Delete RNAgym.croissant.json

RNAgym.croissant.json

@@ -1,206 +0,0 @@
-{
-  "@type": "Dataset",
-  "@context": {
-    "@language": "en",
-    "@vocab": "https://schema.org/",
-    "cr": "http://mlcommons.org/croissant/",
-    "FileSet": "cr:FileSet",
-    "RecordSet": "cr:RecordSet",
-    "Column": "cr:Column",
-    "includes": "cr:includes"
-  },
-
-  "name": "RNAGym",
-  "description": "Benchmark suite for RNA fitness, secondary-structure and tertiary-structure prediction.",
-  "license": "CC-BY-4.0",
-  "version": "0.1.0",
-  "datePublished": "2025-05-15",
-
-  "fileSet": [
-
-    {
-      "@id": "fitness_assays",
-      "@type": "FileSet",
-      "name": "Fitness-prediction assays",
-      "description": "70 deep-mutational-scanning CSVs.",
-      "distribution": {
-        "@type": "DataDownload",
-        "contentUrl": "https://huggingface.co/datasets/Marks-lab/RNAgym/resolve/main/fitness_prediction/",
-        "includes": "fitness_prediction/assays/*.csv",
-        "encodingFormat": "text/csv",
-        "sha256": "f11213c5d5b22ee869e605bbfdcfa5f13d2193247c31c3c58981e3ce97d229d4"
-      },
-      "recordSet": {
-        "@id": "fitness_assays_records",
-        "@type": "RecordSet",
-        "columns": [
-          { "@type": "Column", "name": "mutant",     "column": "mutant"     },
-          { "@type": "Column", "name": "sequence",   "column": "sequence"   },
-          { "@type": "Column", "name": "dms_score",  "column": "DMS_score"  }
-        ]
-      }
-    },
-
-    {
-      "@id": "fitness_reference",
-      "@type": "FileSet",
-      "name": "Fitness-reference sheet",
-      "description": "Supplementary metadata for assays.",
-      "distribution": {
-        "@type": "DataDownload",
-        "contentUrl": "https://huggingface.co/datasets/Marks-lab/RNAgym/resolve/main/fitness_prediction/",
-        "includes": "fitness_prediction/reference_sheet_final.csv",
-        "encodingFormat": "text/csv",
-        "sha256": "f11213c5d5b22ee869e605bbfdcfa5f13d2193247c31c3c58981e3ce97d229d4"
-      }
-    },
-
-    {
-      "@id": "secondary_parquet",
-      "@type": "FileSet",
-      "name": "Secondary-structure Parquet splits",
-      "description": "RMDB s40 train/test in Parquet format.",
-      "distribution": {
-        "@type": "DataDownload",
-        "contentUrl": "https://huggingface.co/datasets/Marks-lab/RNAgym/resolve/main/secondary_structure_prediction/",
-        "includes": "secondary_structure_prediction/RMDB_s40_*.parquet",
-        "encodingFormat": "application/parquet",
-        "sha256": "e8ccbcb268f214a57b3139ef87434db94269e24c3dab5db1e11365148563474e"
-      },
-      "recordSet": {
-        "@id": "secondary_parquet_records",
-        "@type": "RecordSet",
-        "columns": [
-          { "@type": "Column", "name": "sequence",  "column": "sequence"  },
-          { "@type": "Column", "name": "structure", "column": "structure" }
-        ]
-      }
-    },
-
-    {
-      "@id": "secondary_fasta",
-      "@type": "FileSet",
-      "name": "Secondary-structure FASTA sets",
-      "description": "Raw FASTA files (train/test, PDB, Ribonanza).",
-      "distribution": {
-        "@type": "DataDownload",
-        "contentUrl": "https://huggingface.co/datasets/Marks-lab/RNAgym/resolve/main/secondary_structure_prediction/",
-        "includes": [
-          "secondary_structure_prediction/*.fasta"
-        ],
-        "encodingFormat": "text/plain",
-        "sha256": "e8ccbcb268f214a57b3139ef87434db94269e24c3dab5db1e11365148563474e"
-      }
-    },
-
-    {
-      "@id": "secondary_cluster",
-      "@type": "FileSet",
-      "name": "RMDB cluster assignments",
-      "description": "cluster_40.tsv mapping sequences to clusters.",
-      "distribution": {
-        "@type": "DataDownload",
-        "contentUrl": "https://huggingface.co/datasets/Marks-lab/RNAgym/resolve/main/secondary_structure_prediction/",
-        "includes": "secondary_structure_prediction/cluster_40.tsv",
-        "encodingFormat": "text/tab-separated-values",
-        "sha256": "e8ccbcb268f214a57b3139ef87434db94269e24c3dab5db1e11365148563474e"
-      }
-    },
-
-    {
-      "@id": "secondary_archive",
-      "@type": "FileSet",
-      "name": "Compiled RMDB archive",
-      "description": "Full RMDB dataset in compressed tarball.",
-      "distribution": {
-        "@type": "DataDownload",
-        "contentUrl": "https://huggingface.co/datasets/Marks-lab/RNAgym/resolve/main/secondary_structure_prediction/",
-        "includes": "secondary_structure_prediction/compiled_RMDB.tar.gz",
-        "encodingFormat": "application/x-tar",
-        "sha256": "e8ccbcb268f214a57b3139ef87434db94269e24c3dab5db1e11365148563474e"
-      }
-    },
-
-    {
