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:
    - "[object Object]"
    - "[object Object]"
    - "[object Object]"
  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"
