is a Data Source.
PubChem is an open chemistry database that collects information on chemical structures, identifiers, chemical and physical properties, biological activities, patents, health, safety, toxicity data, and other information.
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| pubchem.compounds.asn | PubChem Compounds ASN | ASN | Product | xml | Compound structures, properties, and ... |
| pubchem.compounds.sdf | PubChem Compounds SDF | SDF | Product | sdf | Compound structures, properties, and ... |
| pubchem.substances.asn | PubChem Substances ASN | ASN | Product | xml | PubChem substance information in ASN.... |
| pubchem.substances.sdf | PubChem Substances SDF | SDF | Product | sdf | PubChem substance information in SDF ... |
| pubchem.bioassay.asn | PubChem BioAssay ASN | ASN | Product | xml | PubChem BioAssay data in ASN.1 format |
| pubchem.bioassay.xml | PubChem BioAssay XML | XML | Product | xml | PubChem BioAssay data in XML format |
| pubchem.pug.rest | PubChem PUG REST API | pug-rest | Programming Interface | http | The PubChem Power User Gateway (PUG) ... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| biomarker.bkg.nodes.compound | BKG Compound Nodes | Compound.nodes.zip (871 B) | Graph | csv | had primary source | Nodes from PubChem Database |
| alzkb.browser | AlzKB Graph Database Browser | login | Graphical Interface | http | had primary source | A browser interface for a knowledge g... |
| alzkb.data | AlzKB Data Release (Version 2.0.0) | v2.0.0 | Graph | mixed | had primary source | Memgraph data release for AlzKB. |
| pharmkg.graph | PharmKG graph | 4077338 | Graph | mixed | had primary source | Cleaned benchmark graph (PharmKG-8k) ... |
| microbiomekg.api | MicrobiomeKG Plover TRAPI API | mbkp | Programming Interface | http | had primary source | Plover-hosted TRAPI web API for query... |
| icees-kg.graph | KGX distribution of the ICEES Exposures KP | 1.5.0 | Graph | kgx-jsonl | had primary source | KGX distribution of the ICEES Exposur... |
| icees-kg.trapi | ICEES KG TRAPI API | icees-kg-trapi | Programming Interface | 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... |
| unibiomap.links | UniBioMap Graph Links | unibiomap.links.csv (1.3 GB) | Graph | csv | had primary source | Core UniBioMap graph edges file. |
| unibiomap.auxs | UniBioMap Graph Auxiliaries | unibiomap.auxs.tsv (563.9 MB) | Graph | tsv | had primary source | Auxiliary UniBioMap graph annotations... |
| unibiomap.pred | UniBioMap Predicted Graph | unibiomap.pred.csv (2.3 GB) | Graph | csv | had primary source | Predicted UniBioMap graph edges with ... |
| unibiomap.pred.full | UniBioMap Predicted Graph (Full) | unibiomap.pred.full.csv (5.9 GB) | Graph | csv | had primary source | Full unfiltered UniBioMap predicted g... |
| forum.webapp | FORUM Web Application | forum-webapp.semantic-metabolomics.fr | Graphical Interface | http | had primary source | FORUM web application interface for s... |
| forum.api | FORUM API | openapi-documentation | Programming Interface | http | had primary source | FORUM REST API for programmatic acces... |
| forum.void | FORUM VoID Metadata | void (94.2 KB) | Documentation | ttl | had primary source | FORUM VoID (Vocabulary of Interlinked... |
| reprotox-kg.portal | ReproTox-KG Explorer | reprotox-kg | Graphical Interface | http | had primary source | Public web interface for querying and... |
| reprotox-kg.data | ReproTox-KG Downloads | downloads | Product | http | had primary source | Downloads page listing the ReproTox-K... |
| suppkg.source-data | SuppKG Source Data Repository | SuppKG | Process | http | had primary source | Source data directory used for SuppKG... |
