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--- |
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language: rna |
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tags: |
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- Biology |
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- RNA |
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license: |
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- agpl-3.0 |
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size_categories: |
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- 100K<n<1M |
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source_datasets: |
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- multimolecule/rfam |
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task_categories: |
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- text-generation |
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- fill-mask |
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task_ids: |
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- language-modeling |
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- masked-language-modeling |
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pretty_name: CHANRG |
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library_name: multimolecule |
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--- |
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# Comprehensive Hierarchical Annotation of Non-coding RNA Groups (CHANRG) |
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CHANRG is a database of non-coding RNA families and secondary structures. |
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> [!WARNING] |
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> This dataset is currently in a **Development Preview** state. It is not yet ready for production use and may contain incomplete or experimental features. The MultiMolecule team is actively working on improving this dataset, and we welcome feedback from the community. |
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> |
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> DO NOT DISTRIBUTE, COPY, OR USE THIS DATASET WITHOUT PRIOR WRITTEN PERMISSION FROM THE MULTIMOLECULE TEAM. |
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> NO ACADEMIC, INDUSTRIAL, OR COMMERCIAL USE IS ALLOWED WITHOUT PRIOR WRITTEN PERMISSION FROM THE MULTIMOLECULE TEAM. |
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## Dataset Description |
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- **Homepage**: https://multimolecule.danling.org/datasets/chanrg |
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- **datasets**: https://huggingface.co/datasets/multimolecule/chanrg |
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- **Point of Contact**: [Zhiyuan Chen](mailto:[email protected]) |
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## Example Entry |
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| id | sequence | secondary_structure | structural_annotation | functional_annotation | |
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| --------------- | ----------------------------------- | -------------------------------- | ----------------------------------- | ----------------------------------- | |
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| bpRNA_RFAM_1016 | AUUGCUUCUCGGCCUUUUGGCUAACAUCAAGU... | ......(((.((((....)))).)))...... | EEEEEESSSISSSSHHHHSSSSISSSXXXXXX... | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN... | |
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## Column Description |
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The converted dataset consists of the following columns, each providing specific information about the RNA secondary structures, consistent with the bpRNA standard: |
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- **id**: |
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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. |
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- **sequence**: |
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The nucleotide sequence of the RNA molecule, represented using the standard RNA bases: |
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- **A**: Adenine |
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- **C**: Cytosine |
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- **G**: Guanine |
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- **U**: Uracil |
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- **secondary_structure**: |
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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: |
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- **Dots (`.`)**: Represent unpaired nucleotides. |
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- **Parentheses (`(` and `)`)**: Represent base pairs in standard stems (page 1). |
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- **Square Brackets (`[` and `]`)**: Represent base pairs in pseudoknots (page 2). |
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- **Curly Braces (`{` and `}`)**: Represent base pairs in additional pseudoknots (page 3). |
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- **structural_annotation**: |
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Structural annotations categorizing different regions of the RNA based on their roles within the secondary structure, consistent with bpRNA standards: |
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- **E**: **External Loop** – Regions that are unpaired and external to any loop or helix. |
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- **S**: **Stem** – Paired regions forming helical structures. |
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- **H**: **Hairpin Loop** – Unpaired regions at the end of a stem, forming a loop. |
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- **I**: **Internal Loop** – Unpaired regions between two stems. |
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- **M**: **Multi-loop** – Junctions where three or more stems converge. |
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- **B**: **Bulge** – Unpaired nucleotides on one side of a stem. |
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- **X**: **Ambiguous** or **Undetermined** – Regions where the structure is unknown or cannot be classified. |
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- **K**: **Pseudoknot** – Regions involved in pseudoknots, where base pairs cross each other. |
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- **functional_annotation**: |
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Functional annotations indicating specific functional elements or regions within the RNA sequence, as defined by bpRNA: |
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- **N**: **None** – No specific functional annotation is assigned. |
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- **K**: **Pseudoknot** – Marks nucleotides involved in pseudoknot structures, which can be functionally significant. |
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## License |
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This dataset is licensed under the MultiMolecule Development Preview License. |
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DO NOT DISTRIBUTE, COPY, OR USE THIS DATASET WITHOUT PRIOR WRITTEN PERMISSION FROM THE MULTIMOLECULE TEAM. |
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NO ACADEMIC, INDUSTRIAL, OR COMMERCIAL USE IS ALLOWED WITHOUT PRIOR WRITTEN PERMISSION FROM THE MULTIMOLECULE TEAM. |
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