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pubchem-database
90 / 100 · Low risk
Fine to try. Some of what it can do is expected: a data skill usually connects to databases or online services with your credentials.
By franklee16/academic-research-skills (GitHub) · data · 234 stars · scanned at commit 9a4b2db
Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.
Works with any agent that supports SKILL.md skills.
What this skill can do
Runs commands on your computer
The author does not mention this.
Found in 14 places.
Show 11 more
- science-skills/pubchem_database/SKILL.md, line 66
uv run scripts/pubchem_api.py synonyms --cid 2244 --output result.json - science-skills/pubchem_database/SKILL.md, line 75
uv run scripts/pubchem_api.py safety --cid 2244 --output result.json - science-skills/pubchem_database/SKILL.md, line 82
uv run scripts/pubchem_api.py pharmacology --cid 2244 --output result.json - science-skills/pubchem_database/SKILL.md, line 89
uv run scripts/pubchem_api.py view --cid 3939 --heading "Crystal Structures" --output result.json - science-skills/pubchem_database/SKILL.md, line 96
uv run scripts/pubchem_api.py image --cid 2244 --output result.json - science-skills/pubchem_database/SKILL.md, line 105
uv run scripts/pubchem_api.py similarity --smiles "CC(=O)OC1=CC=CC=C1C(=O)O" --output result.json - science-skills/pubchem_database/SKILL.md, line 111
uv run scripts/pubchem_api.py substructure --smiles "C1=CC=CC=C1" --output result.json - science-skills/pubchem_database/SKILL.md, line 118
uv run scripts/pubchem_api.py assays --cid 2244 --output result.json - science-skills/pubchem_database/SKILL.md, line 127
uv run scripts/pubchem_api.py xrefs --cid 2244 --type "PatentID" --output result.json - science-skills/pubchem_database/SKILL.md, line 136
uv run scripts/pubchem_api.py range --feature molecular_weight --min 400.0 --max 400.05 --output result.json - science-skills/pubchem_database/SKILL.md, line 142
uv run scripts/pubchem_api.py query --path "compound/cid/2244/xrefs/PatentID/JSON" --output result.json
Connects to the internet
The author does not mention this. Expected for a data skill.
Found in 1 place.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'pubchem-database' ] || [ -L ~/.agents/skills/'pubchem-database' ]; then echo 'A skill folder named pubchem-database already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/franklee16/academic-research-skills' "$d" && git -C "$d" checkout --quiet '9a4b2db21fc4b217136ae4a0e6faad42d179ca03' -- 'science-skills/pubchem_database' && mkdir -p ~/.agents/skills && cp -R "$d"/'science-skills/pubchem_database' ~/.agents/skills/'pubchem-database' && rm -rf "$d"; fi
Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'pubchem-database' ~/.claude/skills/'pubchem-database' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.
Badge for your README
The badge for franklee16/academic-research-skills shows the score of its lowest-scoring skill.

[](https://zalavijaysinh.github.io/skilltrust/repos/franklee16/academic-research-skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-07 | 9a4b2db | 90 |