{ "schema": "nmd-vcell-dmd-process-map/1.1", "map_id": "DMD-PROCESS-V1", "disease": "DMD", "organ_scope": "skeletal_muscle", "release_state": "EVIDENCE_AWARE_MECHANISTIC_MAP", "layout_policy": { "algorithm": "manual_hierarchical_dag", "seed": 42, "warning": "Node coordinates encode a reproducible reading order only; position and distance are not biological evidence." }, "edge_line_types": { "DIRECT_CAUSAL": "strong solid arrow", "MEASURED_TRANSITION": "thin solid arrow", "CONTEXTUAL_ASSOCIATION": "dashed arrow", "COMPUTATIONAL_INFERENCE": "dotted arrow", "MISSING_REQUIRED_OUTCOME": "ghost dashed arrow" }, "source_objects": [ { "source_id": "GSE272233", "source_type": "dataset", "label": "DMD-locus correction transcript reference", "route": "/resource/measured-dmd-evidence/", "role": "measured DMD correction and induction reference" }, { "source_id": "PRJNA772047", "source_type": "dataset", "label": "Human DMD patient skeletal muscle reference", "route": "/resource/measured-dmd-evidence/", "role": "measured disease-pathway context" }, { "source_id": "GSE288958", "source_type": "dataset", "label": "Human DMD/BMD/control muscle snRNA-seq and spatial context", "route": "/resource/api/v1.1/context-objects/GSE288958.json", "role": "read-only disease cell-state and spatial context", "analysis_id": "gse288958_sample_aware_module_context_v01", "inferential_unit": "Independent biopsy/sample; cells are nested observations and are not independent disease replicates", "analysis_scope": "Sample-aware stable-module mean summaries across 11 samples, with all-sample reporting and predeclared Normal_2 exclusion sensitivity; no p-values or disease-effect ranking", "pathway_axes": [ "FAP / ECM fibrosis", "Regeneration / stress", "Macrophage inflammatory state", "Oxidative / mitochondrial context", "Vascular / endothelial context" ], "claim_ceiling": "Supports descriptive sample-aware cell-state context and context-only candidate alignment; it does not establish a disease effect, causal transition, therapeutic response, model-training target or functional endpoint.", "artifact_routes": [ { "label": "Sample-aware context object", "route": "/resource/api/v1.1/context-objects/GSE288958.json" }, { "label": "Formal QC gate", "route": "/resource/api/v1.1/gse288958_qc_gate.json" }, { "label": "Reference audit", "route": "/resource/gse288958-audit/" }, { "label": "Reference audit JSON", "route": "/resource/api/v1.1/gse288958_reference_audit.json" }, { "label": "Context brief", "route": "/resource/downloads/GSE288958_CONTEXT_OBJECT.md" }, { "label": "Stable module table", "route": "/resource/downloads/GSE288958_STABLE_MODULE_CONTEXT.tsv" }, { "label": "Candidate context triage", "route": "/resource/downloads/GSE288958_CANDIDATE_CONTEXT_TRIAGE.tsv" } ] }, { "source_id": "GSE277637", "source_type": "dataset", "label": "DMD iPSC-derived skeletal-muscle organoid scRNA-seq", "route": "/resource/api/v1.1/context-objects/GSE277637.json", "role": "line-aware descriptive DMD organoid disease-axis context; 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not a new local measurement" }, { "source_id": "DMD-SPATIAL-CONTEXT", "source_type": "curated_evidence", "label": "DMD spatial degeneration, regeneration and fibrosis context", "route": "/resource/api/v1.1/data_intake_registry.json", "role": "spatial/contextual support; no automatic causal edge" }, { "source_id": "STUDY-CARD-MANIFEST", "source_type": "registry", "label": "21 governed DMD Study Card drafts", "route": "/resource/api/v1.1/study_card_manifest.json", "role": "draft experiment handoff; no registered study or outcome" } ], "nodes": [ { "node_id": "DMD-P001", "process": "DMD genomic lesion", "scale": "gene_molecular", "compartment": "genetic", "cell_type": "disease_anchor", "time_context": "disease_origin", "species_support": [ "human", "mouse" ], "readouts": [ "disease genotype", "dystrophin locus status" ], "claim_ceiling": "DMD disease anchor; does not specify downstream cell-state effect size.