| --- |
| license: cc0-1.0 |
| language: |
| - en |
| pretty_name: COCONUT (2026-10) |
| tags: |
| - chemistry |
| - natural-products |
| - molecular-structures |
| configs: |
| - config_name: full |
| default: true |
| data_files: |
| - split: train |
| path: data/*.parquet |
| --- |
| |
| # COCONUT: 2026-10 source-preserving mirror |
|
|
| This dataset contains **738,794 structure records** and **44 columns** |
| from the full COCONUT CSV export. It contains molecular structures and metadata, |
| not measured spectra. The source download page releases the data under CC0. |
|
|
| Source: [2026-10 full CSV archive](https://coconut.s3.uni-jena.de/prod/downloads/2026-10/coconut_csv-10-2026.zip). |
| See the [upstream download page](https://coconut.naturalproducts.net/download). |
|
|
| ## Data and preprocessing |
|
|
| All source rows, columns, their order, and parsed CSV values are retained. |
| All columns use the string type, including numeric and boolean descriptors. |
| Empty cells remain empty strings. Pipe-delimited metadata remains source text. |
| No molecule standardization, stereochemistry removal, deduplication, or chemistry |
| filter is applied. `canonical_smiles` is the upstream representation, unchanged. |
| Cast descriptor columns explicitly when computing chemical-space statistics. |
|
|
| The `train` split holds the full collection. It is a storage convention, not a |
| scientific training split. No validation or test partition has been created. |
|
|
| ```python |
| from datasets import load_dataset |
| |
| dataset = load_dataset("structure-epflai/coconut", "full", split="train") |
| ``` |
|
|
| ## Validation and provenance |
|
|
| Every parsed CSV value was compared with the generated Parquet value. |
| Unique source identifiers: 738,794; duplicate identifier rows: 0. |
| RDKit parsing was checked on the first 256 structures; |
| 0 failed. This is a smoke check, not a full chemical audit. |
|
|
| `manifest.json` records source/output SHA-256 checksums, row counts, empty-cell |
| counts, software versions, and the source commit and conversion-script hash. |
| The original ZIP is retained under `source/`; the exact conversion script is |
| included as `collate_coconut.py`. Upstream descriptors and annotations have not |
| been independently verified. The CSV export is not the complete database SQL |
| dump, which also includes active/inactive records and relational data. |
|
|
| ## Citation |
|
|
| Venkata Chandrasekhar et al. COCONUT 2.0: a comprehensive overhaul and curation |
| of the collection of open natural products database. Nucleic Acids Research. |
| https://doi.org/10.1093/nar/gkae1063 |
|
|
