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Dataset Card for Dataset Name

This dataset contains the tasks provided by rnaglib, a benchmarking suite for RNA structure-function modelling.

Dataset Details

Dataset Description

This dataset is a Python package wrapping RNA benchmark datasets and tasks. Data access, preprocessing, and task-specific pipelines are implemented in code and not fully expressed through this metadata schema. See documentation at https://github.com/cgoliver/rnaglib.

Curated by: [Luis Wyss, Vincent Mallet, Wissam Karroucha, Carlos Oliver, Karsten Borgwardt]
License: [MIT license]

Dataset Sources [optional]

Repository: https://github.com/cgoliver/rnaglib
Preprint: https://arxiv.org/pdf/2503.21681
Documentation: https://rnaglib.org/en/latest/

Uses

The intended use of these dataset is to train models to elucidate RNA structure-function relationships.

Dataset Structure

Detailed information can be found in the linked paper. This repo contains nine tasks, each coming with their own splitting. The splitting is either based on published splits or on structural dissimilarity.

Dataset Creation

Curation Rationale

We provide datasets replicating published research or generate our own datasets ensuring effective QC, filtering, redundancy removal and splitting.

Source Data

All data originates from RNA structures pulled from the PDB.

Data Collection and Processing

Details can be found in the linked paper.

Who are the source data producers?

The data originates from the PDB, the data producers are the contributors to the PDB.

Annotations [optional]

The data is saved as graphs and annotated with features extracted from th PDB.

Who are the annotators?

rnaglib is used to process the data.

Personal and Sensitive Information

N/A

Bias, Risks, and Limitations

N/A

Citation

BibTeX:

@article{wyss2025comprehensivebenchmarkrna3d, title={A Comprehensive Benchmark for RNA 3D Structure-Function Modeling}, author={Luis Wyss and Vincent Mallet and Wissam Karroucha and Karsten Borgwardt and Carlos Oliver}, year={2025}, eprint={2503.21681}, archivePrefix={arXiv}, primaryClass={q-bio.BM}, url={https://arxiv.org/abs/2503.21681}, }

Dataset Card Contact

[email protected]