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| "description": "Released sample type.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-018" |
| }, |
| "extract": { |
| "column": "sample_type" |
| } |
| } |
| } |
| ], |
| "key": [ |
| { |
| "@id": "train_entries/emd_id" |
| } |
| ] |
| }, |
| { |
| "@type": "cr:RecordSet", |
| "@id": "test_entries", |
| "name": "test_entries", |
| "description": "The full 1,152-entry held-out test pool. Its 618 benchmark targets and 534 remaining entries are disjoint download subsets.", |
| "field": [ |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/emd_id", |
| "name": "emd_id", |
| "description": "EMDB accession identifying the curated map entry.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "emd_id" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/pdb_id", |
| "name": "pdb_id", |
| "description": "PDB identifier of the atomic structure supplied for this entry.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "pdb_id" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/split", |
| "name": "split", |
| "description": "Fixed training or test membership.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "split" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/benchmark_618", |
| "name": "benchmark_618", |
| "description": "Whether this test entry belongs to the common 618-target benchmark.", |
| "dataType": "sc:Boolean", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "benchmark_618" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/resolution_angstrom", |
| "name": "resolution_angstrom", |
| "description": "Reported experimental map resolution in Angstrom.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "resolution_angstrom" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/title", |
| "name": "title", |
| "description": "Released title.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "title" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/release_component", |
| "name": "release_component", |
| "description": "Released release component.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "release_component" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/archive_path", |
| "name": "archive_path", |
| "description": "Containing archive path relative to the HF repository root.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "archive_path" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/download_url", |
| "name": "download_url", |
| "description": "Download URL recorded in the release index.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "download_url" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/entry_directory", |
| "name": "entry_directory", |
| "description": "Directory of the EMD entry relative to the extraction destination.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "entry_directory" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/has_aligned_cif", |
| "name": "has_aligned_cif", |
| "description": "Whether an additional aligned CIF is supplied.", |
| "dataType": "sc:Boolean", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "has_aligned_cif" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/emdb_url", |
| "name": "emdb_url", |
| "description": "Released emdb url.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "emdb_url" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/pdb_url", |
| "name": "pdb_url", |
| "description": "Released pdb url.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "pdb_url" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/source_map_url", |
| "name": "source_map_url", |
| "description": "Released source map url.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "source_map_url" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/map_release_date", |
| "name": "map_release_date", |
| "description": "Released map release date.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "map_release_date" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/structure_determination_method", |
| "name": "structure_determination_method", |
| "description": "Released structure determination method.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "structure_determination_method" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "test_entries/sample_type", |
| "name": "sample_type", |
| "description": "Released sample type.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-017" |
| }, |
| "extract": { |
| "column": "sample_type" |
| } |
| } |
| } |
| ], |
| "key": [ |
| { |
| "@id": "test_entries/emd_id" |
| } |
| ] |
| }, |
| { |
| "@type": "cr:RecordSet", |
| "@id": "benchmark_targets", |
| "name": "benchmark_targets", |
| "description": "The 618 common benchmark entries, all included in test_entries; this is a view of the test split, not an additional set of targets.", |
| "field": [ |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/emd_id", |
| "name": "emd_id", |
| "description": "EMDB accession identifying the curated map entry.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "emd_id" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/pdb_id", |
| "name": "pdb_id", |
| "description": "PDB identifier of the atomic structure supplied for this entry.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "pdb_id" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/split", |
| "name": "split", |
| "description": "Fixed training or test membership.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "split" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/benchmark_618", |
| "name": "benchmark_618", |
| "description": "Whether this test entry belongs to the common 618-target benchmark.", |
