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README.md

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+---
+language: rna
+tags:
+  - Biology
+  - RNA
+license:
+  - agpl-3.0
+size_categories:
+  - 100K<n<1M
+source_datasets:
+  - multimolecule/crw
+  - multimolecule/tmrna_website
+  - multimolecule/srpdb
+  - multimolecule/spr
+  - multimolecule/rnp
+  - multimolecule/rfam
+  - multimolecule/pdb
+task_categories:
+  - text-generation
+  - fill-mask
+task_ids:
+  - language-modeling
+  - masked-language-modeling
+pretty_name: bpRNA-1m
+library_name: multimolecule
+---
+
+# bpRNA-1m
+
+![bpRNA-1m](https://bprna.cgrb.oregonstate.edu/images/bpRNA_structure.png)
+
+bpRNA-1m is a database of single molecule secondary structures annotated using bpRNA.
+
+## Disclaimer
+
+This is an UNOFFICIAL release of the [bpRNA-1m](https://bprna.cgrb.oregonstate.edu/index.html) by Center for Quantitative Life Sciences of the Oregon State University.
+
+**The team releasing bpRNA 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
+- **datasets**: https://huggingface.co/datasets/multimolecule/bprna
+- **Point of Contact**: [Center for Quantitative Life Sciences of the Oregon State University](https://cqls.oregonstate.edu)
+- **Original URL**: https://bprna.cgrb.oregonstate.edu/index.html
+
+## Example Entry
+
+| id            | sequence                                       | secondary_structure                                 | structural_annotation                              | functional_annotation                          |
+| ------------- | ---------------------------------------------- | --------------------------------------------------- | -------------------------------------------------- | ---------------------------------------------- |
+| bpRNA_CRW_170 | GGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGAC... | ((((((((....))))...))))....((((((..........)))))... | EEEEEEEEEEEEEEEEEEEEEEEESSSSSSSSHHHHSSSSBBBSSSS... | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN |
+
+## Column Description
+
+The converted dataset consists of the following columns, each providing specific information about the RNA secondary structures, consistent with the bpRNA standard:
+
+- **id**:
+    A unique identifier for each RNA entry. This ID is derived from the original `.sta` file name and serves as a reference to the specific RNA structure within the dataset.
+
+- **sequence**:
+    The nucleotide sequence of the RNA molecule, represented using the standard RNA bases:
+
+    - **A**: Adenine
+    - **C**: Cytosine
+    - **G**: Guanine
+    - **U**: Uracil
+
+- **secondary_structure**:
+    The secondary structure of the RNA represented in dot-bracket notation, using up to three types of symbols to indicate base pairing and unpaired regions, as per bpRNA's standard:
+
+    - **Dots (`.`)**: Represent unpaired nucleotides.
+    - **Parentheses (`(` and `)`)**: Represent base pairs in standard stems (page 1).
+    - **Square Brackets (`[` and `]`)**: Represent base pairs in pseudoknots (page 2).
+    - **Curly Braces (`{` and `}`)**: Represent base pairs in additional pseudoknots (page 3).
+
+- **structural_annotation**:
+    Structural annotations categorizing different regions of the RNA based on their roles within the secondary structure, consistent with bpRNA standards:
+
+    - **E**: **External Loop** – Regions that are unpaired and external to any loop or helix.
+    - **S**: **Stem** – Paired regions forming helical structures.
+    - **H**: **Hairpin Loop** – Unpaired regions at the end of a stem, forming a loop.
+    - **I**: **Internal Loop** – Unpaired regions between two stems.
+    - **M**: **Multi-loop** – Junctions where three or more stems converge.
+    - **B**: **Bulge** – Unpaired nucleotides on one side of a stem.
+    - **X**: **Ambiguous** or **Undetermined** – Regions where the structure is unknown or cannot be classified.
+    - **K**: **Pseudoknot** – Regions involved in pseudoknots, where base pairs cross each other.
+
+- **functional_annotation**:
+    Functional annotations indicating specific functional elements or regions within the RNA sequence, as defined by bpRNA:
+    - **N**: **None** – No specific functional annotation is assigned.
+    - **K**: **Pseudoknot** – Marks nucleotides involved in pseudoknot structures, which can be functionally significant.
+
+## Variations
+
+This dataset is available in two variants:
+
+- [bpRNA-1m](https://huggingface.co/datasets/multimolecule/bprna): The main bpRNA-1m dataset.
