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Agent skill

Chem Hazard Toxicity

by learningmatter-mit in learningmatter-mit/AtomisticSkills

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

MITAuto-check passedBackend & APIs

Install Chem Hazard Toxicity

skills CLI
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-hazard-toxicity -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install learningmatter-mit/AtomisticSkills chem-hazard-toxicity --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/chem-hazard-toxicity .claude/skills/chem-hazard-toxicity && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
chem-hazard-toxicity
GitHub stars
176
Token cost
~702 tokens
SKILL.md length
213 words
Files
4 (incl. scripts)
Skills in repo
129
Repo updated
First seen
Licence
MIT

At a glance

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

  • Works in 2 steps: Extract Safety Profile by CID → GHS Acute Oral Toxicity Triage Helper
  • Backend & APIs work in your project
  • SKILL.md covers Goal, Instructions and Constraints
  • Runs Python scripts from its folder

What it does

Chem Hazard Toxicity is an agent skill from learningmatter-mit/AtomisticSkills. Extract explicit safety warnings, GHS classifications, LD50 toxicity profiles, and acute oral toxicity triage from PubChem PUG VIEW.

Its SKILL.md is about 700 tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts (for example `examples/caffeine/README.md`, `examples/caffeine/safety_caffeine.json` and `scripts/get_safety_data.py`).

It sits in Backend & APIs. The repository describes itself as: Integrating AtomisticSkills into Agentic IDEs (Cursor, Claude Code, Codex, Google Antigravity, Hermes Agent, etc). The licence is MIT.

When your agent uses it

  • Backend & APIs work in your project

Example prompts

  • “/chem-hazard-toxicity”

Requirements

  • Python 3

Workflow steps

2 steps, taken from the step headings in SKILL.md.

  1. Extract Safety Profile by CID
  2. GHS Acute Oral Toxicity Triage Helper

What it can do on your machine

Read from SKILL.md and the folder at commit 6257444. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 1 file in scripts/ (Python), which the agent can run.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • github.com

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Chem Hazard Toxicity loads about 702 tokens when it runs. Until then it costs about 38 tokens; SKILL.md has 213 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~38
When it runs · the whole SKILL.md, loaded when a task matches
~702

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from learningmatter-mit/AtomisticSkills at commit 6257444, republished under its MIT licence (© learningmatter-mit). 213 words, ~702 tokens.

Download SKILL.mdSave it as .claude/skills/chem-hazard-toxicity/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.
name
chem-hazard-toxicity
description
Extract explicit safety warnings, GHS classifications, LD50 toxicity profiles, and acute oral toxicity triage from PubChem PUG VIEW.
metadata.category
chemistry, drug-discovery
metadata.venv
cpu

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
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/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
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/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

© learningmatter-mit, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files (scripts) in skills/chem-hazard-toxicity of learningmatter-mit/AtomisticSkills.

  • SKILL.md
  • examples/caffeine/README.md
  • examples/caffeine/safety_caffeine.json
  • scripts/get_safety_data.py

Open the folder on GitHubat commit 6257444

Compare with similar skills

Chem Hazard Toxicity next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Chem Hazard Toxicity compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Chem Hazard Toxicity this skilllearningmatter-mit/AtomisticSkills176—~702Automated safety check: PassMIT
Configuring Horizoncoollabsio/coolify63k4 repos~898Automated safety check: PassMIT
Nestjs Best Practicesrolling-scopes/rsschool-app10k6 repos~1.2kAutomated safety check: PassMIT
Sub2API AdminWei-Shaw/sub2api43k1 repos~717Automated safety check: PassLGPL-3.0
Firecrawl Build Onboardingfirecrawl/firecrawl190k1 repos~1.4kAutomated safety check: NotesISC
Obsidian BasesAtmosphere/atmosphere3.8k22 repos~3.2kAutomated safety check: PassApache-2.0

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Categories

Questions about Chem Hazard Toxicity

What does Chem Hazard Toxicity do?

Extract explicit safety warnings, GHS classifications, LD50 toxicity profiles, and acute oral toxicity triage from PubChem PUG VIEW. Chem Hazard Toxicity is an agent skill from learningmatter-mit/AtomisticSkills. Extract explicit safety warnings, GHS classifications, LD50 toxicity profiles, and acute oral toxicity triage from PubChem PUG VIEW.

When should I use Chem Hazard Toxicity?

Chem Hazard Toxicity fits situations like: backend & APIs work in your project.

How do I install Chem Hazard Toxicity in Claude Code?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-hazard-toxicity -a claude-code`. Or copy the skill folder (skills/chem-hazard-toxicity in learningmatter-mit/AtomisticSkills) into .claude/skills/chem-hazard-toxicity in your project. Claude Code loads it when a task matches its description.

How do I install Chem Hazard Toxicity in Codex?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-hazard-toxicity -a codex`. Or copy the skill folder (skills/chem-hazard-toxicity in learningmatter-mit/AtomisticSkills) into .agents/skills/chem-hazard-toxicity in your project. Codex loads it when a task matches its description.

Can I use Chem Hazard Toxicity in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-hazard-toxicity -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/chem-hazard-toxicity, .gemini/skills/chem-hazard-toxicity, .github/skills/chem-hazard-toxicity and .opencode/skills/chem-hazard-toxicity in your project.

What does Chem Hazard Toxicity need to run?

Going by SKILL.md and its folder, Chem Hazard Toxicity needs Python for the scripts in its folder. Our summary lists: Python 3.

Does Chem Hazard Toxicity access the network?

SKILL.md names 1 domain. As links in the text: github.com. This is read from the text; nothing was executed.

Is Chem Hazard Toxicity safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Chem Hazard Toxicity use?

Chem Hazard Toxicity is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Chem Hazard Toxicity use?

About 702 tokens (SKILL.md is roughly 2.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Chem Hazard Toxicity?

Skills that share tags, products or a category with Chem Hazard Toxicity: Configuring Horizon (coollabsio/coolify, 63k stars), Nestjs Best Practices (rolling-scopes/rsschool-app, 10k stars), Sub2API Admin (Wei-Shaw/sub2api, 43k stars) and Firecrawl Build Onboarding (firecrawl/firecrawl, 190k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Chem Hazard Toxicity?

learningmatter-mit (a GitHub organization) maintains it in learningmatter-mit/AtomisticSkills, which has 176 GitHub stars. The repository holds 129 skills in this directory. The repository was last updated on October 7, 2026.

Source: learningmatter-mit/AtomisticSkills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.