| { |
| "protocol_version": 1, |
| "frozen_on": "2026-07-20", |
| "purpose": "Prospective temporal and homology-cold absolute enzyme kinetics benchmark", |
| "development_corpus": { |
| "name": "UniKP/DLKcat kcat development corpus", |
| "sha256": "13643b0b36374f8d3f64d8b014882cf1b3b58946eeaae2b9dcd59e8b2c2d6719", |
| "size_bytes": 12132719, |
| "rows": 17010, |
| "record_level_citations_available": false |
| }, |
| "temporal_gate": { |
| "primary_measurement_article_published_on_or_after": "2023-01-01", |
| "deposit_date_alone_is_not_sufficient": true, |
| "preprints_require_a_stable_doi_and_explicit_dataset_license": true |
| }, |
| "license_gate": { |
| "accepted": [ |
| "CC0-1.0", |
| "CC-BY-4.0" |
| ], |
| "deposit_license_must_cover_the_measurement_table": true, |
| "third_party_database_compilations_require_source_level_redistribution_rights": true |
| }, |
| "record_inclusion": { |
| "direct_experimental_measurement": true, |
| "accepted_endpoints": [ |
| "kcat_s-1", |
| "km_molar", |
| "kcat_per_km_M-1_s-1" |
| ], |
| "primary_endpoint": "log10_kcat_s-1", |
| "full_protein_sequence_or_unambiguous_accession_and_variant": true, |
| "single_defined_substrate_with_structure_identifier": true, |
| "required_provenance": [ |
| "measurement_article_doi", |
| "dataset_doi_or_stable_record_url", |
| "source_file", |
| "source_row_or_table_cell", |
| "organism", |
| "enzyme_identity", |
| "substrate_name", |
| "endpoint", |
| "value", |
| "unit", |
| "assay_temperature_if_reported", |
| "assay_pH_if_reported" |
| ], |
| "derived_kcat_requires_enzyme_concentration_and_documented_formula": true, |
| "model_predictions_pseudolabels_and_relative_activity_are_excluded": true, |
| "bulk_environmental_or_community_apparent_kinetics_are_excluded": true |
| }, |
| "leakage_gates": { |
| "exact_sequence_substrate_overlap_with_development": 0, |
| "mmseqs_min_identity": 0.3, |
| "mmseqs_coverage": 0.8, |
| "mmseqs_coverage_mode": 0, |
| "exclude_all_sequences_with_development_hit": true, |
| "publication_overlap": "exclude_when_known; report unavailable when development citations are absent", |
| "substrate_exact_and_murcko_scaffold_overlap": "report_and_stratify" |
| }, |
| "diversity_and_size_gate": { |
| "minimum_records": 300, |
| "minimum_mmseqs_families": 30, |
| "minimum_unique_substrates": 50, |
| "maximum_records_per_family": 20, |
| "minimum_records_per_reported_family_metric": 3 |
| }, |
| "freeze_policy": { |
| "candidate_metadata_and_homology_may_be_audited_before_freeze": true, |
| "model_predictions_are_prohibited_before_final_selection_freeze": true, |
| "labels_may_not_drive_record_caps_or_family_selection": true, |
| "primary_model_checkpoint_and_metrics_must_be_frozen_before_evaluation": true, |
| "one_final_evaluation_only": true, |
| "failed_readiness_gate_means_no_model_evaluation": true |
| }, |
| "planned_comparators": [ |
| "train_mean", |
| "morgan_mlp", |
| "late_concat", |
| "task_query", |
| "DLKcat_when_training_overlap_is_reported_as_unavailable" |
| ], |
| "claim_boundary": "Until every readiness gate passes, collected records are a curation pool and not an external benchmark. No model may be selected or tuned from this pool." |
| } |
|
|