| "dataType": "sc:Boolean", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "benchmark_618" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/resolution_angstrom", |
| "name": "resolution_angstrom", |
| "description": "Reported experimental map resolution in Angstrom.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "resolution_angstrom" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/title", |
| "name": "title", |
| "description": "Released title.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "title" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/release_component", |
| "name": "release_component", |
| "description": "Released release component.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "release_component" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/archive_path", |
| "name": "archive_path", |
| "description": "Containing archive path relative to the HF repository root.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "archive_path" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/download_url", |
| "name": "download_url", |
| "description": "Download URL recorded in the release index.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "download_url" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/entry_directory", |
| "name": "entry_directory", |
| "description": "Directory of the EMD entry relative to the extraction destination.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "entry_directory" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/has_aligned_cif", |
| "name": "has_aligned_cif", |
| "description": "Whether an additional aligned CIF is supplied.", |
| "dataType": "sc:Boolean", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "has_aligned_cif" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/emdb_url", |
| "name": "emdb_url", |
| "description": "Released emdb url.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "emdb_url" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/pdb_url", |
| "name": "pdb_url", |
| "description": "Released pdb url.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "pdb_url" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/source_map_url", |
| "name": "source_map_url", |
| "description": "Released source map url.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "source_map_url" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/map_release_date", |
| "name": "map_release_date", |
| "description": "Released map release date.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "map_release_date" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/structure_determination_method", |
| "name": "structure_determination_method", |
| "description": "Released structure determination method.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "structure_determination_method" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_targets/sample_type", |
| "name": "sample_type", |
| "description": "Released sample type.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-015" |
| }, |
| "extract": { |
| "column": "sample_type" |
| } |
| } |
| } |
| ], |
| "key": [ |
| { |
| "@id": "benchmark_targets/emd_id" |
| } |
| ] |
| }, |
| { |
| "@type": "cr:RecordSet", |
| "@id": "benchmark_results", |
| "name": "benchmark_results", |
| "description": "3,090 released target-by-method rows: 618 targets times ModelAngelo, CryoAtom2, EMProt, E3-CryoFold and AF3.", |
| "field": [ |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/emd_id", |
| "name": "emd_id", |
| "description": "EMDB accession identifying the curated map entry.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "emd_id" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/method", |
| "name": "method", |
| "description": "Baseline prediction method.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "method" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/pdb_id", |
| "name": "pdb_id", |
| "description": "PDB identifier of the atomic structure supplied for this entry.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "pdb_id" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/category", |
| "name": "category", |
| "description": "Released category.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "category" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/total_residues", |
| "name": "total_residues", |
| "description": "Released total residues.", |
| "dataType": "sc:Integer", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "total_residues" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/resolution", |
| "name": "resolution", |
| "description": "Reported experimental map resolution in Angstrom.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "resolution" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/n_chains", |
| "name": "n_chains", |
| "description": "Released n chains.", |
| "dataType": "sc:Integer", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "n_chains" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/tm_score", |
| "name": "tm_score", |
| "description": "Released target-normalized TM-score.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "tm_score" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/ca_rmsd", |
| "name": "ca_rmsd", |
| "description": "Released C-alpha RMSD measurement in Angstrom; follow the paper protocol for interpretation.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "ca_rmsd" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/residue_coverage", |
| "name": "residue_coverage", |
| "description": "Released residue coverage.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "residue_coverage" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/sequence_match", |