| tera.chebi-to-mesh-csv | ChEBI to MeSH Mapping (CSV) | chebi_to_mesh.csv (76.8 KB) | Mapping | csv | had primary source | Mapping file linking ChEBI identifier... |
| pharmebinet.json | PharMeBINet JSON Release | content (3.4 GB) | Graph | json | was derived from | PharMeBINet V3 JSON release (Zenodo v... |
| pharmebinet.tsv | PharMeBINet TSV Release | content (3.5 GB) | Graph | tsv | was derived from | PharMeBINet V3 TSV release (Zenodo ve... |
| pharmebinet.graphml | PharMeBINet GraphML Release | content (3.8 GB) | Graph | mixed | was derived from | PharMeBINet V3 GraphML release (Zenod... |
| pharmebinet.neo4j | PharMeBINet Neo4j Database | content (7.7 GB) | Graph | neo4j | was derived from | PharMeBINet V3 Neo4j database release... |
| pharmebinet.neo4j.dump | PharMeBINet Neo4j Dump | content (7.5 GB) | Graph | neo4j | was derived from | PharMeBINet V3 Neo4j dump release (Ze... |
| repohub.sample-info.tsv ⚠ | Drug Repurposing Hub Sample Information TSV | repo-sample-annotation-20240610.txt (3.9 MB) | Product | tsv | was informed by | Latest physical sample-level metadata... |
| dsstoxdb.downloads | DSSTox Data Downloads | 5588566 | Mapping | mixed | was informed by | Downloadable Excel and CSV files cont... |
| gtrx.data ⚠ | gTRx Data | metadata | Product | mixed | was informed by | BioThings GTRx association collection... |
| markerdb.api | MarkerDB API | markerdb_api | Programming Interface | 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... |
| chemid.pubchem-source | ChemIDplus in PubChem | ChemIDplus | Graphical Interface | http | used | PubChem source page for ChemIDplus, p... |
| chemid.pubchem-guide | Accessing ChemIDplus Content from PubChem | Accessing_ChemIDplus_Content_from_PubChem.pdf | Documentation | http | used | NLM guide for locating migrated ChemI... |
| foodb.web | FooDB Web Interface | foodb.ca | Graphical Interface | http | 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 | mysql | was informed by | Complete FooDB database as MySQL dump |
| biobtree.api | BioBTree REST API | api | Programming Interface | http | had primary source | REST API for searching identifiers an... |
| genecards.web.interface | GeneCards Web Interface | www.genecards.org | Graphical Interface | http | had primary source | Web-based interface for searching and... |
| biobtree.graph.human-subgraph | BioBTree Knowledge Graph - Human Subgraph (KGX) | 20816742 | Graph | kgx | had primary source | Human-scoped, Neo4j-ready subgraph of... |
| forum.graph.dump | FORUM Knowledge Graph SPARQL Endpoint | sparql | Graph | http | had primary source | Public SPARQL endpoint (OpenLink Virt... |
| biomarker.bkg.edges.compound | BKG Compound Edges | Compound.edges.zip (1.3 KB) | Graph | csv | had primary source | Biomarker to Compound relationships (... |
| gp-kg.graph | GP-KG | GP_KG.txt (46.2 MB) | Graph | txt | was derived from | GP_KG.txt |
| molepro.graph.nodes | Nodes for Molecular Data KP | nodes.tsv (3.4 GB) | Graph | kgx | had primary source | KGX nodes for Molecular Data KP |
| molepro.graph.edges | Edges for Molecular Data KP | edges.tsv (18.8 GB) | Graph | kgx | had primary source | KGX edges for Molecular Data KP |
| unibiomap.compound_desc ⚠ | UniBioMap Compound Descriptions | compound_desc.json | Graph | json | had primary source | UniBioMap compound entity descriptions. |
| biobricks-pubchem-annotations.graph | BioBricks PubChem Annotations Graph | pubchem-annotations-kg | Graph | ttl | was derived from | RDF knowledge graph (Turtle) repackag... |
| ncatsgardkg.graph | NCATS GARD Knowledge Graph | processed | Graph | http | was influenced by | Integrated rare-disease knowledge gra... |
| micromap.api | MicroMap API | docs | Programming Interface | http | was derived from | REST API and MCP server over the prod... |
