Stable Study Card 1.5

SC:v1.0.0-database-resource:GFOD2:1.5-DRAFTDRAFT

GFOD2

evidence import audit Provisional hold · external report not yet audited

Does the author-reported external evidence for GFOD2 meet provenance, context, independence and negative-evidence criteria?

Registration completeness38%

Missing before registration

source accession
numeric effect and interval
denominator and exclusion flow
code/provenance reproducibility
negative-evidence rule

Study Card visual summary

Frozen evidence and registration route

This multi-panel view turns the frozen Study Card fields into a visual audit of what is known, what is missing and what must be registered next.

BoundaryDescriptive frozen evidence snapshot only; no score, rank, cluster, prediction claim or intervention recommendation is generated.

Registration readiness 38% 5 open fields

Current supported level L2 observed same context perturbation Observed evidence ceiling in this record

Highest assessed context L2 observed same context perturbation Assessment does not imply support

Target closure layer L4 DMD functional validation required

DMD source agreement 50% 2/4 sources · conflicted

Muscle expression 2.95 TPM above 1 TPM context flag

Frozen evidence route

L1Resource recordHGNC-resolved typed research object
L2Observed HepG2 perturbation127 observed cells
L3aExternal context screennot assessed
L3bIndependent perturbation replicationsame-perturbation replication absent
L4DMD muscle functional validationDMD-relevant functional validation absent
REGRegistered Study Card5 open fields before registration

Bioinformatics result snapshot

Legacy integrated DMD priorup

Source agreement50%

Skeletal-muscle TPM2.95

External screennot assessed

Dependency cautionnot flagged

DepMap effect-0.077

Evidence-to-experiment route

Context

External-evidence audit only; no new biological escalation until the quantitative import is complete.

Perturb

None. This card imports and audits an existing evidence object.

Endpoint

Completeness, reproducibility and claim-ceiling classification of the imported quantitative result.

Infer

Required import field: preserve the source study’s declared inferential unit exactly.

Model

Reproduce the source model exactly when code and inputs permit; otherwise classify as not reproducible.

Registration gap map

source accession
numeric effect and interval
denominator and exclusion flow
code/provenance reproducibility
negative-evidence rule

These bars are field-state indicators only. They do not create a target score, rank, cluster or prediction claim.

Predeclared design scaffold

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.

Primary endpoint

Completeness, reproducibility and claim-ceiling classification of the imported quantitative result.

Primary estimand

Imported effect estimate with its uncertainty, denominator and exact contrast; no reconstructed estimate is accepted without provenance.

Inferential unit

Required import field: preserve the source study’s declared inferential unit exactly.

Statistical model

Reproduce the source model exactly when code and inputs permit; otherwise classify as not reproducible.

Decision-blocking gap

GAP-09 External quantitative evidence has not been imported and audited

Highest missing evidence layer

L4 dmd functional validation

GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication

Perturbation-direction rationale

Current selection: not applicable

No new perturbation direction is nominated by an evidence-import audit.

Allowed registered hypotheses: not applicable.

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.

Secondary endpoints

Provenance completeness.
Context match.
Negligible-effect interpretation.
Independent reproduction status.

State-transition extension

Mechanism hypothesis and registered time axis

Scientific object: perturbation × cell state × disease context × time × phenotype

Required before registration: state the proposed early molecular mediator, the expected cell-state transition and the downstream functional consequence.

6–12 hearly molecular or signalling response

planning default requires assay calibration

24–48 hregulatory program and cell-state transition

planning default requires assay calibration

4–7 ddifferentiation and functional phenotype

planning default requires assay calibration

Cell context fields

Required before registration: healthy, DMD or isogenic corrected. Required before registration: proliferating myoblast, early differentiation, fusion or maturing myotube. Required before registration; preserve donor-specific estimates.

Cell–cell consequence

Current status: not assessed. Future levels: conditioned medium; two-cell co-culture; three-dimensional muscle model; spatial perturbation model.

Blocking factors

Source study.
Assay batch.
Biological context.
Analysis version.

Assay QC thresholds

Accession resolvable.
Raw or sufficient processed data available.
Target mapping exact.
Effect, interval and denominator present.
Code/provenance sufficient for reproduction.

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.

Prospective planning fields are intentionally not applied: minimally_important_effect, negligible_effect_margin, suggested_sample_size_range, randomisation_unit.

Multiplicity and missing data

Preserve the source family and correction; do not reinterpret an isolated P value.

Define exclusions before unblinding; report all missing units and reasons; do not single-impute primary outcomes without a prespecified sensitivity analysis.

Replication rules

Not applicable unless the imported study reports multiple reagents; if so, preserve reagent-specific results.

Record whether the source result replicates across donors/samples; absence is a limitation, not a negative result.

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.

Time and cost2–10 working days after complete source delivery; planning estimate only. Institution- and assay-dependent; obtain a local itemised quote before registration.

Preregistration statusdraft requires source accession denominator contrast and reproducibility audit

Lifecycle ruleThis draft is editable. Registration requires a timestamp and checksum; a registered revision is immutable and any correction must supersede it.

Escalation ruleRetain, release or formally change the hold only after provenance, independence and negative-evidence gates are audited.

Evidence transitionAuthor report pending import → audited evidence object → governed status decision.

Data-release planRelease 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.