| "name": "sequence_match", |
| "description": "Released sequence match.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "sequence_match" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/sequence_recall", |
| "name": "sequence_recall", |
| "description": "Released sequence-recall measurement.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "sequence_recall" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/completeness", |
| "name": "completeness", |
| "description": "Predicted-to-reference model-length ratio; values may exceed 1.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "completeness" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/gt_score", |
| "name": "gt_score", |
| "description": "Released composite structural-accuracy score.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "gt_score" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/cc_mask", |
| "name": "cc_mask", |
| "description": "Released cc mask.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "cc_mask" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/cc_volume", |
| "name": "cc_volume", |
| "description": "Released cc volume.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "cc_volume" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/cc_peaks", |
| "name": "cc_peaks", |
| "description": "Released cc peaks.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "cc_peaks" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/cc_box", |
| "name": "cc_box", |
| "description": "Released cc box.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "cc_box" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/cc_mean", |
| "name": "cc_mean", |
| "description": "Released cc mean.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "cc_mean" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/qscore", |
| "name": "qscore", |
| "description": "Released qscore.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "qscore" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/recall_qscore", |
| "name": "recall_qscore", |
| "description": "Released recall qscore.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "recall_qscore" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/map_score", |
| "name": "map_score", |
| "description": "Released composite map-agreement score.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "map_score" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/rama_outlier", |
| "name": "rama_outlier", |
| "description": "Released rama outlier.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "rama_outlier" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/rama_favored", |
| "name": "rama_favored", |
| "description": "Released rama favored.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "rama_favored" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/rotamer_outlier", |
| "name": "rotamer_outlier", |
| "description": "Released rotamer outlier.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "rotamer_outlier" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/cbeta_deviations", |
| "name": "cbeta_deviations", |
| "description": "Released cbeta deviations.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "cbeta_deviations" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/clashscore", |
| "name": "clashscore", |
| "description": "Released clashscore.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "clashscore" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/rms_bonds", |
| "name": "rms_bonds", |
| "description": "Released rms bonds.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "rms_bonds" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/rms_angles", |
| "name": "rms_angles", |
| "description": "Released rms angles.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "rms_angles" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/molprobity_score", |
| "name": "molprobity_score", |
| "description": "Released molprobity score.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "molprobity_score" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/geom_steric", |
| "name": "geom_steric", |
| "description": "Released geom steric.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "geom_steric" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/geom_backbone", |
| "name": "geom_backbone", |
| "description": "Released geom backbone.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "geom_backbone" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/geom_sidechn", |
| "name": "geom_sidechn", |
| "description": "Released geom sidechn.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "geom_sidechn" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/geom_bonded", |
| "name": "geom_bonded", |
| "description": "Released geom bonded.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "geom_bonded" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/geom_score", |
| "name": "geom_score", |
| "description": "Released composite stereochemical-quality score.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "geom_score" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/train_pident", |
| "name": "train_pident", |
| "description": "Released observed training-sequence identity annotation; unavailable for AF3 rows.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "train_pident" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark_results/train_bin", |
| "name": "train_bin", |
| "description": "Released sequence-identity category; null is not an observed zero identity.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-003" |
