---
name: pubchem-database-skill-982bb40052c8
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
author: AIPOCH
---
> **Source**: [https://github.com/aipoch/medical-research-skills](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:

```bash
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

```bash
python -c "from scripts.pubchem_ops import get_properties; print(get_properties(query_value='Aspirin', query_type='name'))"
```

Or in Python:

```python
from scripts.pubchem_ops import get_properties

result = get_properties(query_value="Aspirin", query_type="name")
print(result)
```

### 2) Structure search (similarity)

```bash
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:

```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

```bash
python -c "from scripts.pubchem_ops import get_bioactivity; print(get_bioactivity(cid=2244))"
```

Or in Python:

```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`



---
Source attribution: aipoch
Original project: https://github.com/aipoch/medical-research-skills/blob/686e09dfdb45d9fa1a08664f06bb93769b3c9d91/scientific-skills/Evidence%20Insight/pubchem-database-skill/SKILL.md
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Copyright (c) 2026 AIpoch

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: aipoch
Original project: https://github.com/aipoch/medical-research-skills/blob/686e09dfdb45d9fa1a08664f06bb93769b3c9d91/scientific-skills/Evidence%20Insight/pubchem-database-skill/SKILL.md
Attribution basis: Source repository record

Fields of work: Data & Analytics, Development & Engineering, Education & Research
Roles: Data Scientist, ML / AI Engineer, Researcher
Specialties: API
Tools: Pubchem
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: 95362904931bb9e331bf4ba78909147840e2a97ad613621eaf149e3101ea8823