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "DMD-MUSCLE-REVIEW" ], "next_experiment": "Matched genotype and dystrophin-status confirmation in the selected model.", "layout": { "x": 90, "y": 350 }, "legacy_single_axis_label": "MEASURED", "evidence_axes": { "origin": "OBSERVED", "context_match": "CROSS_SPECIES", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P002", "process": "Dystrophin deficiency", "scale": "protein_myofibre", "compartment": "myofibre", "cell_type": "myofibre", "time_context": "disease_origin", "species_support": [ "human", "mouse" ], "readouts": [ "dystrophin protein", "sarcolemmal localization" ], "claim_ceiling": "Disease-associated dystrophin deficiency; not a candidate perturbation response.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "DMD-MUSCLE-REVIEW", "GSE272233" ], "next_experiment": "Quantify dystrophin rescue and membrane integrity in matched DMD/control fibres.", "layout": { "x": 250, "y": 350 }, "legacy_single_axis_label": "MEASURED", "evidence_axes": { "origin": "OBSERVED", "context_match": "LOCUS_CORRECTION", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P003", "process": "Sarcolemmal / mechanical instability", "scale": "cellular_mechanical", "compartment": "myofibre", "cell_type": "myofibre", "time_context": "injury_initiation", "species_support": [ "human", "mouse" ], "readouts": [ "membrane integrity", "mechanical stress response", "injury markers" ], "claim_ceiling": "Mechanistic disease-core context; local transition probability is not calibrated.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "DMD-MUSCLE-REVIEW", "PRJNA772047" ], "next_experiment": "Matched mechanical-stress and membrane-integrity assay with genotype control.", "layout": { "x": 430, "y": 350 }, "legacy_single_axis_label": "CONTEXTUAL", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P004", "process": "Ca2+ / cellular stress state", "scale": "cellular_stress", "compartment": "myofibre", "cell_type": "myofibre", "time_context": "injury_initiation", "species_support": [ "human", "mouse" ], "readouts": [ "calcium handling", "oxidative stress", "metabolic stress", "stress-response pathway delta" ], "claim_ceiling": "Disease-associated stress context; the organoid pathway readout is descriptive and does not provide perturbation-conditioned calcium or metabolic prediction.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "DMD-MUSCLE-REVIEW", "PRJNA772047", "GSE277637" ], "next_experiment": "Time-matched calcium, oxidative and viability readouts after defined mechanical challenge.", "layout": { "x": 600, "y": 210 }, "legacy_single_axis_label": "CONTEXTUAL", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P005", "process": "Myofibre injury", "scale": "tissue_cellular", "compartment": "myofibre", "cell_type": "myofibre", "time_context": "acute_injury", "species_support": [ "human", "mouse" ], "readouts": [ "injury marker", "membrane leakage", "necrotic fraction" ], "claim_ceiling": "Disease injury context; cannot establish candidate-specific injury probability.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "DMD-MUSCLE-REVIEW", "DMD-SPATIAL-CONTEXT" ], "next_experiment": "Prospective injury time course with donor-aware replication.", "layout": { "x": 770, "y": 210 }, "legacy_single_axis_label": "CONTEXTUAL", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P006", "process": "Degeneration / necrosis", "scale": "tissue", "compartment": "tissue", "cell_type": "injured_myofibre", "time_context": "acute_injury", "species_support": [ "human", "mouse" ], "readouts": [ "necrotic area", "debris", "histopathology" ], "claim_ceiling": "Measured disease pathology context; no causal ranking of upstream candidates.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "PRJNA772047", "DMD-SPATIAL-CONTEXT" ], "next_experiment": "Spatially matched injury and immune-clearance sampling across disease stage.", "layout": { "x": 940, "y": 210 }, "legacy_single_axis_label": "MEASURED", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P007", "process": "Damage / inflammatory signalling", "scale": "tissue_signal", "compartment": "tissue", "cell_type": "multicellular", "time_context": "acute_injury", "species_support": [ "human", "mouse" ], "readouts": [ "inflammatory programme", "damage-associated signals", "cytokine module", "pro-inflammatory pathway delta" ], "claim_ceiling": "Inflammatory context; organoid pathway deltas do not resolve cell source, individual ligand activity or causal strength.