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