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PubChem
HealthData.Gov
Updated Oct 29, 2026
About this dataset
PubChem contains the chemical structures of small organic molecules and information on their biological activities. PubChem includes substance information, compound structures, and bioactivity data in three primary databases, PCSubstance, PCCompound, and PCBioAssay, respectively. PubChem is integrated with Entrez, NCBI's primary search engine, and also provides compound neighboring, sub/superstructure, similarity structure, bioactivity data, and other searching features. Technical documentation at http://pubchem.ncbi.nlm.nih.gov/help.html#faq
Data and resources (8)
- HTML
API - PubChem Power User Gateway (PUG)
The PubChem Power User Gateway (PUG) provides access to PubChem services via programmatic interfaces (REST, SOAP, . The basic design principle is straightforward. There is a single CGI (pug.cgi, referred to hereafter as simply PUG) that is the central gateway to multiple PubChem functions. PUG…
Modified Jun 29, 2026
- HTML
PubChem Standardization Service
Standardization in PubChem is the validation and determination of a unique chemical structure that is used to create a PubChem Compound from one or more submitted Substance records. Standardization is part of the PubChem Upload pipeline for submitted records with valid chemical structures. It…
Modified Jun 29, 2026
- HTML
PubChem Structure Search - Query Interface
PubChem Structure Search provides various chemical search types and options.
Modified Jun 29, 2026
- HTML
PubChem Upload
The PubChem Upload tool enables you to submit data to the PubChem Substance and PubChem BioAssay databases, or update your existing data, including chemical structures, experimental biological activity results, annotations, siRNA data and more. Once your submission is reviewed and published in…
Modified Jun 29, 2026
- HTML
PubChem Substance
The PubChem Substance Database contains descriptions of samples, from a variety of sources, and links to biological screening results that are available in PubChem BioAssay. If the chemical contents of a sample are known, the description includes links to PubChem Compound.
Modified Jun 29, 2026
- HTML
PubChem Compound
The PubChem Compound Database contains validated chemical depiction information provided to describe substances in PubChem Substance. Structures stored within PubChem Compounds are pre-clustered and cross-referenced by identity and similarity groups.
Modified Jun 29, 2026
- HTML
PubChem BioAssay
The PubChem BioAssay Database contains bioactivity screens of chemical substances described in PubChem Substance. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to that screening procedure.
Modified Jun 29, 2026
- HTML
Downloading PubChem Data
Modified Jun 29, 2026