| }, |
| "extract": { |
| "column": "train_bin" |
| } |
| } |
| } |
| ], |
| "key": [ |
| { |
| "@id": "benchmark_results/emd_id" |
| }, |
| { |
| "@id": "benchmark_results/method" |
| } |
| ] |
| }, |
| { |
| "@type": "cr:RecordSet", |
| "@id": "training_utility", |
| "name": "training_utility", |
| "description": "1,236 released target-by-checkpoint rows from the two ModelAngelo CNN retraining conditions. AVERAGE rows from the raw CSVs are excluded from this target-only view.", |
| "field": [ |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/emd_id", |
| "name": "emd_id", |
| "description": "EMDB accession identifying the curated map entry.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "emd_id" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/checkpoint", |
| "name": "checkpoint", |
| "description": "Retrained ModelAngelo CNN condition: MA_CryoAtlas or MA_Cryo2StructData.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "checkpoint" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/pdb_id", |
| "name": "pdb_id", |
| "description": "PDB identifier of the atomic structure supplied for this entry.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "pdb_id" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/category", |
| "name": "category", |
| "description": "Released category.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "category" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/total_residues", |
| "name": "total_residues", |
| "description": "Released total residues.", |
| "dataType": "sc:Integer", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "total_residues" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/resolution", |
| "name": "resolution", |
| "description": "Reported experimental map resolution in Angstrom.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "resolution" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/n_chains", |
| "name": "n_chains", |
| "description": "Released n chains.", |
| "dataType": "sc:Integer", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "n_chains" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/tm_score", |
| "name": "tm_score", |
| "description": "Released target-normalized TM-score.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "tm_score" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/ca_rmsd", |
| "name": "ca_rmsd", |
| "description": "Released C-alpha RMSD measurement in Angstrom; follow the paper protocol for interpretation.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "ca_rmsd" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/residue_coverage", |
| "name": "residue_coverage", |
| "description": "Released residue coverage.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "residue_coverage" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/sequence_match", |
| "name": "sequence_match", |
| "description": "Released sequence match.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "sequence_match" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/sequence_recall", |
| "name": "sequence_recall", |
| "description": "Released sequence-recall measurement.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "sequence_recall" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/completeness", |
| "name": "completeness", |
| "description": "Predicted-to-reference model-length ratio; values may exceed 1.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "completeness" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/gt_score", |
| "name": "gt_score", |
| "description": "Released composite structural-accuracy score.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "gt_score" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/cc_mask", |
| "name": "cc_mask", |
| "description": "Released cc mask.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "cc_mask" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/cc_volume", |
| "name": "cc_volume", |
| "description": "Released cc volume.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "cc_volume" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/cc_peaks", |
| "name": "cc_peaks", |
| "description": "Released cc peaks.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "cc_peaks" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/cc_box", |
| "name": "cc_box", |
| "description": "Released cc box.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "cc_box" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/cc_mean", |
| "name": "cc_mean", |
| "description": "Released cc mean.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "cc_mean" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/qscore", |
| "name": "qscore", |
| "description": "Released qscore.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "qscore" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/recall_qscore", |
| "name": "recall_qscore", |
| "description": "Released recall qscore.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "recall_qscore" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/map_score", |
| "name": "map_score", |
| "description": "Released composite map-agreement score.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "map_score" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/rama_outlier", |
| "name": "rama_outlier", |
| "description": "Released rama outlier.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "rama_outlier" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/rama_favored", |
| "name": "rama_favored", |
| "description": "Released rama favored.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "rama_favored" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/rotamer_outlier", |