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "PRJNA772047", "DMD-SPATIAL-CONTEXT", "GSE277637" ], "next_experiment": "Matched spatial and temporal measurement of damage signals and responding compartments.", "layout": { "x": 1110, "y": 210 }, "legacy_single_axis_label": "CONTEXTUAL", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P008", "process": "Monocyte / myeloid recruitment", "scale": "cell_population", "compartment": "immune", "cell_type": "monocyte_myeloid", "time_context": "inflammation_clearance", "species_support": [ "human", "mouse" ], "readouts": [ "myeloid abundance", "recruitment markers", "spatial localization" ], "claim_ceiling": "Disease-associated myeloid recruitment context; no cell-specific causal effect estimate.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "PRJNA772047", "DMD-SPATIAL-CONTEXT" ], "next_experiment": "Donor- and stage-matched myeloid recruitment measurement with spatial coordinates.", "layout": { "x": 1270, "y": 130 }, "legacy_single_axis_label": "MEASURED", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P009", "process": "Phagocytic / clearance macrophage state", "scale": "cell_state", "compartment": "immune", "cell_type": "macrophage", "time_context": "inflammation_clearance", "species_support": [ "human", "mouse" ], "readouts": [ "phagocytosis", "debris clearance", "macrophage state programme" ], "claim_ceiling": "State-associated macrophage context; not an M1/M2 assignment or causal clearance estimate.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "DMD-SPATIAL-CONTEXT", "GSE288958" ], "next_experiment": "State-resolved phagocytosis and clearance assay in matched DMD/control context.", "layout": { "x": 1430, "y": 40 }, "legacy_single_axis_label": "CONTEXTUAL", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P010", "process": "Repair-associated macrophage state", "scale": "cell_state", "compartment": "immune", "cell_type": "macrophage", "time_context": "repair_regeneration", "species_support": [ "human", "mouse" ], "readouts": [ "repair programme", "pro-regenerative signals", "state abundance" ], "claim_ceiling": "State-associated repair context; no direct repair efficacy or fate probability.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "DMD-SPATIAL-CONTEXT", "GSE288958" ], "next_experiment": "Time-resolved state annotation with functional repair co-readout.", "layout": { "x": 1430, "y": 180 }, "legacy_single_axis_label": "CONTEXTUAL", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P011", "process": "Fibrosis-associated macrophage state", "scale": "cell_state", "compartment": "immune", "cell_type": "macrophage", "time_context": "remodelling_failure", "species_support": [ "human", "mouse" ], "readouts": [ "fibrotic macrophage programme", "SPP1-associated state", "spatial co-localization" ], "claim_ceiling": "Association and candidate communication only; macrophage-to-FAP causality is not established.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "DMD-SPATIAL-CONTEXT", "GSE288958" ], "next_experiment": "Matched macrophage-conditioned or SPP1 perturbation study on DMD FAP phenotype.", "layout": { "x": 1430, "y": 320 }, "legacy_single_axis_label": "CONTEXTUAL", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P012", "process": "MuSC activation", "scale": "cell_state", "compartment": "myogenic", "cell_type": "satellite_cell", "time_context": "repair_regeneration", "species_support": [ "human", "mouse" ], "readouts": [ "MuSC activation markers", "state abundance", "entry into cycle" ], "claim_ceiling": "Myogenic activation context; no DMD perturbation-conditioned transition probability.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "GSE288958", "GSE52529" ], "next_experiment": "Donor-aware MuSC activation time course in DMD and matched control.", "layout": { "x": 1270, "y": 430 }, "legacy_single_axis_label": "CONTEXTUAL", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P013", "process": "Myogenic proliferation", "scale": "cell_state", "compartment": "myogenic", "cell_type": "myogenic_progenitor", "time_context": "repair_regeneration", "species_support": [ "human", "mouse" ], "readouts": [ "proliferation", "cell-state occupancy", "myogenic programme" ], "claim_ceiling": "Reference myogenic state context; not a DMD perturbation outcome.", "model_readiness": "REFERENCE_ONLY", "source_ids": [ "GSE52529", "GSE293514" ], "next_experiment": "Matched DMD/control perturbation with donor and state-resolved proliferation.", "layout": { "x": 1110, "y": 430 }, "legacy_single_axis_label": "CONTEXTUAL", "evidence_axes": { "origin": "OBSERVED", "context_match": "SAME_TISSUE", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P014", "process": "Myogenic differentiation", "scale": "cell_state", "compartment": "myogenic", "cell_type": "myogenic_progenitor", "time_context": "repair_regeneration", "species_support": [ "human", "mouse" ], "readouts": [ "differentiation markers", "state occupancy", "pathway programme", "myogenesis pathway delta" ], "claim_ceiling": "Measured unperturbed human-myogenic trajectory plus line-aware DMD organoid pathway context; DMD perturbation response and cell-state transition remain not measured.", "model_readiness": "REFERENCE_ONLY", "source_ids": [ "GSE52529", "GSE272233", "GSE277637" ], "next_experiment": "Matched DMD/control perturbation and differentiation endpoint with frozen Study Card.", "layout": { "x": 940, "y": 430 }, "legacy_single_axis_label": "MEASURED", "evidence_axes": { "origin": "OBSERVED", "context_match": "LOCUS_CORRECTION", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P015", "process": "Myoblast fusion", "scale": "cell_function", "compartment": "myogenic", "cell_type": "fusion_competent_myoblast", "time_context": "repair_regeneration", "species_support": [ "human", "mouse" ], "readouts": [ "fusion index", "myotube morphology", "viability" ], "claim_ceiling": "Healthy-human-myoblast fusion context is observed; it is not DMD replication or treatment efficacy.", "model_readiness": "CONTEXT_ONLY", "source_ids": [ "GSE293514" ], "next_experiment": "DMD/control matched perturbation with fusion, membrane and viability endpoints.", "layout": { "x": 770, "y": 430 }, "legacy_single_axis_label": "MEASURED", "evidence_axes": { "origin": "OBSERVED", "context_match": "SAME_TISSUE", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P016", "process": "Regenerated myofibre", "scale": "tissue_cellular", "compartment": "myofibre", "cell_type": "regenerated_myofibre", "time_context": "repair_regeneration", "species_support": [ "human", "mouse" ], "readouts": [ "regenerated fibre morphology", "dystrophin status", "contractile markers" ], "claim_ceiling": "Regeneration context; no calibrated regenerated-fibre probability or function prediction.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "GSE272233", "DMD-SPATIAL-CONTEXT" ], "next_experiment": "Longitudinal regenerated-fibre identity and function in matched DMD/control.", "layout": { "x": 600, "y": 430 }, "legacy_single_axis_label": "CONTEXTUAL", "evidence_axes": { "origin": "OBSERVED", "context_match": "LOCUS_CORRECTION", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P017", "process": "FAP activation", "scale": "cell_state", "compartment": "stromal", "cell_type": "FAP", "time_context": "repair_regeneration", "species_support": [ "human", "mouse" ], "readouts": [ "FAP state markers", "ECM programme", "secretome" ], "claim_ceiling": "Disease-associated FAP state; macrophage-to-FAP causality is not established.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "GSE288958", "DMD-SPATIAL-CONTEXT" ], "next_experiment": "Macrophage-conditioned or SPP1 perturbation study with DMD FAP fibrotic readouts.", "layout": { "x": 1270, "y": 570 }, "legacy_single_axis_label": "CONTEXTUAL", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P018", "process": "Regeneration-supportive stromal state", "scale": "cell_state", "compartment": "stromal", "cell_type": "FAP_stromal", "time_context": "repair_regeneration", "species_support": [ "human", "mouse" ], "readouts": [ "niche-support programme", "secretome", "myogenic support" ], "claim_ceiling": "Contextual niche-support state; no cell-cell causal effect is measured.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "GSE288958", "DMD-SPATIAL-CONTEXT" ], "next_experiment": "Co-culture or conditioned-medium assay with matched myogenic readouts.", "layout": { "x": 1110, "y": 570 }, "legacy_single_axis_label": "CONTEXTUAL", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P019", "process": "Fibrotic stromal / FAP state", "scale": "cell_state", "compartment": "stromal", "cell_type": "FAP_stromal", "time_context": "remodelling_failure", "species_support": [ "human", "mouse" ], "readouts": [ "fibrotic programme", "ECM genes", "collagen secretion" ], "claim_ceiling": "Disease-associated fibrotic stromal context; no intervention efficacy estimate.