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chem-hazard-toxicity

Extract explicit safety warnings, GHS classifications, LD50 toxicity profiles, and acute oral toxicity triage from PubChem PUG VIEW.

Examiner la source Voir sur GitHub

Prix non confirmé★ 161 Stars GitHubRegistre mis à jour · 6 sept. 2026agent-skill

Vue d’ensemble

Extract explicit safety warnings, GHS classifications, LD50 toxicity profiles, and acute oral toxicity triage from PubChem PUG VIEW.

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Documentation source, pas des instructions pour ce site. Vérifiez les permissions avant d’exécuter des commandes.

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.

Author: Bowen Deng Contact: GitHub @learningmatter-mit

Voir la source ↗

Métadonnées du fichier

name: chem-hazard-toxicity
description: Extract explicit safety warnings, GHS classifications, LD50 toxicity profiles, and acute oral toxicity triage from PubChem PUG VIEW.
category: [chemistry, drug-discovery]

Voir le texte original

---
name: chem-hazard-toxicity
description: Extract explicit safety warnings, GHS classifications, LD50 toxicity profiles, and acute oral toxicity triage from PubChem PUG VIEW.
category: [chemistry, drug-discovery]
---

# 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.

```bash
# 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:

```bash
# 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:

```python
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.

---
---

**Author:** Bowen Deng
**Contact:** [GitHub @learningmatter-mit](https://github.com/learningmatter-mit)

Examiner la source

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Licence: MIT
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Source du skill enregistrée

Un chemin vers les instructions est enregistré. Cela ne constitue pas un test, une garantie de sécurité ou de compatibilité.

Réviser avant installation: Éviter l’installation automatique

Licence: MIT

Dependency or permission surface needs review
Permission surface may require sandboxing
The SKILL.md excerpt is truncated in the review material, but the full file appears complete and well-structured.
The script relies on external PubChem API; network availability is a dependency but handled with backoff.
Quality score needs review
Permission surface needs review: secrets or environment access, shell or command execution
Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
Dependency/runtime risk: command execution surface, credential or environment access
Permission surface: secrets or environment access, shell or command execution

Ouvrir l’audit complet

Les outils sont des indications de métadonnées, pas une compatibilité testée. Les prompts sont des suggestions.

Commencer par une petite tâche

1Lisez la source et confirmez entrées, résultats, dépendances et permissions.
2Demandez un plan à l’agent. Approuvez la configuration et les coûts avant un test isolé.
3Vérifiez résultats et fichiers modifiés. Signalez uniquement ce qui a été exécuté et conservez la révision source.

Vérifiez les dépendances, clés API et frais externes dans la source. Un dépôt public ne rend pas tous les services gratuits.

Source et conseils d’utilisation

Répertorié

Métadonnées et examens sont indicatifs. Popularité, découverte et exécution réussie sont des faits distincts.

Dépôt source: learningmatter-mit/AtomisticSkills
Licence: MIT
Version: 1.0.0
Dernier push GitHub: 3 sept. 2026
Registre mis à jour: 6 sept. 2026
Chemin des instructions: .agents/skills/chem-hazard-toxicity/SKILL.md @ d1f7ecfda2cd

Version déclarée dans le registre ; vérifiez les versions de la source.

Qualité

66/100

Prometteur

Confiance

56/100

Do not auto-install

Audit

72/100

Revue nécessaire

Ouvrir l’audit complet Voir le rapport d’évaluation

Dependency or permission surface needs review
Permission surface may require sandboxing
The SKILL.md excerpt is truncated in the review material, but the full file appears complete and well-structured.
The script relies on external PubChem API; network availability is a dependency but handled with backoff.
Quality score needs review
Permission surface needs review: secrets or environment access, shell or command execution
Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
Dependency/runtime risk: command execution surface, credential or environment access
Permission surface: secrets or environment access, shell or command execution

Verified installs: —
Résultats: —

Copier ne signifie pas installer. Les compteurs nécessitent un rapport de réussite et ne garantissent pas la qualité globale.

Accès agent

L’API Registry fournit les signaux de décision, confiance, audit, cas d’usage et installation sans analyser l’interface.

Ouvrir l’API d’installation Format texte LLM Ouvrir Manifest Plan de résolution auto

Plus de détails

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Créateur: learningmatter-mit
Source: learningmatter-mit/AtomisticSkills
Indexé par: Index communautaire OpenAgentSkill

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