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README.md

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+---
+language: rna
+tags:
+  - Biology
+  - RNA
+license:
+  - agpl-3.0
+size_categories:
+  - 10K<n<100K
+source_datasets:
+  - multimolecule/bprna
+  - multimolecule/pdb
+task_categories:
+  - text-generation
+  - fill-mask
+task_ids:
+  - language-modeling
+  - masked-language-modeling
+pretty_name: bpRNA-spot
+library_name: multimolecule
+---
+
+# bpRNA-spot
+
+bpRNA-spot is a collection of the datasets used by SPOT-RNA for RNA secondary structure prediction.
+
+The dataset is released as a composite repository, `bpRNA-spot`, and three numbered component repositories:
+
+- `bpRNA-spot-0`: the initial bpRNA split, `TR0`, `VL0`, and `TS0`.
+- `bpRNA-spot-1`: the PDB transfer-learning split, `TR1`, `VL1`, and `TS1`.
+- `bpRNA-spot-2`: the NMR-only evaluation split, `TS2`.
+
+`bpRNA-spot` concatenates the components in order:
+
+- `train`: `TR0 + TR1`
+- `validation`: `VL0 + VL1`
+- `test`: `TS0 + TS1 + TS2`
+
+The `TR0`/`VL0`/`TS0` split is a subset of [bpRNA-1m](../bprna).
+It applies [CD-HIT (CD-HIT-EST)](https://sites.google.com/view/cd-hit) to remove sequences with more than 80% sequence similarity from bpRNA-1m.
+It further randomly splits the remaining sequences into training, validation, and test sets with a ratio of approximately 8:1:1.
+
+The `TR1`/`VL1`/`TS1` split contains high-resolution PDB RNAs used for transfer learning.
+`TS2` contains 39 RNAs solved by NMR and is used for post-training evaluation.
+
+All secondary structures are stored as dot-bracket notation.
+For the sequence/label splits, base pairs that would make a nucleotide pair with multiple partners are removed before converting to dot-bracket notation.
+Non-`A/C/G/U` symbols in those sequence files are normalized to `N`.
+
+## Schema
+
+| Column | Description |
+| --- | --- |
+| `id` | Identifier of the sequence. |
+| `sequence` | RNA sequence. |
+| `secondary_structure` | Secondary structure in dot-bracket notation. Pseudoknots may use bracket tiers beyond `()`. |
+| `structural_annotation` | bpRNA-style structural annotation generated from the stored dot-bracket structure. |
+| `functional_annotation` | bpRNA-style functional annotation generated from the stored dot-bracket structure. |
+
+## Disclaimer
+
+This is an UNOFFICIAL release of the bpRNA-spot by Jaswinder Singh, et al.
+
+**The team releasing bpRNA-spot did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.**
+
+## Dataset Description
+
+- **Homepage**: https://multimolecule.danling.org/datasets/bprna-spot
+- **datasets**: https://huggingface.co/datasets/multimolecule/bprna-spot
+- **Point of Contact**: [Kuldip Paliwal](mailto:k.paliwal@griffith.edu.au) and [Yaoqi Zhou](mailto:yaoqi.zhou@griffith.edu.au)
+
+## Related Datasets
+
+- [bpRNA-1m](https://huggingface.co/datasets/multimolecule/bprna): A database of single molecule secondary structures annotated using bpRNA.
+- [bpRNA-new](https://huggingface.co/datasets/multimolecule/bprna-new): A dataset of newly discovered RNA families from Rfam 14.2, designed for cross-family validation to assess generalization capability.
+- [RNAStrAlign](https://huggingface.co/datasets/multimolecule/rnastralign): A database of RNA secondary with the same families as ArchiveII, usually used for training.
+
+## License
+
+This dataset is licensed under the [GNU Affero General Public License](license.md).
+
+For additional terms and clarifications, please refer to our [License FAQ](license-faq.md).
+
+```spdx
+SPDX-License-Identifier: AGPL-3.0-or-later
+```
+## Citation
+
+```bibtex
+@article{singh2019rna,
+  author    = {Singh, Jaswinder and Hanson, Jack and Paliwal, Kuldip and Zhou, Yaoqi},
+  journal   = {Nature Communications},
+  month     = nov,
+  number    = 1,
+  pages     = {5407},
+  publisher = {Springer Science and Business Media LLC},
+  title     = {{RNA} secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning},
+  volume    = 10,
+  year      = 2019
+}
+
+@article{darty2009varna,
+  author    = {Darty, K{\'e}vin and Denise, Alain and Ponty, Yann},
+  journal   = {Bioinformatics},
+  month     = aug,
+  number    = 15,
+  pages     = {1974--1975},
+  publisher = {Oxford University Press (OUP)},
+  title     = {{VARNA}: Interactive drawing and editing of the {RNA} secondary structure},
+  volume    = 25,
+  year      = 2009
+}
+
+@article{berman2000protein,
+  author    = {Berman, H M and Westbrook, J and Feng, Z and Gilliland, G and Bhat, T N and Weissig, H and Shindyalov, I N and Bourne, P E},
+  journal   = {Nucleic Acids Research},
+  month     = jan,
+  number    = 1,
+  pages     = {235--242},
+  publisher = {Oxford University Press (OUP)},
+  title     = {The Protein Data Bank},
+  volume    = 28,
+  year      = 2000
+}
+```
+
+> [!NOTE]
+> The artifacts distributed in this repository are part of the MultiMolecule project.
+> If you use MultiMolecule in your research, you must cite the MultiMolecule project as follows:
+
+```bibtex
+@software{chen_2024_12638419,
+  author    = {Chen, Zhiyuan and Zhu, Sophia Y.},
+  title     = {MultiMolecule},
+  doi       = {10.5281/zenodo.12638419},
+  publisher = {Zenodo},
+  url       = {https://doi.org/10.5281/zenodo.12638419},
+  year      = 2024,
+  month     = may,
+  day       = 4
+}
+```

test.parquet

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train.parquet

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validation.parquet

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