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "GSE288958", "DMD-SPATIAL-CONTEXT" ], "next_experiment": "State-matched anti-fibrotic perturbation with ECM and myogenic consequence readouts.", "layout": { "x": 1270, "y": 710 }, "legacy_single_axis_label": "MEASURED", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P020", "process": "ECM deposition / remodeling", "scale": "tissue_matrix", "compartment": "ecm", "cell_type": "extracellular_matrix", "time_context": "remodelling_failure", "species_support": [ "human", "mouse" ], "readouts": [ "ECM composition", "collagen deposition", "matrix organization", "extracellular-matrix pathway delta" ], "claim_ceiling": "Measured tissue/remodeling context with a descriptive organoid ECM axis; no causal edge to a candidate gene or FAP intervention is established.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "DMD-SPATIAL-CONTEXT", "PRJNA772047", "GSE277637" ], "next_experiment": "Spatial ECM quantification paired with FAP and myogenic state measurements.", "layout": { "x": 1110, "y": 710 }, "legacy_single_axis_label": "MEASURED", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P021", "process": "Fibrosis / adipogenic remodeling", "scale": "tissue", "compartment": "tissue", "cell_type": "fibrotic_adipogenic_tissue", "time_context": "remodelling_failure", "species_support": [ "human", "mouse" ], "readouts": [ "fibrosis area", "adipogenic programme", "tissue stiffness" ], "claim_ceiling": "Disease tissue-remodeling endpoint; no therapeutic efficacy or patient outcome prediction.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "PRJNA772047", "DMD-SPATIAL-CONTEXT" ], "next_experiment": "Stage- and region-matched fibrosis/adipogenic quantification with function.", "layout": { "x": 940, "y": 710 }, "legacy_single_axis_label": "MEASURED", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P022", "process": "Endothelial / vascular response", "scale": "cell_state_tissue", "compartment": "vascular", "cell_type": "endothelial", "time_context": "repair_regeneration", "species_support": [ "human", "mouse" ], "readouts": [ "endothelial state", "perfusion support", "vascular markers" ], "claim_ceiling": "Vascular context only; no perfusion or cross-compartment causal estimate.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "GSE288958", "DMD-SPATIAL-CONTEXT" ], "next_experiment": "Spatial vascular profiling paired with injury and regeneration stage.", "layout": { "x": 770, "y": 700 }, "legacy_single_axis_label": "CONTEXTUAL", "evidence_axes": { "origin": "OBSERVED", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P023", "process": "Regenerative niche", "scale": "multicellular", "compartment": "multicellular", "cell_type": "myogenic_immune_stromal_vascular_niche", "time_context": "repair_regeneration", "species_support": [ "human", "mouse" ], "readouts": [ "neighbourhood composition", "state co-occurrence", "repair support" ], "claim_ceiling": "Spatial/contextual niche hypothesis; communication inference is not causal validation.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "GSE288958", "DMD-SPATIAL-CONTEXT" ], "next_experiment": "Matched spatial perturbation or co-culture study with pre-registered interaction readouts.", "layout": { "x": 600, "y": 590 }, "legacy_single_axis_label": "COMPUTATIONAL", "evidence_axes": { "origin": "COMPUTATIONAL", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "node_id": "DMD-P024", "process": "Functional muscle output", "scale": "organ_function", "compartment": "function", "cell_type": "muscle_tissue", "time_context": "chronic_failure", "species_support": [ "human", "mouse" ], "readouts": [ "fusion", "membrane integrity", "calcium/contraction", "viability" ], "claim_ceiling": "Functional endpoint is required for disease-relevant success; current candidate-level DMD outcome is absent.", "model_readiness": "NOT_CALIBRATED", "source_ids": [ "STUDY-CARD-MANIFEST" ], "next_experiment": "Matched DMD/control perturbation with molecular, functional, toxicity and replication endpoints.", "layout": { "x": 430, "y": 590 }, "legacy_single_axis_label": "MISSING", "evidence_axes": { "origin": "MISSING", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "DRAFT", "outcome_evaluability": "MISSING_TARGET_CONTEXT_OUTCOME", "outcome_direction": "NOT_APPLICABLE" } } ], "edges": [ { "edge_id": "DMD-E001", "source": "DMD-P001", "target": "DMD-P002", "relation": "causes", "direction": "genotype_to_protein", "causal_status": "DIRECT_CAUSAL", "human_support": true, "animal_support": true, "spatial_support": false, "temporal_support": false, "computational_support": false, "direct_perturbation_support": false, "claim_ceiling": "Disease anchor relationship; no downstream effect size.", "next_test": "Dystrophin-status confirmation in matched model.", "line_type": "DIRECT_CAUSAL", "source_ids": [ "DMD-MUSCLE-REVIEW" ], "legacy_single_axis_label": "MEASURED", "evidence_axes": { "origin": "OBSERVED", "context_match": "CROSS_SPECIES", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "edge_id": "DMD-E002", "source": "DMD-P002", "target": "DMD-P003", "relation": "destabilizes", "direction": "protein_to_mechanical_state", "causal_status": "DIRECT_MECHANISTIC", "human_support": true, "animal_support": true, "spatial_support": false, "temporal_support": false, "computational_support": false, "direct_perturbation_support": false, "claim_ceiling": "Mechanistic disease-core relationship; 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no cell-cell causal effect.", "next_test": "Matched niche perturbation with differentiation and fusion endpoints.", "line_type": "COMPUTATIONAL_INFERENCE", "source_ids": [ "DMD-SPATIAL-CONTEXT", "GSE52529" ], "legacy_single_axis_label": "COMPUTATIONAL", "evidence_axes": { "origin": "COMPUTATIONAL", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "RELEASED", "outcome_evaluability": "EVALUABLE", "outcome_direction": "AMBIGUOUS" } }, { "edge_id": "DMD-E027", "source": "DMD-P014", "target": "DMD-P024", "relation": "changes", "direction": "differentiation_to_function", "causal_status": "REQUIRES_DMD_OUTCOME", "human_support": false, "animal_support": false, "spatial_support": false, "temporal_support": false, "computational_support": false, "direct_perturbation_support": false, "claim_ceiling": "Transcriptome-to-function bridge is not calibrated in DMD perturbation context.", "next_test": "Molecular plus fusion, membrane, calcium/contraction and viability panel.", "line_type": "MISSING_REQUIRED_OUTCOME", "source_ids": [ "STUDY-CARD-MANIFEST" ], "legacy_single_axis_label": "MISSING", "evidence_axes": { "origin": "MISSING", "context_match": "TARGET_CONTEXT", "unit_structure": "source_defined_biological_unit", "lifecycle": "DRAFT", "outcome_evaluability": "MISSING_TARGET_CONTEXT_OUTCOME", "outcome_direction": "NOT_APPLICABLE" } }, { "edge_id": "DMD-E028", "source": "DMD-P019", "target": "DMD-P024", "relation": "impairs", "direction": "fibrotic_state_to_function", "causal_status": "REQUIRES_FUNCTIONAL_TEST", "human_support": true, "animal_support": true, "spatial_support": true, "temporal_support": false, "computational_support": false, "direct_perturbation_support": false, "claim_ceiling": "Fibrotic state is disease-associated; 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current calibrated process ModelRun count is zero.", "experiments": "Show draft Study Card handoffs separately from registered studies and measured outcomes; current registered study and outcome counts are zero." }, "claim_boundary": "DMD Biological Process Map V1.0 is an evidence-aware mechanistic map. It is not a causal network, perturbation-conditioned virtual-cell prediction, patient simulation, treatment ranking or clinical decision system. Missing is not negative, and layout is not biology.", "evidence_contract_axes": { "origin": [ "OBSERVED", "COMPUTATIONAL", "MISSING" ], "context_match": [ "TARGET_CONTEXT", "SAME_TISSUE", "EXTERNAL_CELL_CONTEXT", "LOCUS_CORRECTION", "CROSS_SPECIES", "CLINICAL" ], "unit_structure": [ "source_defined_biological_unit", "donor", "line", "culture", "library", "cell", "pathway", "process_node" ], "lifecycle": [ "DRAFT", "FROZEN", "REGISTERED", "RUNNING", "COMPLETED", "RELEASED", "SUPERSEDED" ], "outcome_evaluability": [ "EVALUABLE", "NOT_EVALUABLE", "PARTIALLY_EVALUABLE", "MISSING_TARGET_CONTEXT_OUTCOME" ], "outcome_direction": [ "CONCORDANT", "DISCORDANT", "EQUIVALENT_NULL", "AMBIGUOUS", "NOT_APPLICABLE" ] }, "legacy_single_axis_policy": "legacy_single_axis_label is retained for migration/audit only. 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