate citation. Commercial reuse requires explicit permission; see the downloads page for terms.
Contact form available via the portal for inquiries and permissions.
Created: August 12, 2025 | Last modified: May 30, 2026