---
license: cc-by-4.0
task_categories:
- other
language:
- en
tags:
- chemistry
- reactions
- smiles
- atom-mapping
- graphies
- reaction smiles
- rxnmapper
- ITS
pretty_name: MappedCRD
size_categories:
- 1M<n<10M
configs:
- config_name: rxnmapper
  data_files: rxnmapper/train-*.parquet
- config_name: its
  data_files: its/train-*.parquet
- config_name: its-nomod
  data_files: its-nomod/train-*.parquet
---

# MappedCRD — Mapped Chemical Reactions Database

This dataset is a processed version of the [Chemical Reactions Database (CRD)](https://kmt.vander-lingen.nl/) ([Zenodo](https://doi.org/10.5281/zenodo.18109268)), providing atom-mapped reaction SMILES and imaginary transition state (ITS) graph encodings for large-scale cheminformatics and machine-learning use.

## Dataset Description

The CRD is a curated collection of chemical reactions. This dataset distributes two subsets derived from it:

| Subset | Examples | Description |
|--------|----------|-------------|
| `rxnmapper` | 1,446,478 | Full reaction SMILES mapped with [RXNMapper](https://github.com/rxn4chemistry/rxnmapper) |
| `its` | 1,405,109 | Reactions encoded as imaginary transition state (ITS) graphs using [graphies](https://github.com/lukasmki/graphies) and [SynKit](https://github.com/TieuLongPhan/SynKit) |
| `its-nomod` | 1,405,109 | ITS graphies without charge and hydrogen modifiers |

## Subsets

### `rxnmapper`

Atom-mapped reactions produced by RXNMapper. Each row contains:

| Column | Type | Description |
|--------|------|-------------|
| `reaction` | string | Original reaction SMILES (unmapped) |
| `mapped_reaction` | string | Atom-mapped reaction SMILES |
| `confidence` | float64 | RXNMapper confidence score (0–1) |

### `its`

Reactions that were successfully processed into ITS graphs and encoded with graphies. Each row contains:

| Column | Type | Description |
|--------|------|-------------|
| `original_rsmi` | string | Original reaction SMILES |
| `mapped_rxn` | string | Atom-mapped reaction SMILES |
| `its_graphies` | string | graphies-encoded ITS graph string |

The ITS (imaginary transition state) representation encodes both reactant and product bond changes in a single molecular graph, enabling direct graph-based learning on reaction data.

## Usage

```python
from datasets import load_dataset

# Atom-mapped reactions
ds_mapped = load_dataset("lukasmki/MappedCRD", name="rxnmapper", split="train")

# ITS graph encodings
ds_its = load_dataset("lukasmki/MappedCRD", name="its", split="train")

# ITS graph encodings without charge/hydrogens
ds_its = load_dataset("lukasmki/MappedCRD", name="its-nomod", split="train")
```

## Source Data

- CRD source: https://kmt.vander-lingen.nl/
- CRD Zenodo archive: https://doi.org/10.5281/zenodo.18109268

## Tools

- Atom mapping: [RXNMapper](https://github.com/rxn4chemistry/rxnmapper)
- ITS encoding: [graphies](https://github.com/lukasmki/graphies) and [SynKit](https://github.com/TieuLongPhan/SynKit)

## Citation

If you use this dataset, please cite the original CRD:

```
@misc{crd,
  doi = {10.5281/ZENODO.18109268},
  url = {https://zenodo.org/doi/10.5281/zenodo.18109268},
  author = {van der Lingen,  Rik},
  language = {en},
  title = {Organic reaction SMILES 1.44M dataset},
  publisher = {Zenodo},
  year = {2025},
  copyright = {Creative Commons Attribution 4.0 International}
}
```