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pubchem-database-skill

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.

Published by aipoch ↗aipoch/medical-research-skills

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pubchem-database-skill

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Use pubchem-database-skill to look up [compound identifier] and return its physicochemical properties plus available bioactivity and target information.

Required inputs

  • [compound identifier]

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SKILL.md

name: pubchem-database-skilldescription: 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: MITauthor: AIPOCH

Source: https://github.com/aipoch/medical-research-skills

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

  • 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_type must match supported types (e.g., name, cid, smiles, inchi, formula).
    • search_type must be similarity or substructure.

  • Error handling:

    • Returns structured error or None if compound is not found.
    • Handles PubChem rate limits (≤ 5 requests/sec).

  • Troubleshooting considerations:

    • Ensure network access to pubchem.ncbi.nlm.nih.gov.
    • Verify query format (e.g., valid SMILES or InChI) if results are empty.

  • Additional reference:

    • API documentation pointers: references/api_reference.md