node_id	process	scale	compartment	cell_type	time_context	legacy_single_axis_label	evidence_axes	model_readiness	claim_ceiling	source_ids	next_experiment
DMD-P001	DMD genomic lesion	gene_molecular	genetic	disease_anchor	disease_origin	MEASURED	{"origin":"OBSERVED","context_match":"CROSS_SPECIES","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	DMD disease anchor; does not specify downstream cell-state effect size.	DMD-MUSCLE-REVIEW	Matched genotype and dystrophin-status confirmation in the selected model.
DMD-P002	Dystrophin deficiency	protein_myofibre	myofibre	myofibre	disease_origin	MEASURED	{"origin":"OBSERVED","context_match":"LOCUS_CORRECTION","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Disease-associated dystrophin deficiency; not a candidate perturbation response.	DMD-MUSCLE-REVIEW | GSE272233	Quantify dystrophin rescue and membrane integrity in matched DMD/control fibres.
DMD-P003	Sarcolemmal / mechanical instability	cellular_mechanical	myofibre	myofibre	injury_initiation	CONTEXTUAL	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Mechanistic disease-core context; local transition probability is not calibrated.	DMD-MUSCLE-REVIEW | PRJNA772047	Matched mechanical-stress and membrane-integrity assay with genotype control.
DMD-P004	Ca2+ / cellular stress state	cellular_stress	myofibre	myofibre	injury_initiation	CONTEXTUAL	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Disease-associated stress context; the organoid pathway readout is descriptive and does not provide perturbation-conditioned calcium or metabolic prediction.	DMD-MUSCLE-REVIEW | PRJNA772047 | GSE277637	Time-matched calcium, oxidative and viability readouts after defined mechanical challenge.
DMD-P005	Myofibre injury	tissue_cellular	myofibre	myofibre	acute_injury	CONTEXTUAL	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Disease injury context; cannot establish candidate-specific injury probability.	DMD-MUSCLE-REVIEW | DMD-SPATIAL-CONTEXT	Prospective injury time course with donor-aware replication.
DMD-P006	Degeneration / necrosis	tissue	tissue	injured_myofibre	acute_injury	MEASURED	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Measured disease pathology context; no causal ranking of upstream candidates.	PRJNA772047 | DMD-SPATIAL-CONTEXT	Spatially matched injury and immune-clearance sampling across disease stage.
DMD-P007	Damage / inflammatory signalling	tissue_signal	tissue	multicellular	acute_injury	CONTEXTUAL	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Inflammatory context; organoid pathway deltas do not resolve cell source, individual ligand activity or causal strength.	PRJNA772047 | DMD-SPATIAL-CONTEXT | GSE277637	Matched spatial and temporal measurement of damage signals and responding compartments.
DMD-P008	Monocyte / myeloid recruitment	cell_population	immune	monocyte_myeloid	inflammation_clearance	MEASURED	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Disease-associated myeloid recruitment context; no cell-specific causal effect estimate.	PRJNA772047 | DMD-SPATIAL-CONTEXT	Donor- and stage-matched myeloid recruitment measurement with spatial coordinates.
DMD-P009	Phagocytic / clearance macrophage state	cell_state	immune	macrophage	inflammation_clearance	CONTEXTUAL	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	State-associated macrophage context; not an M1/M2 assignment or causal clearance estimate.	DMD-SPATIAL-CONTEXT | GSE288958	State-resolved phagocytosis and clearance assay in matched DMD/control context.
DMD-P010	Repair-associated macrophage state	cell_state	immune	macrophage	repair_regeneration	CONTEXTUAL	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	State-associated repair context; no direct repair efficacy or fate probability.	DMD-SPATIAL-CONTEXT | GSE288958	Time-resolved state annotation with functional repair co-readout.
DMD-P011	Fibrosis-associated macrophage state	cell_state	immune	macrophage	remodelling_failure	CONTEXTUAL	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Association and candidate communication only; macrophage-to-FAP causality is not established.	DMD-SPATIAL-CONTEXT | GSE288958	Matched macrophage-conditioned or SPP1 perturbation study on DMD FAP phenotype.
DMD-P012	MuSC activation	cell_state	myogenic	satellite_cell	repair_regeneration	CONTEXTUAL	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Myogenic activation context; no DMD perturbation-conditioned transition probability.	GSE288958 | GSE52529	Donor-aware MuSC activation time course in DMD and matched control.
DMD-P013	Myogenic proliferation	cell_state	myogenic	myogenic_progenitor	repair_regeneration	CONTEXTUAL	{"origin":"OBSERVED","context_match":"SAME_TISSUE","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	REFERENCE_ONLY	Reference myogenic state context; not a DMD perturbation outcome.	GSE52529 | GSE293514	Matched DMD/control perturbation with donor and state-resolved proliferation.
