{ "schema": "nmd-vcell-module-semantic-contract/1.0", "interface_build": "EA-20260806-50", "resource_release": "v1.2.0-measured-dmd-evidence", "audited_at": "2026-08-06T00:00:00.000Z", "module_count": 8, "ordering_policy": "Navigation order encodes the evidence-to-experiment workflow; it is not a ranking of diseases, genes or models.", "global_claim_boundary": "No module emits a calibrated patient-level disease prediction, treatment ranking or clinical recommendation.", "modules": [ { "module_id": "diseases", "label": "Diseases", "route": "/resource/diseases/", "status": "FOUR_DISEASE_TYPED_EVIDENCE_AVAILABLE", "disease_scope": "DMD, FSHD, DM1 and SMA disease-specific evidence modules; each retains its own biological model, statistical unit and claim ceiling.", "research_question": "What has been measured, induced, corrected, perturbed or remains missing in each disease?", "evidence_unit": "Dataset-specific biological unit—donor, biopsy, clone, well or donor-derived line; individual cells are not treated as independent biological replicates by default.", "current_output": "Typed disease summary, dataset registry, role-typed candidate objects, strict evidence states and a disease-specific next experiment.", "claim_ceiling": "No pooled cross-disease score, disease winner, treatment ranking, calibrated patient simulation or clinical recommendation.", "next_handoff": "Choose a disease route; use the DMD interactive workflow where supported or follow the disease-specific next experiment.", "next_route": "/resource/diseases/compare/" }, { "module_id": "questions", "label": "Questions", "route": "/resource/virtual-cell/", "status": "DMD_INTERACTIVE_GATE_OTHER_DISEASES_EVIDENCE_ONLY", "disease_scope": "The interactive six-input predictability checker is DMD-specific. FSHD, DM1 and SMA currently expose bounded evidence routes, not an inference engine.", "research_question": "Can the current release answer this prespecified DMD cell-state perturbation question?", "evidence_unit": "One question object with disease, cell state, perturbation, time, endpoint and requested output fixed together.", "current_output": "Answer state, available evidence layers, missing truth, claim boundary and the next discriminating experiment.", "claim_ceiling": "No calibrated DMD response, candidate pathway outcome, patient trajectory, efficacy estimate or clinical recommendation.", "next_handoff": "Inspect the relevant context in Browse, then compare DMD candidate evidence or freeze a Study Card.", "next_route": "/resource/cell-browser/" }, { "module_id": "browse", "label": "Browse", "route": "/resource/cell-browser/", "status": "DMD_CONTEXT_MAP_AND_SOURCE_LINKED_RECORDS_AVAILABLE", "disease_scope": "The interactive cell-compartment map is DMD muscle context. Four-disease datasets and measured evidence are browsed through the disease atlas.", "research_question": "Which gene, cell compartment, dataset and measured context are relevant to the question?", "evidence_unit": "A source-linked gene, dataset or compartment record with explicit provenance and biological/statistical unit.", "current_output": "A context map or stable evidence record that shows what is observed, contextual and missing.", "claim_ceiling": "No cell-specific causal effect, cell–cell interaction estimate or perturbation-conditioned DMD fate is inferred from browsing.", "next_handoff": "Open a gene record, compare DMD candidates, or return to a disease module for disease-level evidence.", "next_route": "/resource/genes/" }, { "module_id": "gene_compare", "label": "Gene compare", "route": "/resource/compare", "status": "DMD_EVIDENCE_DIMENSION_COMPARISON_AVAILABLE", "disease_scope": "Compares mapped gene and DMD-candidate evidence dimensions. Disease-level