By name: safety-assessment description: Based on a compound, get its safety info. Assess compound safety profile including toxicity, hazard classifications, and regulatory information using PubChem and PubMed.
Safety Assessment Skill
Assess compound safety via PubChem (GHS hazards, toxicity, regulatory) and PubMed (literature evidence).
Workflow
- Resolve compound → PubChem CID
- Safety data → GHS hazard classifications
- Toxicity info → LD50, carcinogenicity, mutagenicity, reproductive toxicity
- Regulatory info → FDA, EPA, REACH status
- PubMed search → Supporting safety literature
- Format output → Assessment with literature references
Step 1: Resolve Compound Identifier
Use the appropriate PubChem search tool based on input type:
- By name:
PubChem:search_compounds(query="<name>") - By SMILES:
PubChem:search_by_smiles(smiles="<SMILES>") - By InChI:
PubChem:search_by_inchi(inchi="<InChI>") - By CAS:
PubChem:search_by_cas_number(cas_number="<CAS>")
Step 2: Get Safety Data
DO NOT call get_safety_data. This tool returns millions of characters of irrelevant classification hierarchies (ChEBI Ontology, patent classifications, etc.) that will exceed the context window and crash the agent. Skip this step entirely — toxicity and regulatory data from Steps 3 and 4 provide sufficient safety information.
Step 3: Get Toxicity Information
PubChem:get_toxicity_info(cid=<CID>) — returns LD50/LC50 values, IARC/NTP carcinogenicity classifications, Ames test mutagenicity, and reproductive toxicity data.
For environmental toxicity: PubChem:assess_environmental_fate(cid=<CID>)
Step 4: Get Regulatory Information
PubChem:get_regulatory_info(cid=<CID>) — returns FDA approval/warnings, EPA registration, REACH status, and other agency data.
Step 5: Search PubMed for Evidence
PubMed:search_articles(query="<compound> toxicity", max_results=10)
Also search for: <compound> carcinogenicity, <compound> safety, <compound> adverse effects.
Get metadata for relevant PMIDs: PubMed:get_article_metadata(pmids=[...])
Cross-reference with: PubChem:get_literature_references(cid=<CID>)
Step 6: Format Output
Present as structured markdown with sections for GHS classification, toxicity data (acute, carcinogenicity, mutagenicity, reproductive), regulatory status, supporting literature table (PMID, title, journal, year), and a brief safety summary.
Error Handling
- Compound not found: Suggest alternative names or ask for CID
- Limited data: Note gaps; some compounds lack comprehensive testing
- No PubMed results: Note absence; suggest broader search terms
- Conflicting data: Present all sources and note discrepancies