+- [bpRNA-1m(90)](https://huggingface.co/datasets/multimolecule/bprna-90): bpRNA_1m(90) is a subset of bpRNA_1m containing RNAs with less than 90% sequence similarity.
+
+## License
+
+This dataset is licensed under the [AGPL-3.0 License](https://www.gnu.org/licenses/agpl-3.0.html).
+
+```spdx
+SPDX-License-Identifier: AGPL-3.0-or-later
+```
+
+## Citation
+
+```bibtex
+@article{danaee2018bprna,
+  author  = {Danaee, Padideh and Rouches, Mason and Wiley, Michelle and Deng, Dezhong and Huang, Liang and Hendrix, David},
+  journal = {Nucleic Acids Research},
+  month   = jun,
+  number  = 11,
+  pages   = {5381--5394},
+  title   = {{bpRNA}: large-scale automated annotation and analysis of {RNA} secondary structure},
+  volume  = 46,
+  year    = 2018
+}
+
+@article{cannone2002comparative,
+  author    = {Cannone, Jamie J and Subramanian, Sankar and Schnare, Murray N and Collett, James R and D'Souza, Lisa M and Du, Yushi and Feng, Brian and Lin, Nan and Madabusi, Lakshmi V and M{\"u}ller, Kirsten M and Pande, Nupur and Shang, Zhidi and Yu, Nan and Gutell, Robin R},
+  copyright = {https://www.springernature.com/gp/researchers/text-and-data-mining},
+  journal   = {BMC Bioinformatics},
+  month     = jan,
+  number    = 1,
+  pages     = {2},
+  publisher = {Springer Science and Business Media LLC},
+  title     = {The comparative {RNA} web ({CRW}) site: an online database of comparative sequence and structure information for ribosomal, intron, and other {RNAs}},
+  volume    = 3,
+  year      = 2002
+}
+
+@article{zwieb2003tmrdb,
+  author    = {Zwieb, Christian and Gorodkin, Jan and Knudsen, Bjarne and Burks, Jody and Wower, Jacek},
+  journal   = {Nucleic Acids Research},
+  month     = jan,
+  number    = 1,
+  pages     = {446--447},
+  publisher = {Oxford University Press (OUP)},
+  title     = {{tmRDB} ({tmRNA} database)},
+  volume    = 31,
+  year      = 2003
+}
+
+@article{rosenblad2003srpdb,
+  author    = {Rosenblad, Magnus Alm and Gorodkin, Jan and Knudsen, Bjarne and Zwieb, Christian and Samuelsson, Tore},
+  journal   = {Nucleic Acids Research},
+  month     = jan,
+  number    = 1,
+  pages     = {363--364},
+  publisher = {Oxford University Press (OUP)},
+  title     = {{SRPDB}: Signal Recognition Particle Database},
+  volume    = 31,
+  year      = 2003
+}
+
+@article{sprinzl2005compilation,
+  author    = {Sprinzl, Mathias and Vassilenko, Konstantin S},
+  journal   = {Nucleic Acids Research},
+  month     = jan,
+  number    = {Database issue},
+  pages     = {D139--40},
+  publisher = {Oxford University Press (OUP)},
+  title     = {Compilation of {tRNA} sequences and sequences of {tRNA} genes},
+  volume    = 33,
+  year      = 2005
+}
+
+@article{brown1994ribonuclease,
+  author    = {Brown, J W and Haas, E S and Gilbert, D G and Pace, N R},
+  journal   = {Nucleic Acids Research},
+  month     = sep,
+  number    = 17,
+  pages     = {3660--3662},
+  publisher = {Oxford University Press (OUP)},
+  title     = {The Ribonuclease {P} database},
+  volume    = 22,
+  year      = 1994
+}
+
+@article{griffiths2003rfam,
+  author    = {Griffiths-Jones, Sam and Bateman, Alex and Marshall, Mhairi and Khanna, Ajay and Eddy, Sean R},
+  journal   = {Nucleic Acids Research},
+  month     = jan,
+  number    = 1,
+  pages     = {439--441},
+  publisher = {Oxford University Press (OUP)},
+  title     = {Rfam: an {RNA} family database},
+  volume    = 31,
+  year      = 2003
+}
+
+@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
+}
+```

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