| --- |
| language: rna |
| tags: |
| - Biology |
| - RNA |
| license: |
| - cc-by-4.0 |
| source_datasets: |
| - multimolecule/bprna |
| - multimolecule/rfam |
| task_categories: |
| - text-generation |
| - fill-mask |
| task_ids: |
| - language-modeling |
| - masked-language-modeling |
| pretty_name: IPknot++ |
| library_name: multimolecule |
| --- |
| |
| # IPknot++ |
|
|
| IPknot++ is a benchmark dataset released with the IPknot++ RNA secondary structure prediction paper. |
| It is intended as an external evaluation set rather than a training split. |
| A common use is to train or tune RNA secondary structure prediction models on SPOT-RNA-style splits such as [bpRNA-spot](../bprna_spot), then evaluate generalization on IPknot++. |
|
|
| The original release does not define train, validation, and test partitions. |
| The converted dataset follows the paper's benchmark blocks as four splits: |
|
|
| - `bprna_1m`: single-sequence structures from bpRNA-1m. |
| - `rfam_14_5`: single-sequence structures from Rfam 14.5. |
| - `rfam_14_5_ref`: Rfam 14.5 reference alignments for common-structure prediction. |
| - `rfam_14_5_mafft`: Rfam 14.5 MAFFT alignments for common-structure prediction. |
|
|
| For alignment entries, `sequence` and `secondary_structure` are taken from the corresponding single-sequence BPSEQ file, and the full alignment is stored in `aligned_ids` and `aligned_sequences`. |
|
|
| ## Schema |
|
|
| | Column | Description | |
| | --- | --- | |
| | `id` | Identifier of the benchmark entry. | |
| | `sequence` | Ungapped RNA sequence for the benchmark target. | |
| | `secondary_structure` | Target secondary structure in dot-bracket notation. | |
| | `aligned_ids` | Sequence IDs in the alignment. Single-sequence entries contain only their own ID. | |
| | `aligned_sequences` | Aligned sequences, preserving gap characters. Single-sequence entries contain only the ungapped sequence. | |
|
|
| ## Disclaimer |
|
|
| This is an UNOFFICIAL release of the IPknot++ benchmark dataset by Kengo Sato and Yuki Kato. |
|
|
| **The team releasing IPknot++ did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.** |
|
|
| ## Dataset Description |
|
|
| - **Homepage**: https://www.sato-lab.org/en/publication/sato-2022-qk/ |
| - **datasets**: https://huggingface.co/datasets/multimolecule/ipknot-plus-plus |
| - **Original URL**: https://zenodo.org/records/4923158 |
|
|
| ## License |
|
|
| The original IPknot++ benchmark dataset is licensed under the [Creative Commons Attribution 4.0 International](https://creativecommons.org/licenses/by/4.0/) license. |
|
|
| ```spdx |
| SPDX-License-Identifier: CC-BY-4.0 |
| ``` |
|
|
| ## Citation |
|
|
| ```bibtex |
| @article{sato2022prediction, |
| author = {Sato, Kengo and Kato, Yuki}, |
| journal = {Briefings in Bioinformatics}, |
| month = jan, |
| number = 1, |
| title = {Prediction of {RNA} secondary structure including pseudoknots for long sequences}, |
| volume = 23, |
| year = 2022 |
| } |
| ``` |
|
|
| ```bibtex |
| @dataset{sato2021ipknot, |
| author = {Sato, Kengo and Kato, Yuki}, |
| title = {{IPknot++} benchmark dataset}, |
| publisher = {Zenodo}, |
| doi = {10.5281/zenodo.4923158}, |
| year = 2021 |
| } |
| ``` |
|
|
| > [!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 |
| } |
| ``` |
|
|