comparison is a separate categorical route.", "research_question": "How do selected genes differ across evidence depth, source agreement, context and the experiment-blocking gap?", "evidence_unit": "One mapped gene record per identifier, preserving original input, mapping provenance and separate evidence dimensions.", "current_output": "A stable comparison object and rule-traced gap-closing study suggestion without a scalar winner.", "claim_ceiling": "No target rank, therapeutic priority, pooled cross-disease score or silent conversion of missing evidence to zero.", "next_handoff": "Send the selected evidence gap to Design and freeze the estimand, endpoint and stopping rule.", "next_route": "/resource/planner" }, { "module_id": "design", "label": "Design", "route": "/resource/planner", "status": "TWENTY_ONE_DMD_DRAFT_STUDY_CARDS_AVAILABLE", "disease_scope": "Versioned Study Cards currently cover the 21 governed DMD candidates. Other disease modules provide bounded next-experiment recommendations, not registered Study Cards.", "research_question": "What falsifiable experiment would close the named evidence gap and what result would change the decision?", "evidence_unit": "One versioned Study Card with estimand, endpoint, replication, QC, analysis and stopping rule.", "current_output": "A downloadable draft design object with explicit registration gaps and links to its evidence inputs.", "claim_ceiling": "A draft is not a registered study, executed experiment, measured outcome, target validation or efficacy result.", "next_handoff": "Inspect lifecycle state in Registry; registration and execution remain prospective.", "next_route": "/resource/registry" }, { "module_id": "models", "label": "Models", "route": "/resource/models/", "status": "BOUNDED_MODELRUN_LEDGER_NO_CALIBRATED_DISEASE_MODEL", "disease_scope": "Frozen DMD/assay benchmark runs and model audits are available. FSHD, DM1 and SMA do not currently have calibrated NMD-VCell model runs.", "research_question": "What actually ran on a frozen task, against which baseline, with which split, metric, failure reason and permitted use?", "evidence_unit": "One ModelRun bound to a task, data revision, split, baseline, seed, metrics and gate decision.", "current_output": "Model cards, a six-run execution ledger, benchmark contracts, negative results and explicit readiness gates.", "claim_ceiling": "Published external performance is not inherited; no calibrated DMD or multi-disease predictor is released.", "next_handoff": "Carry only a frozen, gate-passing run into prospective registration and outcome comparison.", "next_route": "/resource/registry" }, { "module_id": "registry", "label": "Registry", "route": "/resource/registry", "status": "READ_ONLY_LIFECYCLE_AND_EVIDENCE_REGISTRY_AVAILABLE", "disease_scope": "Two layers are explicit: the DMD prospective lifecycle and the released four-disease evidence contract.", "research_question": "What is draft, frozen, registered, running, measured, released, superseded or intentionally absent?", "evidence_unit": "One immutable versioned research object; a missing record is never interpreted as a negative result.", "current_output": "Lifecycle states for comparisons, Study Cards, protocols, ModelRuns, predictions and outcomes, including honest zero states.", "claim_ceiling": "The public registry is read-only; it does not accept uploads, create persistence or promote zero outcomes into validation.", "next_handoff": "Contribute a traceable outcome or evidence object, then apply the formal transition rules.", "next_route": "/resource/contribute/" }, { "module_id": "data_api", "label": "Data & API", "route": "/resource/downloads", "status": "VERSIONED_MACHINE_READABLE_OBJECTS_AVAILABLE", "disease_scope": "Covers