-      "@id": "tertiary_monomer",
-      "@type": "FileSet",
-      "name": "Tertiary-structure monomer scores",
-      "description": "Structural similarity metrics for monomer RNAs.",
-      "distribution": {
-        "@type": "DataDownload",
-        "contentUrl": "https://huggingface.co/datasets/Marks-lab/RNAgym/resolve/main/tertiary_structure/",
-        "includes": "tertiary_structure/monomer.csv",
-        "encodingFormat": "text/csv",
-        "sha256": "001c93cb93b24e3f47d732291a013df88dbca4a174db7caea4973dfcf25abdb0"
-      },
-      "recordSet": {
-        "@id": "tertiary_monomer_records",
-        "@type": "RecordSet",
-        "columns": [
-          { "@type": "Column", "name": "pdb_id",                          "column": "PDB ID" },
-          { "@type": "Column", "name": "asym_chain_id",                  "column": "Asym. Chain ID" },
-          { "@type": "Column", "name": "auth_chain_id",                  "column": "Auth. Chain ID" },
-          { "@type": "Column", "name": "af3_tm",                         "column": "AF3 MONOMERS TM Score" },
-          { "@type": "Column", "name": "af3_inf_wc",                     "column": "AF3 MONOMERS INF_WC" },
-          { "@type": "Column", "name": "af3_inf_nwc",                    "column": "AF3 MONOMERS INF_NWC" },
-          { "@type": "Column", "name": "nu_tm",                          "column": "NU MONOMERS TM Score" },
-          { "@type": "Column", "name": "nu_inf_wc",                      "column": "NU MONOMERS INF_WC" },
-          { "@type": "Column", "name": "nu_inf_nwc",                     "column": "NU MONOMERS INF_NWC" },
-          { "@type": "Column", "name": "rf2na_tm",                       "column": "RF2NA MONOMERS TM Score" },
-          { "@type": "Column", "name": "rf2na_inf_wc",                   "column": "RF2NA MONOMERS INF_WC" },
-          { "@type": "Column", "name": "rf2na_inf_nwc",                  "column": "RF2NA MONOMERS INF_NWC" },
-          { "@type": "Column", "name": "rho_tm",                         "column": "RHO MONOMERS TM Score" },
-          { "@type": "Column", "name": "rho_inf_wc",                     "column": "RHO MONOMERS INF_WC" },
-          { "@type": "Column", "name": "rho_inf_nwc",                    "column": "RHO MONOMERS INF_NWC" },
-          { "@type": "Column", "name": "trrna_tm",                       "column": "TRRNA MONOMERS TM Score" },
-          { "@type": "Column", "name": "trrna_inf_wc",                   "column": "TRRNA MONOMERS INF_WC" },
-          { "@type": "Column", "name": "trrna_inf_nwc",                  "column": "TRRNA MONOMERS INF_NWC" }
-        ]
-      }
-    },
-
-    {
-      "@id": "tertiary_multimer",
-      "@type": "FileSet",
-      "name": "Tertiary-structure multimer scores",
-      "description": "Structural similarity metrics for multimer RNAs.",
-      "distribution": {
-        "@type": "DataDownload",
-        "contentUrl": "https://huggingface.co/datasets/Marks-lab/RNAgym/resolve/main/tertiary_structure/",
-        "includes": "tertiary_structure/multimer.csv",
-        "encodingFormat": "text/csv",
-        "sha256": "001c93cb93b24e3f47d732291a013df88dbca4a174db7caea4973dfcf25abdb0"
-      },
-      "recordSet": {
-        "@id": "tertiary_multimer_records",
-        "@type": "RecordSet",
-        "columns": [
-          { "@type": "Column", "name": "pdb_id",          "column": "PDB ID" },
-          { "@type": "Column", "name": "asym_chain_id",   "column": "Asym. Chain ID" },
-          { "@type": "Column", "name": "auth_chain_id",   "column": "Auth. Chain ID" },
-          { "@type": "Column", "name": "af3_tm",          "column": "AF3 MULTIMERS TM Score" },
-          { "@type": "Column", "name": "af3_inf_wc",      "column": "AF3 MULTIMERS INF_WC" },
-          { "@type": "Column", "name": "af3_inf_nwc",     "column": "AF3 MULTIMERS INF_NWC" },
-          { "@type": "Column", "name": "rf2na_tm",        "column": "RF2NA MULTIMERS TM Score" },
-          { "@type": "Column", "name": "rf2na_inf_wc",    "column": "RF2NA MULTIMERS INF_WC" },
-          { "@type": "Column", "name": "rf2na_inf_nwc",   "column": "RF2NA MULTIMERS INF_NWC" }
-        ]
-      }
-    },
-
-    {
-      "@id": "tertiary_msa",
-      "@type": "FileSet",
-      "name": "Tertiary-structure MSAs",
-      "description": "Multiple-sequence alignments in AFA format.",
-      "distribution": {
-        "@type": "DataDownload",
-        "contentUrl": "https://huggingface.co/datasets/Marks-lab/RNAgym/resolve/main/tertiary_structure/",
-        "includes": "tertiary_structure/msa/*.afa",
-        "encodingFormat": "text/plain",
-        "sha256": "001c93cb93b24e3f47d732291a013df88dbca4a174db7caea4973dfcf25abdb0"
-      }
-    }
-
-  ]
-}