| "name": "rotamer_outlier", |
| "description": "Released rotamer outlier.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "rotamer_outlier" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/cbeta_deviations", |
| "name": "cbeta_deviations", |
| "description": "Released cbeta deviations.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "cbeta_deviations" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/clashscore", |
| "name": "clashscore", |
| "description": "Released clashscore.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "clashscore" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/rms_bonds", |
| "name": "rms_bonds", |
| "description": "Released rms bonds.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "rms_bonds" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/rms_angles", |
| "name": "rms_angles", |
| "description": "Released rms angles.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "rms_angles" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/molprobity_score", |
| "name": "molprobity_score", |
| "description": "Released molprobity score.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "molprobity_score" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/geom_steric", |
| "name": "geom_steric", |
| "description": "Released geom steric.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "geom_steric" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/geom_backbone", |
| "name": "geom_backbone", |
| "description": "Released geom backbone.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "geom_backbone" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/geom_sidechn", |
| "name": "geom_sidechn", |
| "description": "Released geom sidechn.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "geom_sidechn" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/geom_bonded", |
| "name": "geom_bonded", |
| "description": "Released geom bonded.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "geom_bonded" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "training_utility/geom_score", |
| "name": "geom_score", |
| "description": "Released composite stereochemical-quality score.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-011" |
| }, |
| "extract": { |
| "column": "geom_score" |
| } |
| } |
| } |
| ], |
| "key": [ |
| { |
| "@id": "training_utility/emd_id" |
| }, |
| { |
| "@id": "training_utility/checkpoint" |
| } |
| ] |
| }, |
| { |
| "@type": "cr:RecordSet", |
| "@id": "archive_catalog", |
| "name": "archive_catalog", |
| "description": "71 main download archives: 68 training shards, two test archives, and one benchmark resource archive. Metadata-only bundles are separate auxiliary resources.", |
| "field": [ |
| { |
| "@type": "cr:Field", |
| "@id": "archive_catalog/path", |
| "name": "path", |
| "description": "Released path.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-014" |
| }, |
| "extract": { |
| "column": "path" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "archive_catalog/bytes", |
| "name": "bytes", |
| "description": "Exact compressed file size in bytes.", |
| "dataType": "sc:Integer", |
| "source": { |
| "fileObject": { |
| "@id": "file-014" |
| }, |
| "extract": { |
| "column": "bytes" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "archive_catalog/sha256", |
| "name": "sha256", |
| "description": "SHA-256 of the complete compressed file.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-014" |
| }, |
| "extract": { |
| "column": "sha256" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "archive_catalog/component", |
| "name": "component", |
| "description": "Released component.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-014" |
| }, |
| "extract": { |
| "column": "component" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "archive_catalog/entries", |
| "name": "entries", |
| "description": "Number of map entries in a training/test archive; null for the mixed resource package.", |
| "dataType": "sc:Integer", |
| "source": { |
| "fileObject": { |
| "@id": "file-014" |
| }, |
| "extract": { |
| "column": "entries" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "archive_catalog/size_gb", |
| "name": "size_gb", |
| "description": "Released size gb.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-014" |
| }, |
| "extract": { |
| "column": "size_gb" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "archive_catalog/download_url", |
| "name": "download_url", |
| "description": "Download URL recorded in the release index.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-014" |
| }, |
| "extract": { |
| "column": "download_url" |
| } |
| } |
| } |
| ], |
| "key": [ |
| { |
| "@id": "archive_catalog/path" |
| } |
| ] |
| }, |
| { |
| "@type": "cr:RecordSet", |
| "@id": "source_accessions", |
| "name": "source_accessions", |
| "description": "17,809 source-accession rows; PDB identifiers match the structures supplied in the fixed release.", |
| "key": [ |
| { |
| "@id": "source_accessions/emd_id" |
| } |
| ], |
| "field": [ |
| { |
| "@type": "cr:Field", |
| "@id": "source_accessions/emd_id", |
| "name": "emd_id", |
| "description": "EMDB accession identifying the curated map entry.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-096" |
| }, |
| "extract": { |
| "column": "emd_id" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "source_accessions/pdb_id", |
| "name": "pdb_id", |
| "description": "PDB identifier of the atomic structure supplied for this entry.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-096" |
| }, |
| "extract": { |