the DMD workbench and the additive four-disease v2 evidence contract through versioned files and static APIs.", "research_question": "Which exact bytes, schema, identifier, checksum and release boundary support a displayed result?", "evidence_unit": "One versioned file or API object with a declared schema, provenance path and checksum identity.", "current_output": "JSON, TSV, schemas, manifests, checksums, release bundles and a portable RO-Crate contract.", "claim_ceiling": "Machine readability or file availability does not expand biological claims; hosting exclusions remain declared rather than silently omitted.", "next_handoff": "Verify the object, then return to the module whose scientific question it supports.", "next_route": "/resource/meaning-map/" } ], "disease_scope_matrix": [ { "disease_id": "DMD", "disease_route": "/resource/disease/dmd/", "diseases": "FULL_TYPED_MODULE", "questions": "INTERACTIVE_SIX_INPUT_EVIDENCE_GATE", "browse": "DMD_MUSCLE_CONTEXT_MAP_AND_GENE_RECORDS", "gene_compare": "TWENTY_ONE_CANDIDATE_EVIDENCE_COMPARISON", "design": "TWENTY_ONE_DRAFT_STUDY_CARDS", "models": "BOUNDED_ASSAY_AND_DMD_RUN_LEDGER_NO_CALIBRATED_MODEL", "registry": "PROSPECTIVE_LIFECYCLE_ZERO_REGISTERED_OUTCOMES", "data_api": "V1_1_WORKBENCH_AND_V2_DISEASE_OBJECTS" }, { "disease_id": "FSHD", "disease_route": "/resource/disease/fshd/", "diseases": "FULL_TYPED_MODULE_WITH_REGISTERED_SINGLE_CELL_EXTENSION", "questions": "BOUNDED_EVIDENCE_ROUTE_NO_INTERACTIVE_PREDICTOR", "browse": "DISEASE_DATASETS_AND_SINGLE_CELL_STATE_LOCALIZATION", "gene_compare": "NOT_SUPPORTED_NO_CROSS_DISEASE_GENE_POOLING", "design": "NEXT_EXPERIMENT_RECOMMENDATIONS_NOT_FROZEN_STUDY_CARDS", "models": "NO_CALIBRATED_DISEASE_MODEL", "registry": "RELEASED_EVIDENCE_OBJECTS_NO_PROSPECTIVE_OUTCOMES", "data_api": "V2_TYPED_DISEASE_OBJECTS" }, { "disease_id": "DM1", "disease_route": "/resource/disease/dm1/", "diseases": "FULL_TYPED_MODULE_WITH_SPLICING_SPECIFIC_CORRECTION", "questions": "BOUNDED_EVIDENCE_ROUTE_NO_INTERACTIVE_PREDICTOR", "browse": "DISEASE_DATASETS_AND_BULK_SPLICING_EVIDENCE", "gene_compare": "NOT_SUPPORTED_NO_CROSS_DISEASE_GENE_POOLING", "design": "NEXT_EXPERIMENT_RECOMMENDATIONS_NOT_FROZEN_STUDY_CARDS", "models": "NO_CALIBRATED_DISEASE_MODEL", "registry": "RELEASED_EVIDENCE_OBJECTS_NO_PROSPECTIVE_OUTCOMES", "data_api": "V2_TYPED_DISEASE_OBJECTS" }, { "disease_id": "SMA", "disease_route": "/resource/disease/sma/", "diseases": "FULL_TYPED_MODULE_WITH_REGISTERED_SINGLE_CELL_EXTENSION", "questions": "BOUNDED_EVIDENCE_ROUTE_NO_INTERACTIVE_PREDICTOR", "browse": "DISEASE_DATASETS_AND_LINE_AWARE_STATE_LOCALIZATION", "gene_compare": "NOT_SUPPORTED_NO_CROSS_DISEASE_GENE_POOLING", "design": "NEXT_EXPERIMENT_RECOMMENDATIONS_NOT_FROZEN_STUDY_CARDS", "models": "NO_CALIBRATED_DISEASE_MODEL", "registry": "RELEASED_EVIDENCE_OBJECTS_NO_PROSPECTIVE_OUTCOMES", "data_api": "V2_TYPED_DISEASE_OBJECTS" } ], "flow_edges": [ { "from": "diseases", "to": "questions", "meaning": "DMD interactive question" }, { "from": "diseases", "to": "browse", "meaning": "all-disease evidence browsing" }, { "from": "questions", "to": "browse", "meaning": "locate context and evidence" }, { "from": "browse", "to": "gene_compare", "meaning": "contrast DMD gene evidence" }, { "from": "gene_compare", "to": "design", "meaning": "freeze the gap-closing study" }, { "from": "design", "to": "models", "meaning": "bind task, baseline and metric" }, { "from": "models", "to": "registry", "meaning": "preserve run and gate state" }, { "from": "registry", "to": "diseases", "meaning": "return measured outcomes without overwriting history" }, { "from": "data_api", "to": "all_modules", "meaning": "schema, provenance and checksum foundation" } ] }