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Retrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
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| name | general-chemical-literature |
| description | Retrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem. |
| category | ["general","chemistry","drug-discovery","materials"] |
To programmatically check if a specific chemical compound exists in recent literature or patent databases. This skill uses PubChem's PUG-REST XRefs endpoint to extract an exhaustive list of associated PubMed IDs and Patent numbers.
This is incredibly useful as an autonomous "novelty check" for generated molecules.
Provide the CID of the target molecule. By default, the script will output the absolute total number of hits but limits the JSON save array to 1000 to prevent memory flooding for ubiquitous molecules (like Aspirin, which has over 100,000 patents). Adjust --limit as needed.
# Env: base-agent
python .agents/skills/general-chemical-literature/scripts/get_xrefs.py \
--cid 2244 \
--limit 50 \
--outdir research/aspirin_literature \
--output xrefs_aspirin.json
We can pull cross-references for Aspirin (CID: 2244), saving the top 50 identifiers.
# Env: base-agent
python .agents/skills/general-chemical-literature/scripts/get_xrefs.py \
--cid 2244 \
--limit 50 \
--outdir .agents/skills/general-chemical-literature/examples/aspirin \
--output xrefs_aspirin.json
pubmed.ncbi.nlm.nih.gov/ and patents.google.com/patent/) for the top 5 results for immediate verification.Author: Bowen Deng Contact: GitHub @learningmatter-mit