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