aipoch/pubchem-database-skill
scientific-skills/Evidence Insights/pubchem-database-skill/SKILL.md
Programmatic access to the PubChem database (via PUG-REST API and PubChemPy) for searching chemical compounds, retrieving physicochemical properties, performing structure similarity/substructure searches, and obtaining bioactivity data.
$ install --global
skillsauthnpx skillsauth add aipoch/medical-research-skills pubchem-database-skillInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- pubchem-database-skill
- description:
- Programmatic access to the PubChem database (via PUG-REST API and PubChemPy) for searching chemical compounds, retrieving physicochemical properties, performing structure similarity/substructure searches, and obtaining bioactivity data.
- license:
- MIT
- skill-author:
- AIPOCH
When to Use
- You need to search for chemical compounds by name, CID, SMILES, InChI, or molecular formula.
- You want to retrieve physicochemical properties (e.g., molecular weight, LogP, TPSA, H-bond donors/acceptors).
- You need to perform structure-based searches, such as similarity or substructure queries.
- You want to obtain bioactivity data (e.g., assay summaries, target information) for a given compound.
- You are building an automated cheminformatics or drug discovery workflow that requires programmatic access to PubChem.
Key Features
-
Flexible compound search by name, CID, SMILES, InChI, or formula.
-
Property retrieval via PubChem PUG-REST and PubChemPy (e.g., MW, LogP, Canonical SMILES).
-
Structure search:
- Similarity search
- Substructure search
-
Bioactivity retrieval linked to PubChem BioAssay records.
-
Rate-limit aware implementation (respects PubChem’s limit of max 5 requests/sec).
-
Python function interface for seamless integration into scientific pipelines.
Dependencies
Install the required Python packages:
uv pip install pubchempy requests
pubchempy(version: not pinned)requests(version: not pinned)
Example Usage
Primary module:
scripts/pubchem_ops.py
1) Get compound properties
python -c "from scripts.pubchem_ops import get_properties; print(get_properties(query_value='Aspirin', query_type='name'))"
Or in Python:
from scripts.pubchem_ops import get_properties
result = get_properties(query_value="Aspirin", query_type="name")
print(result)
2) Structure search (similarity)
python -c "from scripts.pubchem_ops import structure_search; print(structure_search(query_value='CC(=O)OC1=CC=CC=C1C(=O)O', search_type='similarity'))"
Or in Python:
from scripts.pubchem_ops import structure_search
smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"
result = structure_search(query_value=smiles, search_type="similarity")
print(result)
3) Get bioactivity data
python -c "from scripts.pubchem_ops import get_bioactivity; print(get_bioactivity(cid=2244))"
Or in Python:
from scripts.pubchem_ops import get_bioactivity
result = get_bioactivity(cid=2244)
print(result)
Implementation Details
-
Primary script:
scripts/pubchem_ops.py -
Data sources / endpoints:
- Compound & properties:
pubchem.ncbi.nlm.nih.gov/rest/pug - Bioactivity: PubChem BioAssay endpoints
- Python wrapper:
PubChemPy
- Compound & properties:
-
Supported operations:
get_properties: retrieve physicochemical properties by name/CID/SMILES/InChI/formula.structure_search: perform similarity or substructure search.get_bioactivity: retrieve assay and bioactivity-related data by CID.
-
Input constraints:
query_typemust match supported types (e.g.,name,cid,smiles,inchi,formula).search_typemust besimilarityorsubstructure.
-
Error handling:
- Returns structured error or
Noneif compound is not found. - Handles PubChem rate limits (≤ 5 requests/sec).
- Returns structured error or
-
Troubleshooting considerations:
- Ensure network access to
pubchem.ncbi.nlm.nih.gov. - Verify query format (e.g., valid SMILES or InChI) if results are empty.
- Ensure network access to
-
Additional reference:
- API documentation pointers:
references/api_reference.md
- API documentation pointers:
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