Overview
PubChem integrates substance submissions, standardized compound records and bioassay information. It is useful for identifier reconciliation and candidate-reference lookup.
What can this tool do?
Common uses
- Resolve compound identifiers and synonyms.
- Retrieve candidate structures for an annotation workflow.
Scientific fit
Primary function
Reference data and database search
Data compatibility
Inputs
Compound list or annotations, Molecular structures
Outputs
Compound list or annotations, Molecular structures
Input formats
Other, Names, identifiers or structures
Output formats
SDF, JSON
Scope and considerations
Designed for
- Resolve compound identifiers and synonyms.
Not designed for
- Demonstrating that a compound is present in a biological sample.
Important requirements
- A chemical name, identifier, structure or supported search query.
Considerations
- Check stereochemistry, charge and salt forms when matching records; contributed annotations retain source-specific evidence.
Access and documentation
Public NIH resource; attribution and reuse terms can vary across contributing data sources.
Evidence and review
Documentation-based editorial review on 7 September 2026. Scope and limitations summarize the linked official sources; software execution and developer verification were not assessed.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Kim S, Chen J, Cheng T, et al. PubChem 2025 update. Nucleic Acids Res 53, D1516-D1525 (2025). doi:10.1093/nar/gkae1059
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-08 · Entry update
Audit core publications across existing tools
View change · Entry at this revision - 2026-09-07 · First committed entry
Add 50 documented metabolomics resources
View change · Entry at this revision