| onco.all_json | OnCo full corpus (JSON) | all.json (30.0 MB) | Graph | json | had primary source | Every OnCo record in one JSON file, e... |
| mps-db.portal ⚠ | MPS-Db Web Portal | mps.csb.pitt.edu | Graphical Interface | http | had primary source | MPS-Db web portal for browsing, analy... |
| klocd.portal | KLOCD Web Interface | www.organchip.cn | Graphical Interface | http | had primary source | KLOCD web interface for searching its... |
| molepro.api | MolePro API | api | Programming Interface | http | had primary source | MolePro API providing access to the k... |
| molepro.trapi | MolePro TRAPI Interface | ui | Programming Interface | http | had primary source | TRAPI-compliant interface for MolePro... |
| molepro.catalog | MolePro Knowledge Sources Catalog | transformers (2.0 MB) | Product | json | had primary source | Catalog of MolePro knowledge sources ... |
| stitch.portal | STITCH Web Portal | stitch-db.org | Product | http | had primary source | Web interface for searching and visua... |
| stitch.downloads | STITCH Data Downloads | download.pl | Product | tsv | had primary source | Downloadable data files containing ch... |
| stitch.api | STITCH API | access.pl?footer_active_subpage=apis | Programming Interface | http | had primary source | API for programmatic access to STITCH... |
| mychem.api | MyChem.info API | query | Programming Interface | json | had primary source | MyChem.info REST API (v1) for queryin... |
| babel.compendia | Babel Compendia | compendia | Product | json | had primary source | Babel compendia, one file per Biolink... |
| rdf-portal.sparql.pubchem | RDF Portal PubChem SPARQL Endpoint | sparql | Programming Interface | http | was derived from | SPARQL endpoint for PubChem RDF. |
| drugshot.drugrif | DrugRIF Drug-Publication Associations | DrugRIF.tsv.gz (8.6 MB) | Product | tsv | had primary source | About 2 million drug to PubMed articl... |
| comptox-dashboard.portal | CompTox Chemicals Dashboard Web Application | dashboard | Graphical Interface | http | was derived from | Web interface to the CompTox Chemical... |
| echemportal.portal | eChemPortal Search Portal | echemportal | Graphical Interface | http | was derived from | Web portal for searching participatin... |
| drugmonizome.libraries ⚠ | Drugmonizome Drug Set Libraries | libraries | Product | json | was derived from | The 35 Drugmonizome drug set librarie... |
| l1000fwd.drug-metadata | L1000FWD Drug Metadata | Drugs_metadata.csv (7.4 MB) | Product | csv | was informed by | Metadata for the profiled drugs and s... |
| sep-l1000.smiles-metadata | SEP-L1000 Compound SMILES Metadata | meta_SMILES.csv (3.8 MB) | Product | csv | was informed by | Compound metadata for 41,774 LINCS L1... |
| linked-discoveries.site | Linked Discoveries Web Interface | linkeddiscoveries.ncbi.nlm.nih.gov | Graphical Interface | http | was derived from | Interactive web interface for explori... |
PubChem is a database of chemical molecules and their activities against biological assays maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, which is part of the United States National Institutes of Health (NIH).
The system contains three primary databases:
PubChem data is available through a web interface, programmatically via the PUG REST API, and as bulk downloads via FTP. The system supports structure searches, chemical property information, biological activities, safety and toxicity information, patents, literature citations, and links to related resources.
All PubChem data is in the public domain and can be freely downloaded and used for both commercial and non-commercial purposes.
Created: May 04, 2025 | Last modified: July 14, 2026