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README.md

@@ -13,63 +13,78 @@ task_categories:
 task_ids:
   - language-modeling
   - masked-language-modeling
-pretty_name: EternaBench-CM
+pretty_name: EternaBench-ChemMapping
 library_name: multimolecule
 ---
 
-# EternaBench-CM
+# EternaBench-ChemMapping
 
-![EternaBench](https://eternagame.org/sites/default/files/thumb_eternabench_paper.png)
+![EternaBench-ChemMapping](https://eternagame.org/sites/default/files/thumb_eternabench_paper.png)
 
-EternaBench is a database comprising the diverse high-throughput structural data gathered through the crowdsourced RNA design project Eterna, to evaluate the performance of a wide set of structure algorithms.
+EternaBench-ChemMapping is a synthetic RNA dataset comprising 12,711 RNA constructs that have been chemically mapped using SHAPE and MAP-seq methods.
+These RNA sequences are probed to obtain experimental data on their nucleotide reactivity, which indicates whether specific regions of the RNA are flexible or structured.
+The dataset provides high-resolution, large-scale data that can be used for studying RNA folding and stability.
 
 ## Disclaimer
 
-This is an UNOFFICIAL release of the [EternaBench](https://github.com/eternagame/EternaBench) by Hannah K. Wayment-Steele, et al.
+This is an UNOFFICIAL release of the [EternaBench-ChemMapping](https://github.com/eternagame/EternaBench) by Hannah K. Wayment-Steele, et al.
 
-**The team releasing EternaBench did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.**
+**The team releasing EternaBench-ChemMapping 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/eternabench
+- **Homepage**: https://multimolecule.danling.org/datasets/eternabench_cm
+- **datasets**: https://huggingface.co/datasets/multimolecule/eternabench-cm
 - **Point of Contact**: [Rhiju Das](https://biochemistry.stanford.edu/people/rhiju-das/)
 
+The dataset includes a large set of synthetic RNA sequences with experimental chemical mapping data, which provides a quantitative readout of RNA nucleotide reactivity. These data are ensemble-averaged and serve as a critical benchmark for evaluating secondary structure prediction algorithms in their ability to model RNA folding dynamics.
+
 ## Example Entry
 
-| ID       | design_name            | sequence         | structure        | reactivity                 | errors                      | signal_to_noise |
-| -------- | ---------------------- | ---------------- | ---------------- | -------------------------- | --------------------------- | --------------- |
-| 769337-1 | d+m plots weaker again | GGAAAAAAAAAAA... | ................ | [0.642,1.4853,0.1629, ...] | [0.3181,0.4221,0.1823, ...] | 3.227           |
+| index    | design                 | sequence         | secondary_structure | reactivity                 | errors                      | signal_to_noise |
+| -------- | ---------------------- | ---------------- | ------------------- | -------------------------- | --------------------------- | --------------- |
+| 769337-1 | d+m plots weaker again | GGAAAAAAAAAAA... | ................    | [0.642,1.4853,0.1629, ...] | [0.3181,0.4221,0.1823, ...] | 3.227           |
 
 ## Column Description
 
-The EternaBench dataset consists of the following columns, providing crucial insights for understanding RNA stability for vaccine design:
+The EternaBench-ChemMapping dataset consists of the following columns, providing crucial insights for understanding RNA stability for vaccine design:
 
 - **ID**:
-  A unique identifier for each RNA sequence entry.
+    A unique identifier for each RNA sequence entry.
 
 - **design_name**:
-  The name given to each RNA design by contributors, used for easy reference.
+    The name given to each RNA design by contributors, used for easy reference.
 
 - **sequence**:
-  The nucleotide sequence of the RNA, using standard bases.
+    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:
 
-- **structure**:
-  The predicted secondary structure of the RNA, represented using dot-bracket notation.
-  The structure helps determine the likely secondary interactions within each RNA molecule.
+    - **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).
 
 - **reactivity**:
-  A list of floating-point values that provide an estimate of the likelihood of the RNA backbone being cut at each nucleotide position.
-  These values help determine the stability of the RNA structure under various experimental conditions.
+    A list of normalized reactivity values for each nucleotide, representing the likelihood that a nucleotide is unpaired.
+    High reactivity indicates high flexibility (unpaired regions), and low reactivity corresponds to paired or structured regions.
 
 - **errors**:
-  Arrays of floating-point numbers indicating the experimental errors corresponding to the measurements in the **reactivity**.
-  These values help quantify the uncertainty in the degradation rates and reactivity measurements.
+    Arrays of floating-point numbers indicating the experimental errors corresponding to the measurements in the **reactivity**.
+    These values help quantify the uncertainty in the degradation rates and reactivity measurements.
 
-## Variations
+- **signal_to_noise**:
+    The signal-to-noise ratio calculated from the reactivity and error values, providing a measure of data quality.
 
-This dataset is available in two subsets:
+## Related Datasets
 
-- [EternaBench-CM](https://huggingface.co/datasets/multimolecule/eternabench-cm)
+- [EternaBench-ChemMapping](https://huggingface.co/datasets/multimolecule/eternabench-cm)
 - [EternaBench-Switch](https://huggingface.co/datasets/multimolecule/eternabench-switch)
 
 ## License

test.parquet

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train.parquet

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