PubChem PUG REST API
Provides programmatic access to NIH's PubChem database of 100M+ chemical compounds, including structures, properties, safety data, bioactivity assays, and synonyms via a RESTful URL-based query system.
Score Breakdown
⚙ Agent Friendliness
🔒 Security
HTTPS enforced. No authentication means no scope concerns. Public read-only data. PubChemPy library is community-maintained and infrequently updated.
⚡ Reliability
Best When
An agent needs to look up, validate, or enrich chemical compound data including structure, properties, or safety information.
Avoid When
You need bulk data exports (use FTP), proprietary compound databases, or real-time computational chemistry.
Use Cases
- • Looking up chemical properties (molecular weight, formula, InChI) by name or structure
- • Retrieving safety and hazard data (GHS, SDS) for chemicals
- • Performing structure similarity or substructure searches
- • Mapping chemical synonyms and CAS numbers to PubChem CIDs
- • Fetching bioactivity data and assay results for drug discovery
Not For
- • Real-time reaction prediction or synthesis planning
- • Proprietary or unpublished compound data
- • High-throughput bulk downloads (use FTP data dumps instead)
Interface
Authentication
No authentication required. Fully public API operated by NCBI/NIH. Rate limiting is enforced automatically (5 requests/second, 400 requests/minute) without requiring a key.
Pricing
Completely free public API operated by NCBI. Rate limits apply but no paid tier exists.
Agent Metadata
Known Gotchas
- ⚠ Rate limit of 5 req/sec is easy to hit in loops; agents must add backoff or use batch endpoints
- ⚠ URL-path-based query syntax (e.g., /compound/name/{name}/property/{prop}/JSON) is non-standard and can confuse agents expecting query params
- ⚠ Async job pattern required for slow operations (structure search): must poll a job URL, not a direct response
- ⚠ Compound names with special characters must be URL-encoded carefully; some names still fail
- ⚠ PUG View and PUG REST have different URL schemes and capabilities — easy to conflate
Alternatives
Full Evaluation Report
Detailed scoring breakdown, competitive positioning, security analysis, and improvement recommendations for PubChem PUG REST API.
Scores are editorial opinions as of 2026-03-06.