| "column": "pdb_id" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "source_accessions/split", |
| "name": "split", |
| "description": "Fixed training or test membership.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-096" |
| }, |
| "extract": { |
| "column": "split" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "source_accessions/emdb_map_url", |
| "name": "emdb_map_url", |
| "description": "Released emdb map url.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-096" |
| }, |
| "extract": { |
| "column": "emdb_map_url" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "source_accessions/map_filename", |
| "name": "map_filename", |
| "description": "Released map filename.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-096" |
| }, |
| "extract": { |
| "column": "map_filename" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "source_accessions/resolution", |
| "name": "resolution", |
| "description": "Reported experimental map resolution in Angstrom.", |
| "dataType": "sc:Float", |
| "source": { |
| "fileObject": { |
| "@id": "file-096" |
| }, |
| "extract": { |
| "column": "resolution" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "source_accessions/structure_determination_method", |
| "name": "structure_determination_method", |
| "description": "Released structure determination method.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-096" |
| }, |
| "extract": { |
| "column": "structure_determination_method" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "source_accessions/sample_type", |
| "name": "sample_type", |
| "description": "Released sample type.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-096" |
| }, |
| "extract": { |
| "column": "sample_type" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "source_accessions/map_release_date", |
| "name": "map_release_date", |
| "description": "Released map release date.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-096" |
| }, |
| "extract": { |
| "column": "map_release_date" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "source_accessions/title", |
| "name": "title", |
| "description": "Released title.", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "file-096" |
| }, |
| "extract": { |
| "column": "title" |
| } |
| } |
| } |
| ] |
| } |
| ], |
| "rai:dataLimitations": [ |
| "The modeling and benchmark tasks focus on protein chains. Deposited coordinate files may retain additional molecular components; the release is not a nucleotide-modeling benchmark.", |
| "Entries require a usable experimental map, deposited atomic model, protein sequence and quality screening. Deposited coordinates and metadata can still contain errors; curation does not establish atomic correctness in every region.", |
| "The 618-target comparison subset depends on overlap/length eligibility and successful method outputs, and may underrepresent large or computationally difficult assemblies. The full fixed test pool has 1,152 entries.", |
| "A map is treated as a static target. Whole-structure metrics do not exhaustively characterize heterogeneous conformations or functionally important local regions. Generated predictions require validation against experimental density before biological interpretation.", |
| "Clinical decision-making and treating model predictions as experimentally validated structures are not established uses." |
| ], |
| "rai:dataBiases": [ |
| "Coverage follows EMDB/PDB deposition and the availability of paired maps, coordinates and protein sequences, not a balanced sample of biological structures.", |
| "Resolution-dependent quality filtering favors entries with strong map support and can reduce coverage of lower-resolution experimental maps.", |
| "The common benchmark has method-completion and computational-resource selection effects. Compare stratified results and report training-data overlap instead of interpreting aggregate scores as universal generalization." |
| ], |
| "rai:personalSensitiveInformation": [ |
| "No newly collected human-subject, clinical or person-level health records are included. Macromolecular sequences and organism metadata describe scientific structures rather than identifiable participants.", |
| "Original deposited CIF metadata can retain publicly available depositor names or contact information. These source attribution fields are inherited from public PDB records." |
| ], |
| "rai:dataUseCases": [ |
| "Research on protein atomic model building from experimental cryo-EM density maps and sequences; development and testing on the fixed train/test split.", |
| "Reproducible comparison of structural accuracy, experimental map agreement and stereochemical quality using complementary released raw/composite metrics.", |
| "Analysis by resolution, sequence length, chain count and training-sequence similarity. Metadata indexes and example previews support retrieval and inspection; they are not separate training/evaluation populations.", |
| "The benchmark characterizes modeling behavior under its published eligibility, input and tool assumptions. Fairness guarantees, clinical validity and general nucleotide modeling have not been established." |
| ], |
| "rai:dataSocialImpact": "The intended benefit is more reproducible structural-biology research and evaluation. Potential harms include over-reliance on plausible but incorrect generated structures, misleading downstream biological conclusions and general misuse of structural-modeling tools. Retained source accessions, fixed splits, file hashes, complementary measurements and explicit limitations support verification; predictions should be checked against experimental density.", |
| "rai:hasSyntheticData": true, |
