{
  "capability_atlas_schema": "nmd-vcell-capability-atlas/1.0",
  "interface_build": "EA-20260730-33",
  "resource_release": "v1.0.0-database-resource",
  "status_vocabulary": {
    "available": "Released evidence objects and validation contracts exist.",
    "partial": "A reference or context layer exists but not the requested disease-conditioned response.",
    "limited": "An executed model task exists only inside a bounded assay context.",
    "locked": "Required training, truth or validation objects do not exist."
  },
  "counts": {
    "capability_levels": 5,
    "available_or_partial_levels": 2,
    "limited_model_levels": 1,
    "locked_levels": 2,
    "registered_predictions": 0,
    "independent_dmd_outcomes": 0
  },
  "levels": [
    {
      "level": "VC-1",
      "name": "Evidence resource",
      "state": "available",
      "status": "Available now",
      "purpose": "Find and connect disease evidence without converting it into a prediction.",
      "input": "Gene identifiers, DMD source rows, perturbation records and provenance",
      "output": "Source-linked evidence record, uncertainty state and decision-blocking gap",
      "evaluation": "Schema validation, checksums, source traceability and release invariants",
      "evidence": "17,921 gene records · 123 detailed audit records · 5 frozen comparisons",
      "blocker": "This layer organizes evidence; it does not estimate a DMD response.",
      "href": "/resource/genes/",
      "action": "Explore the evidence"
    },
    {
      "level": "VC-2",
      "name": "Cell-state context",
      "state": "partial",
      "status": "Partially available",
      "purpose": "Place a question in a biological compartment or myogenic transition.",
      "input": "Unperturbed human-myogenic time course and qualified context screens",
      "output": "Reference-state placement and evidence-availability map",
      "evaluation": "Physical timepoint QC, context coverage and explicit missing-state labels",
      "evidence": "271 cells · 0/24/48/72 h · 20/21 genes measured · 9/21 in myoblast screen",
      "blocker": "No released trajectory is both DMD-specific and perturbation-conditioned.",
      "href": "/resource/cell-browser/",
      "action": "Open the cell ecosystem"
    },
    {
      "level": "VC-3",
      "name": "Same-context perturbation baseline",
      "state": "limited",
      "status": "Available · limited",
      "purpose": "Test whether a model can recover held-out responses inside one processed assay.",
      "input": "Observed HepG2 CRISPRi response substrate for 21 candidates",
      "output": "Held-out 2,000-feature mean response vector",
      "evaluation": "Repeated target-level folds · RMSE · raw and residual cosine · simple baselines",
      "evidence": "Small average-error improvement; direction unreliable; external transfer unsupported",
      "blocker": "Same-assay performance does not establish transport to muscle or DMD.",
      "href": "/resource/benchmarks/core/",
      "action": "Inspect the benchmark"
    },
    {
      "level": "VC-4",
      "name": "DMD state-transition predictor",
      "state": "locked",
      "status": "Locked · no disease outcomes",
      "purpose": "Predict molecular and functional response in matched DMD and control muscle states.",
      "input": "Required: independent DMD/control perturbations with donor, state, time and function",
      "output": "Desired: response distribution, functional effect, toxicity and calibrated uncertainty",
      "evaluation": "Planned unseen donor, state, laboratory and disease holdouts with abstention",
      "evidence": "0 registered predictions · 0 independent DMD perturbation outcomes",
      "blocker": "The training and external truth objects required for this task do not exist.",
      "href": "/resource/minimum-perturbome/",
      "action": "See the data required"
    },
    {
      "level": "VC-5",
      "name": "Patient digital twin",
      "state": "locked",
      "status": "Locked · not available",
      "purpose": "Estimate a patient-specific disease trajectory under an intervention.",
      "input": "Required: longitudinal patient-linked state, intervention and outcome data",
      "output": "Desired: patient-specific trajectory with uncertainty and prospective calibration",
      "evaluation": "Required: prospective patient holdout, safety analysis and clinical governance",
      "evidence": "No patient-linked longitudinal perturbation trajectory is released",
      "blocker": "No patient-specific prediction or treatment simulation is scientifically permitted.",
      "href": "/resource/trajectory/",
      "action": "Inspect the trajectory boundary"
    }
  ],
  "coverage_matrix": [
    {
      "context": "DMD evidence sources",
      "state": "Disease-associated observations",
      "perturbation": "No matched perturbation",
      "molecular": "Source-linked direction and conflict",
      "function": "Not measured",
      "status": "available",
      "label": "Evidence only"
    },
    {
      "context": "Human myogenic reference",
      "state": "0 / 24 / 48 / 72 h",
      "perturbation": "Unperturbed",
      "molecular": "Reference program trajectory",
      "function": "Differentiation context only",
      "status": "partial",
      "label": "Measured reference"
    },
    {
      "context": "HepG2",
      "state": "One processed assay context",
      "perturbation": "21 observed CRISPRi targets",
      "molecular": "2,000-feature response vector",
      "function": "Not a muscle endpoint",
      "status": "limited",
      "label": "Limited baseline"
    },
    {
      "context": "DMD muscle",
      "state": "Myoblast → mature/function",
      "perturbation": "Candidate perturbation",
      "molecular": "Required but unavailable",
      "function": "Required but unavailable",
      "status": "locked",
      "label": "Not yet tested"
    },
    {
      "context": "FAP · immune · vascular",
      "state": "Disease microenvironment",
      "perturbation": "Cell-specific perturbation",
      "molecular": "Required but unavailable",
      "function": "Cross-cell consequence unavailable",
      "status": "locked",
      "label": "Not yet tested"
    },
    {
      "context": "Individual patient",
      "state": "Longitudinal disease state",
      "perturbation": "Therapy or intervention",
      "molecular": "No calibrated output",
      "function": "No clinical outcome prediction",
      "status": "locked",
      "label": "Not available"
    }
  ],
  "claim_boundary": "Capability status describes released evidence and evaluation readiness. It is not a disease-response probability, therapeutic recommendation or patient-specific prediction."
}