| --- |
| 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} |
| } |
| ``` |
|
|