| "rai:dataCollection": "Paired public EMDB maps, PDB coordinates and protein sequences from records available up to March 2026 were assembled and curated. The experimental dataset has 17,809 fixed map-model-sequence entries. Model-generated CIF predictions and evaluation outputs are included separately in the benchmark resource package.", |
| "rai:dataCollectionType": [ |
| "Secondary Data analysis", |
| "Software Collection", |
| "Web API" |
| ], |
| "rai:dataCollectionRawData": "Experimental density maps and accession metadata originate from EMDB; deposited atomic structures and sequences originate from PDB. Model predictions are outputs of ModelAngelo, CryoAtom2, EMProt, E3-CryoFold, AlphaFold 3 and two ModelAngelo CNN retraining conditions. These outputs are labeled by method/condition and are not experimental reference coordinates.", |
| "rai:dataCollectionMissingData": "Entries without paired usable structures or protein sequences were excluded. Unmodeled residues are represented in the aligned/trimmed FASTA representations rather than filled with invented atomic coordinates. The complete fixed test pool remains available beyond the 618-target common comparison subset.", |
| "rai:dataPreprocessingProtocol": [ |
| "The documented curation protocol checks map-model coordinate agreement, performs realignment where needed, aligns sequences to modeled chains and supplies terminal-trimmed sequence representations.", |
| "Q-score-based and unmodeled-density screening retained 17,809 of the 21,229 eligible paired candidates. Reported resolutions and split membership are retained in the published metadata.", |
| "MMseqs2-based sequence clustering and complex-level grouping define the fixed 16,657-entry training and 1,152-entry test split. The benchmark is the common 618-target eligible comparison subset.", |
| "Dataset files are packaged by complete EMD entries. Dataset catalogs use the PDB identifiers of the packaged structures; per-file inventories and archive SHA-256 values describe the published bytes.", |
| "The image previews are independently scaled maximum-intensity projections of ten existing maps along stored array axes. They are display aids, not new experimental densities or quantitative quality labels." |
| ], |
| "rai:dataManipulationProtocol": "Map/structure coordinate alignment, sequence alignment/trimming, quality screening, fixed splitting, benchmark selection and release packaging are documented transformations. Experimental map/CIF/FASTA payloads are kept distinct from model-generated prediction files. Catalog and normalized result views do not recompute or rescale published measurements.", |
| "rai:dataImputationProtocol": "No experimental map voxels or reference atomic coordinates are imputed as new ground truth. Generated model predictions are separate benchmark outputs; unresolved reference sequence regions remain unmodeled.", |
| "rai:dataAnnotationProtocol": [ |
| "Scientific attribution and deposited coordinates are inherited from EMDB/PDB. Split membership, curation annotations, sequence-similarity measurements and modeling metrics are software-derived. No crowdsourced labeling or newly recruited human annotators were used.", |
| "The synthetic component consists of the released prediction CIFs from the named modeling methods and CNN retraining conditions. This metadata does not rerun those models or introduce new predictions. Methods and conditions are identified by folder/table columns; the official reference and retraining result sets are separate." |
| ], |
| "rai:machineAnnotationTools": [ |
| "UCSF ChimeraX", |
| "Clustal Omega", |
| "MMseqs2", |
| "Phenix", |
| "US-align", |
| "the named modeling methods" |
| ], |
| "rai:dataReleaseMaintenancePlan": "CryoAtlas v1.0 is a fixed public snapshot hosted on Hugging Face. Data-file URLs in this Croissant are pinned to repository commit 0779e539e03d62a238eb77427586f9261d3e52c7. Archive hashes, split lists and file inventories define the snapshot. The authors maintain the project website and release documentation. Corrections or additions should be documented as a subsequent revision/version with updated metadata and checksums; fixed split changes require a new version.", |
| "prov:wasDerivedFrom": [ |
| { |
| "@id": "https://www.ebi.ac.uk/emdb/", |
| "@type": "prov:Entity", |
| "name": "Electron Microscopy Data Bank" |
| }, |
| { |
| "@id": "https://www.rcsb.org/", |
| "@type": "prov:Entity", |
| "name": "Protein Data Bank" |
| } |
| ], |
| "prov:wasGeneratedBy": [ |
| { |
| "@type": "prov:Activity", |
| "prov:label": "Pairing, alignment and curation", |
| "description": "Collect paired EMDB/PDB map-model-sequence records through March 2026; check coordinate agreement, align sequences, apply quality criteria and preserve source accessions." |
| }, |
| { |
| "@type": "prov:Activity", |
| "prov:label": "Fixed split and benchmark selection", |
| "description": "Construct the fixed train/test split and the 618-target common comparison subset using the published sequence, eligibility and completion rules." |
| }, |
| { |
| "@type": "prov:Activity", |
| "prov:label": "Prediction and metric generation", |
| "description": "Release previously generated baseline and retrained ModelAngelo predictions and their evaluation tables. Model-generated structures are separate from experimental maps and deposited reference models." |
| }, |
| { |
| "@type": "prov:Activity", |
| "prov:label": "Versioned publication", |
| "description": "Publish 68 independent training archives, two test archives and the complete benchmark resource package, with typed catalogs, frozen file lists and SHA-256 checksums." |
| } |
| ] |
| } |
|
|
