ok: Merge pull request #3067 from jnwei/patch-1

Revise OpenFold3 dataset description and citation

Author: berylrab

datasets/openfold3.yaml

@@ -1,8 +1,16 @@
 Name: OpenFold3 Training Data
-Description: This dataset contains MSAs and predicted structures for 13 million long (sequence length >= 200 amino acids) monomers from the MGNIFY database. These MSAs were generated using the AF3 protocol, and were used to predict structures with AlphaFold2. This data serves as the long monomer distillation set for Openfold3, an open-source, all-atom ligand, RNA and protein structure prediction software.
-Documentation: https://github.com/aqlaboratory/openfold3-training-data-RODA/tree/main
-Contact: https://github.com/aqlaboratory/openfold3-training-data-RODA/issues
-ManagedBy: OpenFold
+Description: | 
+  This dataset contains MSAs and predicted structures used to train  OpenFold3 preview, an open-source, all-atom ligand, RNA and protein structure prediction software. This includes - 
+    - PDB - 245k structures and alignments from the RCSB Protein Data Bank - https://www.rcsb.org/
+    - Long monomer distillation set - ~13 million long (sequence length >= 200 amino acids) monomers from the MGNIFY database - https://www.ebi.ac.uk/metagenomics/.
+    - Short monomer distillation set - 400k short (sequence length < 200 amino acid) monomers from the MGNIFY database - https://www.ebi.ac.uk/metagenomics/.
+    - Disordered set - AF2-predicted structures for unresolved segments missing from the PDB
+    - RNA - OF3p2-predicted RNA monomer structures generated from a clustered version of RFAM (current version)
+  For the distillation sets MSAs were generated using the AF3 protocol, and were used to predict structures with AlphaFold2, more details can be found in our whitepaper - https://portal.openfold.omsf.io/reports/of3p2_technical_report.pdf
+  For a full description and an interactive data explorer, please visit https://portal.openfold.omsf.io/datasets
+Documentation: https://portal.openfold.omsf.io/datasets
+Contact: https://github.com/aqlaboratory/openfold-3/issues
+ManagedBy: OpenFold Consortium
 UpdateFrequency: Never
 Tags:
   - openfold
@@ -14,7 +22,7 @@ Tags:
   - life sciences
   - aws-pds
 License: "[CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)"
-Citation: "Additionally, please cite [our prior manuscript](https://www.nature.com/articles/s41592-024-02272-z)."
+Citation: "Additionally, please cite [our repository](https://doi.org/10.5281/zenodo.19001000) and [our prior manuscript](https://www.nature.com/articles/s41592-024-02272-z)."
 Resources:
   - Description: A repository of MSAs and 3D protein structural coordinates used to train OpenFold3.
     ARN: arn:aws:s3:::openfold3-data
@@ -27,9 +35,9 @@ DataAtWork:
       AuthorName: Glòria Macià
       AuthorURL: https://www.linkedin.com/in/gloriamacia/
   Publications:
-    - Title: "OpenProteinSet: Training data for structural biology at scale"
-      URL: "https://arxiv.org/abs/2308.05326"
-      AuthorName: Ahdritz, Gustaf; Bouatta, Nazim; Kadyan, Sachin; Jarosch, Lukas; Berenberg, Daniel; Fisk, Ian, et al
+    - Title: OpenFold3-preview2 Technical Report
+      URL: https://portal.openfold.omsf.io/reports/of3p2_technical_report.pdf
+      AuthorName: The OpenFold3 Team
     - Title: "OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization"
-      URL: "https://www.nature.com/articles/s41592-024-02272-z"
+      URL: https://www.nature.com/articles/s41592-024-02272-z
       AuthorName: Ahdritz, Gustaf; Bouatta, Nazim; Kadyan, Sachin; Xia, Qinghui; Gerecke, William; O'Donnell, Timothy J, et al