DMD-P014	Myogenic differentiation	cell_state	myogenic	myogenic_progenitor	repair_regeneration	MEASURED	{"origin":"OBSERVED","context_match":"LOCUS_CORRECTION","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	REFERENCE_ONLY	Measured unperturbed human-myogenic trajectory plus line-aware DMD organoid pathway context; DMD perturbation response and cell-state transition remain not measured.	GSE52529 | GSE272233 | GSE277637	Matched DMD/control perturbation and differentiation endpoint with frozen Study Card.
DMD-P015	Myoblast fusion	cell_function	myogenic	fusion_competent_myoblast	repair_regeneration	MEASURED	{"origin":"OBSERVED","context_match":"SAME_TISSUE","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	CONTEXT_ONLY	Healthy-human-myoblast fusion context is observed; it is not DMD replication or treatment efficacy.	GSE293514	DMD/control matched perturbation with fusion, membrane and viability endpoints.
DMD-P016	Regenerated myofibre	tissue_cellular	myofibre	regenerated_myofibre	repair_regeneration	CONTEXTUAL	{"origin":"OBSERVED","context_match":"LOCUS_CORRECTION","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Regeneration context; no calibrated regenerated-fibre probability or function prediction.	GSE272233 | DMD-SPATIAL-CONTEXT	Longitudinal regenerated-fibre identity and function in matched DMD/control.
DMD-P017	FAP activation	cell_state	stromal	FAP	repair_regeneration	CONTEXTUAL	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Disease-associated FAP state; macrophage-to-FAP causality is not established.	GSE288958 | DMD-SPATIAL-CONTEXT	Macrophage-conditioned or SPP1 perturbation study with DMD FAP fibrotic readouts.
DMD-P018	Regeneration-supportive stromal state	cell_state	stromal	FAP_stromal	repair_regeneration	CONTEXTUAL	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Contextual niche-support state; no cell-cell causal effect is measured.	GSE288958 | DMD-SPATIAL-CONTEXT	Co-culture or conditioned-medium assay with matched myogenic readouts.
DMD-P019	Fibrotic stromal / FAP state	cell_state	stromal	FAP_stromal	remodelling_failure	MEASURED	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Disease-associated fibrotic stromal context; no intervention efficacy estimate.	GSE288958 | DMD-SPATIAL-CONTEXT	State-matched anti-fibrotic perturbation with ECM and myogenic consequence readouts.
DMD-P020	ECM deposition / remodeling	tissue_matrix	ecm	extracellular_matrix	remodelling_failure	MEASURED	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Measured tissue/remodeling context with a descriptive organoid ECM axis; no causal edge to a candidate gene or FAP intervention is established.	DMD-SPATIAL-CONTEXT | PRJNA772047 | GSE277637	Spatial ECM quantification paired with FAP and myogenic state measurements.
DMD-P021	Fibrosis / adipogenic remodeling	tissue	tissue	fibrotic_adipogenic_tissue	remodelling_failure	MEASURED	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Disease tissue-remodeling endpoint; no therapeutic efficacy or patient outcome prediction.	PRJNA772047 | DMD-SPATIAL-CONTEXT	Stage- and region-matched fibrosis/adipogenic quantification with function.
DMD-P022	Endothelial / vascular response	cell_state_tissue	vascular	endothelial	repair_regeneration	CONTEXTUAL	{"origin":"OBSERVED","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Vascular context only; no perfusion or cross-compartment causal estimate.	GSE288958 | DMD-SPATIAL-CONTEXT	Spatial vascular profiling paired with injury and regeneration stage.
DMD-P023	Regenerative niche	multicellular	multicellular	myogenic_immune_stromal_vascular_niche	repair_regeneration	COMPUTATIONAL	{"origin":"COMPUTATIONAL","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"RELEASED","outcome_evaluability":"EVALUABLE","outcome_direction":"AMBIGUOUS"}	NOT_CALIBRATED	Spatial/contextual niche hypothesis; communication inference is not causal validation.	GSE288958 | DMD-SPATIAL-CONTEXT	Matched spatial perturbation or co-culture study with pre-registered interaction readouts.
DMD-P024	Functional muscle output	organ_function	function	muscle_tissue	chronic_failure	MISSING	{"origin":"MISSING","context_match":"TARGET_CONTEXT","unit_structure":"source_defined_biological_unit","lifecycle":"DRAFT","outcome_evaluability":"MISSING_TARGET_CONTEXT_OUTCOME","outcome_direction":"NOT_APPLICABLE"}	NOT_CALIBRATED	Functional endpoint is required for disease-relevant success; current candidate-level DMD outcome is absent.	STUDY-CARD-MANIFEST	Matched DMD/control perturbation with molecular, functional, toxicity and replication endpoints.