{ "registry_schema": "nmd-vcell-product-contract-registry/1.0", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-16", "generated_by": "scripts/apply-evidence-atlas-product-overlay.mjs", "contract_count": 4, "flagship_count": 4, "contracts": [ { "contract_id": "PRODUCT-CONTRACT-DATASET-CARD-1.0", "label": "Dataset Card", "product_role": "Turn a stored matrix or source accession into a citable, task-qualified biological data object.", "primary_question": "What was measured, in which biological units, and what can this dataset validly support?", "required_sections": [ "Identity and version", "Disease, tissue, cell state and perturbation context", "Sample, donor and statistical-unit design", "Matrix, feature, metadata and checksum inventory", "Access, licence and source provenance", "Readiness, permitted use and prohibited use", "Linked ModelRuns, benchmarks and studies" ], "required_links": [ "source record", "download or access object", "readiness gate", "downstream run or study" ], "current_route": "/resource/datasets/", "current_state": "RELEASED_PARTIAL_STANDARDIZATION", "next_gate": "Render the same required sections for every dataset and reject model-ready status when donor, feature or perturbation identity is unresolved.", "inspired_by": [ "CELLxGENE", "Tahoe-100M", "DepMap" ], "claim_boundary": "Dataset scale or availability does not establish independent biological replication or task suitability." }, { "contract_id": "PRODUCT-CONTRACT-MODEL-CARD-1.0", "label": "Model Card", "product_role": "Bind a model identity to one task, one execution history and one bounded claim surface.", "primary_question": "What did this exact model version receive, return, beat or fail, and where must it abstain?", "required_sections": [ "Model identity, version and provider", "Task, input and output object", "Training and evaluation context", "Split, leakage and baseline controls", "Metrics, seeds and local execution result", "Failure, abstention and prohibited claims", "Artifacts, run receipts and reproducibility links" ], "required_links": [ "ModelRun", "dataset digest", "benchmark task", "artifact or source", "failure analysis" ], "current_route": "/resource/models/", "current_state": "RELEASED_AUDITED", "next_gate": "Expose a uniform adapter and quickstart only after the same model identity is reproducible across documentation, API and run receipts.", "inspired_by": [ "CZI Virtual Cells Platform", "X-Cell", "NVIDIA BioNeMo" ], "claim_boundary": "Architecture reputation and external performance are not local NMD or DMD validation." }, { "contract_id": "PRODUCT-CONTRACT-BENCHMARK-CARD-1.0", "label": "Benchmark Card", "product_role": "Make model evaluation a frozen scientific task rather than a movable leaderboard claim.", "primary_question": "On which sealed outcomes, split, baselines and metrics did a model advance or stop?", "required_sections": [ "Scientific question and task identifier", "Frozen data, target context and outcome object", "Split, leakage groups and hidden-label policy", "Permanent simple baselines", "Metric families, seeds and uncertainty", "Advance or no-advance decision gate", "Immutable result and negative-run history" ], "required_links": [ "benchmark schema", "split manifest", "baseline runs", "ModelRuns", "result download" ], "current_route": "/resource/benchmarks", "current_state": "RELEASED_TASK_BOUNDED", "next_gate": "Add external adapters only on compatible frozen tasks and retain every stopped or negative result.", "inspired_by": [ "Arc Virtual Cell Challenge", "CZI Virtual Cells benchmarks" ], "claim_boundary": "A same-assay benchmark result cannot be transferred to DMD muscle or a different output distribution." }, { "contract_id": "PRODUCT-CONTRACT-WORKFLOW-OUTCOME-CARD-1.0", "label": "Workflow / Outcome Card", "product_role": "Connect a biological question to a frozen experiment, returned outcome and explicit evidence update.", "primary_question": "What experiment can change the conclusion, and how will every positive, null, toxic or failed outcome return?", "required_sections": [ "Question, estimand and hypothesis", "Intervention, cell context, dose, time and comparator", "Biological unit, controls, endpoints and QC", "Lifecycle, preregistration and immutable decision rule", "Prediction freeze when applicable", "Measured outcome, provenance and failure state", "Evidence transition and claim update" ], "required_links": [ "Study Card", "Prediction Card when applicable", "Outcome object", "source evidence", "release update" ], "current_route": "/resource/planner", "current_state": "SCHEMA_RELEASED_OUTCOME_REGISTRY_EMPTY", "next_gate": "Register one immutable DMD study and return its outcome through the same identifiers without suppressing null, toxic or failed branches.", "inspired_by": [ "Recursion OS", "Cellular Intelligence", "VCell" ], "claim_boundary": "A study design is prospective infrastructure, not a measured intervention effect." } ], "flagship_modules": [ { "module_id": "FLAGSHIP-EVIDENCE-ATLAS", "title": "Evidence Atlas", "audience": "Biologists and translational researchers", "question": "What is known in this disease, cell state and biological process?", "inputs": [ "disease", "cell context", "gene or process", "source evidence" ], "outputs": [ "source-linked evidence", "conflicts", "missing layers", "claim ceiling" ], "primary_route": "/resource/diseases/", "supporting_routes": [ "/resource/process/", "/resource/cell-browser/", "/resource/data-universe/" ], "current_outcome": "Four disease modules and donor-aware context objects are visible; evidence depth differs by disease.", "status": "RELEASED_EVIDENCE_BOUNDARY" }, { "module_id": "FLAGSHIP-VIRTUAL-CELL-MODELS", "title": "Virtual Cell Models", "audience": "Computational biologists and model developers", "question": "Can this exact task be computed, and what did each registered model actually do?", "inputs": [ "task-qualified dataset", "frozen split", "model version", "baseline contract" ], "outputs": [ "ModelRun", "benchmark decision", "failure analysis", "abstention" ], "primary_route": "/resource/models/", "supporting_routes": [ "/resource/benchmarks", "/resource/prediction_readiness", "/resource/virtual-cell/" ], "current_outcome": "Six frozen runs are registered; no calibrated candidate-level DMD model is released.", "status": "RELEASED_LIMITED_NO_DMD_PREDICTOR" }, { "module_id": "FLAGSHIP-EXPERIMENT-ENGINE", "title": "Experiment Engine", "audience": "Experimental teams and collaborators", "question": "Which controlled experiment would close the decision-critical evidence gap?", "inputs": [ "missing edge", "estimand", "cell system", "controls and endpoints" ], "outputs": [ "Study Card", "frozen decision rule", "QC plan", "return path" ], "primary_route": "/resource/planner", "supporting_routes": [ "/resource/decisions/", "/resource/study-card/ZNF133", "/resource/contribute/" ], "current_outcome": "Prospective Study Cards are available; they remain designs until registered and run.", "status": "RELEASED_DESIGN_LAYER" }, { "module_id": "FLAGSHIP-OUTCOME-REGISTRY", "title": "Outcome Registry", "audience": "Study owners, reviewers and downstream modelers", "question": "What was registered, measured, failed or released—and what conclusion changed?", "inputs": [ "registered study", "frozen prediction if applicable", "measured outcome", "provenance" ], "outputs": [ "Outcome object", "evidence transition", "updated claim boundary", "future benchmark outcome" ], "primary_route": "/resource/registry", "supporting_routes": [ "/resource/release", "/resource/api/v1.1/prospective_lifecycle.json" ], "current_outcome": "The lifecycle and schemas are public; qualifying candidate-level DMD outcomes remain 0/21.", "status": "RELEASED_EMPTY_BY_DESIGN" } ], "operating_rule": "Every public asset must resolve to a typed card, every card must name its claim boundary and next gate, and every experiment-capable path must return through the outcome registry.", "claim_boundary": "These contracts standardize presentation, provenance and decisions. They do not create missing measurements, model performance or biological validation." }