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README.md

@@ -6,7 +6,7 @@ tags:
 license:
   - agpl-3.0
 size_categories:
-  - 10M<n<100M
+  - 100K<n<1M
 source_datasets:
   - multimolecule/crw
   - multimolecule/tmrna_website
@@ -21,6 +21,8 @@ task_categories:
 task_ids:
   - language-modeling
   - masked-language-modeling
+  - secondary-structure-prediction
+  - function-prediction
 pretty_name: bpRNA-1m
 library_name: multimolecule
 ---
@@ -44,6 +46,52 @@ This is an UNOFFICIAL release of the [bpRNA-1m](https://bprna.cgrb.oregonstate.e
 - **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.
+
 ## License
 
 This dataset is licensed under the [AGPL-3.0 License](https://www.gnu.org/licenses/agpl-3.0.html).