Chemical Hazard and Toxicity Profiling

Goal

To programmatically extract critical safety information from the PubChem PUG-VIEW API. This skill pulls GHS Classifications, Hazard Classes, and Toxicological properties (like LD50/LC50 experimental animal records) for a given compound based on its CID, and performs GHS Acute Toxicity Category assignment and hazard statement consistency analysis.

Instructions

1. Extract Safety Profile by CID

Provide the precise CID of the molecule to query safety metadata.

# Env: base-agent
python .agents/skills/chem-hazard-toxicity/scripts/get_safety_data.py \
  --cid 2519 \
  --outdir research/caffeine_safety \
  --output safety_caffeine.json

2. GHS Acute Oral Toxicity Triage Helper

Use --triage to extract consensus GHS statements ($\ge 50%$), lowest rat oral LD50, GHS acute oral category (1–5 or unclassified), and check oral hazard code consistency:

# Env: base-agent
python .agents/skills/chem-hazard-toxicity/scripts/get_safety_data.py \
  --cid 2519 \
  --triage \
  --outdir research/caffeine_safety \
  --output triage_caffeine.json

Python API Integration

Import helper functions directly into python scripts:

from scripts.get_safety_data import (
    extract_consensus_ghs_codes,
    extract_lowest_rat_oral_ld50,
    assign_acute_oral_category,
    check_oral_code_consistency,
    profile_compound,
)

profile = profile_compound(2519, threshold_percent=50.0)
# Returns dict with cid, consensus_ghs_codes, oral_rat_ld50_mg_kg, oral_rat_ld50_evidence, acute_oral_category, ghs_oral_code_consistent

GHS Category & Code Consistency Rule:

• Category 1 ($\le 5\text{ mg/kg}$) & Category 2 ($5 < \text{LD}_{50} \le 50\text{ mg/kg}$) $\rightarrow$ expected GHS oral code H300 (Fatal if swallowed).
• Category 3 ($50 < \text{LD}_{50} \le 300\text{ mg/kg}$) $\rightarrow$ H301 (Toxic if swallowed).
• Category 4 ($300 < \text{LD}_{50} \le 2000\text{ mg/kg}$) $\rightarrow$ H302 (Harmful if swallowed).
• Category 5 ($2000 < \text{LD}_{50} \le 5000\text{ mg/kg}$) $\rightarrow$ H303 (May be harmful if swallowed).
• unclassified ($> 5000\text{ mg/kg}$) $\rightarrow$ empty set ({}).

Constraints

• Data Availability: Relies on experimental or reported data listed in PubChem.
• Network Limits: Automatically handles standard HTTP 503/429 rate limiting via exponential backoff.

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Author: Bowen Deng Contact: GitHub @learningmatter-mit