README.md

---
license: cc-by-4.0
task_categories:
  - tabular-classification
tags:
  - chemistry
  - drug-discovery
  - pubchem
  - bioassay
  - smiles
  - rdkit
---

# Simeonov2008: PubChem Bioassay Active Compounds

## Overview

Active compounds from PubChem qHTS bioassay screenings (AIDs: 587, 588, 590, 591, 592, 593, 594) based on Simeonov et al. (2008). SMILES were sanitized using RDKit MolStandardize.

| Metric | Value |
|--------|-------|
| Total rows | 7109 |
| Unique compounds | 6743 |
| Assays | 6 |

## Quick Start

```python
from datasets import load_dataset

# Load dataset
dataset = load_dataset("jpraise/Simeonov2008")

# Get full data as DataFrame
df = dataset['full'].to_pandas()
print(df.head())
```

## Data Fields

| Column | Description |
|--------|-------------|
| AID | PubChem Assay ID |
| CID | PubChem Compound ID |
| SMILES | Original SMILES from PubChem |
| InChI | IUPAC InChI identifier |
| InChIKey | Hashed InChI key |
| SMILES_sanitized | Standardized SMILES via RDKit |

## Assays

| AID | Link |
|-----|------|
| 587 | [PubChem](https://pubchem.ncbi.nlm.nih.gov/bioassay/587) |
| 588 | [PubChem](https://pubchem.ncbi.nlm.nih.gov/bioassay/588) |
| 590 | [PubChem](https://pubchem.ncbi.nlm.nih.gov/bioassay/590) |
| 591 | [PubChem](https://pubchem.ncbi.nlm.nih.gov/bioassay/591) |
| 592 | [PubChem](https://pubchem.ncbi.nlm.nih.gov/bioassay/592) |
| 593 | [PubChem](https://pubchem.ncbi.nlm.nih.gov/bioassay/593) |
| 594 | [PubChem](https://pubchem.ncbi.nlm.nih.gov/bioassay/594) |

## SMILES Sanitization

RDKit MolStandardize pipeline:
1. LargestFragmentChooser - Remove salts/counterions
2. Normalizer - Standardize functional groups
3. Uncharger - Neutralize charges
4. TautomerEnumerator - Canonicalize tautomers

## Citation

```bibtex
@article{simeonov2008,
  title={Fluorescence spectroscopic profiling of compound libraries},
  author={Simeonov, Anton and Jadhav, Ajit and Thomas, Craig J and others},
  journal={Journal of Medicinal Chemistry},
  volume={51},
  number={8},
  pages={2363--2371},
  year={2008},
  doi={10.1021/jm701301m}
}
```

## License

CC-BY-4.0. Source data from PubChem (public domain).