Indexado en Registry

chem-hazard-toxicity

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

Revisar el código fuente Ver en GitHub

Precio sin confirmar★ 161 Estrellas de GitHubRegistro actualizado · 6 sept 2026agent-skill

Resumen

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

Leer documentación completa

Documentación de origen, no instrucciones para este sitio. Revisa los permisos antes de ejecutar comandos.

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

Ver fuente ↗

Metadatos del archivo

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]

Ver texto 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)

Revisar el código fuente

Precio y costes de ejecución

Obtener el skill: Precio sin confirmar
Ejecutarlo: Requisitos sin confirmar. Consulta los costes del agente, API y servicios en la fuente.
Licencia: MIT
Precio sin confirmar: No hemos confirmado el precio. Los enlaces existentes al código y a la instalación siguen disponibles.

Obtener gratis no significa ejecutar gratis. El precio no es una evaluación de seguridad. Enviar información de precio →

Fuente del skill registrada

La ruta de instrucciones está registrada. No implica pruebas de ejecución, seguridad ni compatibilidad.

Revisar antes de instalar: Evitar instalación automática

Licencia: 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

Abrir auditoría completa

Las herramientas son indicios de metadatos, no compatibilidad probada. Los prompts son sugerencias.

Empieza con una tarea pequeña

1Lee la fuente y confirma entradas, resultados, dependencias y permisos.
2Pide un plan al agente. Aprueba la configuración y los costes antes de probar en un entorno aislado.
3Comprueba resultados y archivos modificados. Informa solo de lo ejecutado y conserva la revisión de la fuente.

Consulta dependencias, claves API y costes externos en la fuente. Un repositorio público no implica servicios gratuitos.

Fuente y notas de uso

Indexado

Los metadatos y revisiones son orientativos. Popularidad, descubrimiento y ejecución correcta son hechos distintos.

Repositorio fuente: learningmatter-mit/AtomisticSkills
Licencia: MIT
Versión: 1.0.0
Último push de GitHub: 3 sept 2026
Registro actualizado: 6 sept 2026
Ruta de instrucciones: .agents/skills/chem-hazard-toxicity/SKILL.md @ d1f7ecfda2cd

Versión declarada en el registro; consulta las versiones de la fuente.

Calidad

66/100

Prometedor

Confianza

56/100

Do not auto-install

Auditoría

72/100

Requiere revisión

Abrir auditoría completa Ver informe de evaluación

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: —
Resultados: —

Copiar no es instalar. Los recuentos requieren un informe de instalación correcta, no garantizan calidad general.

Acceso para agentes

La API Registry expone señales de decisión, confianza, auditoría, casos de uso e instalación sin raspar la interfaz.

Abrir API de instalación Formato de texto LLM Abrir Manifest Plan de resolución automática

Más detalles

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}

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Creador: learningmatter-mit
Fuente: learningmatter-mit/AtomisticSkills
Indexado por: Índice comunitario de OpenAgentSkill

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[![Listed on OpenAgentSkill](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-hazard-toxicity?metric=listed&label=Listed)](https://www.openagentskill.com/skills/learningmatter-mit-chem-hazard-toxicity?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)
[![OpenAgentSkill Trust](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-hazard-toxicity?metric=trust&label=Trust)](https://www.openagentskill.com/skills/learningmatter-mit-chem-hazard-toxicity?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)
[![OpenAgentSkill Audit](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-hazard-toxicity?metric=audit&label=Audit)](https://www.openagentskill.com/skills/learningmatter-mit-chem-hazard-toxicity/audit)
[![Agent Proven](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-hazard-toxicity?metric=proven&label=Agent%20Proven)](https://www.openagentskill.com/skills/learningmatter-mit-chem-hazard-toxicity?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)

Vista previa de insignia Abrir auditoría Kit para creadores

Señal de comunidad

Comparte si este skill resulta útil para tu flujo de Agent. Los comentarios agregados mejoran la clasificación con el tiempo.