{ "object_id": "SC:v1.0.0-database-resource:GFOD2:1.5-DRAFT", "card_schema": "nmd-vcell-study-card/1.5", "card_version": "1.5", "resource_release": "v1.0.0-database-resource", "evidence_freeze": "2026-07-25", "interface_build": "EA-20260729-18", "gene": "GFOD2", "card_type": "evidence_import_audit", "current_action_code": "hold_pending_external_audit", "current_action": "Provisional hold · external report not yet audited", "lifecycle": { "state": "DRAFT", "revision": 1, "immutable": false, "registered_at": null, "supersedes": null, "immutable_after_registration": true }, "decision_blocking_gap": { "code": "GAP-09", "label": "External quantitative evidence has not been imported and audited" }, "highest_missing_evidence_layer": "L4_dmd_functional_validation", "secondary_gaps": [ "GAP-02 independent muscle-context perturbation", "GAP-03 DMD-relevant functional validation", "GAP-07 independent replication" ], "frozen_evidence_snapshot": { "snapshot_schema": "nmd-vcell-study-card-frozen-evidence-snapshot/1.0", "source_record": "gene/GFOD2", "highest_supported_level": "L2_observed_same_context_perturbation", "highest_assessed_level": "L2_observed_same_context_perturbation", "observed_hepg2_perturbation": { "assessment_status": "assessed", "support_status": "supported", "observed_cells": 127 }, "external_context_screen": { "assessment_status": "not_assessed", "support_status": null, "hit": null, "effect_size": null, "fdr": null, "interpretation": null }, "dmd_prior": { "integrated_prior_direction": "up", "source_direction_state": "conflicted", "source_agreement_proportion": 0.5, "agreeing_sources": 2, "assessed_sources": 4, "coverage_state": "4_of_4_sources", "uncertainty_state": "direction_conflict_retained" }, "context_metrics": { "skeletal_muscle_median_tpm": 2.94732, "depmap_median_gene_effect": -0.0768458591182602, "moderate_dependency_flag": false }, "visual_boundary": "Descriptive frozen evidence snapshot only; no score, rank, cluster, prediction claim or intervention recommendation is generated." }, "unresolved_question": "Does the author-reported external evidence for GFOD2 meet provenance, context, independence and negative-evidence criteria?", "biological_context": "External-evidence audit only; no new biological escalation until the quantitative import is complete.", "perturbation_modality": "None. This card imports and audits an existing evidence object.", "comparator_and_controls": [ "Dataset accession and source owner.", "Raw/processed availability.", "Target mapping and assay context.", "Primary endpoint, effect size and uncertainty.", "Independent reproduction and import acceptance criteria." ], "primary_endpoint": "Completeness, reproducibility and claim-ceiling classification of the imported quantitative result.", "secondary_endpoints": [ "Provenance completeness.", "Context match.", "Negligible-effect interpretation.", "Independent reproduction status." ], "primary_estimand": "Imported effect estimate with its uncertainty, denominator and exact contrast; no reconstructed estimate is accepted without provenance.", "state_transition_design": { "scientific_object": "perturbation × cell state × disease context × time × phenotype", "mechanism_hypothesis": "Required before registration: state the proposed early molecular mediator, the expected cell-state transition and the downstream functional consequence.", "cell_context_fields": { "disease_background": "Required before registration: healthy, DMD or isogenic corrected.", "myogenic_state": "Required before registration: proliferating myoblast, early differentiation, fusion or maturing myotube.", "donor_or_isogenic_pair": "Required before registration; preserve donor-specific estimates." }, "timepoint_plan": [ { "window": "6–12 h", "role": "early molecular or signalling response", "status": "planning_default_requires_assay_calibration" }, { "window": "24–48 h", "role": "regulatory program and cell-state transition", "status": "planning_default_requires_assay_calibration" }, { "window": "4–7 d", "role": "differentiation and functional phenotype", "status": "planning_default_requires_assay_calibration" } ], "endpoint_domains": { "target_engagement": [ "mRNA", "protein where validated", "perturbation efficiency" ], "functional": [ "fusion", "morphology", "membrane integrity", "calcium", "contraction" ], "safety": [ "viability", "proliferation", "differentiation blockade", "global stress" ], "replication": [ "reagent", "donor or isogenic pair", "future batch" ] }, "cell_cell_consequence": { "current_status": "not_assessed", "future_levels": [ "conditioned medium", "two-cell co-culture", "three-dimensional muscle model", "spatial perturbation model" ] }, "response_archetype": { "current_status": "not_assessed", "allowed_values": [ "robust_responder", "dmd_specific_responder", "donor_variable", "state_specific", "toxic_responder", "null_with_equivalence_margin", "discordant", "qc_failure", "inconclusive" ] } }, "perturbation_direction_rationale": { "selected_hypothesis": "not_applicable", "allowed_hypotheses": [ "not_applicable" ], "required_justification": "No new perturbation direction is nominated by an evidence-import audit." }, "minimally_important_effect": null, "negligible_effect_margin": null, "suggested_sample_size_range": null, "randomisation_unit": null, "blocking_factors": [ "Source study.", "Assay batch.", "Biological context.", "Analysis version." ], "statistical_model": "Reproduce the source model exactly when code and inputs permit; otherwise classify as not reproducible.", "multiple_testing_family": "Preserve the source family and correction; do not reinterpret an isolated P value.", "missing_data_rule": "Define exclusions before unblinding; report all missing units and reasons; do not single-impute primary outcomes without a prespecified sensitivity analysis.", "assay_qc_thresholds": [ "Accession resolvable.", "Raw or sufficient processed data available.", "Target mapping exact.", "Effect, interval and denominator present.", "Code/provenance sufficient for reproduction." ], "guide_concordance_rule": "Not applicable unless the imported study reports multiple reagents; if so, preserve reagent-specific results.", "donor_replication_rule": "Record whether the source result replicates across donors/samples; absence is a limitation, not a negative result.", "estimated_time_band": "2–10 working days after complete source delivery; planning estimate only.", "estimated_cost_band": "Institution- and assay-dependent; obtain a local itemised quote before registration.", "preregistration_status": "draft_requires_source_accession_denominator_contrast_and_reproducibility_audit", "inferential_unit": "Required import field: preserve the source study’s declared inferential unit exactly.", "evidence_import_requirements": [ "Source accession and owner.", "Raw and processed data availability.", "Exact denominator and exclusion flow.", "Effect estimate, interval and primary contrast.", "Original allocation and inferential unit.", "Preregistration status.", "Code and environment reproducibility.", "Reagent and donor replication.", "Negative-result definition.", "Selective-reporting assessment." ], "planning_fields_not_applicable": [ "minimally_important_effect", "negligible_effect_margin", "suggested_sample_size_range", "randomisation_unit" ], "stop_rules": [ "Stop or classify as infeasible if a required numeric QC threshold fails.", "Do not interpret a nonsignificant result as no material effect without a negligible-effect interval.", "Do not change canonical candidate status automatically; require governed review." ], "escalation_rule": "Retain, release or formally change the hold only after provenance, independence and negative-evidence gates are audited.", "evidence_transition": "Author report pending import → audited evidence object → governed status decision.", "data_release_plan": "Release the frozen card, protocol identifiers, analysis code, complete denominators and results irrespective of direction; never overwrite the registered card.", "boundary": "This Study Card is an evidence-gated design scaffold, not a protocol, power calculation, safety claim, prediction or therapeutic recommendation.", "stable_url": "study-card/GFOD2", "exports": { "json": "api/v1.1/study-cards/GFOD2.json", "yaml": "downloads/study-cards/GFOD2.yaml", "tsv": "downloads/study-cards/GFOD2.tsv" } }