{ "openapi": "3.0.3", "info": { "title": "NMD-VCell Research Workbench canonical static API", "version": "1.1", "description": "Typed schema 1.1; evidence release v1.0.0-database-resource; frozen 2026-07-25. Static endpoints do not rank genes or run inference.", "x-version-axes": { "resource_release": "v1.0.0-database-resource", "evidence_freeze": "2026-07-25", "schema_version": "1.1", "model_release": "ridge-safe-v2.3", "benchmark_release": "repeated-fold-v2.2", "interface_label": "Research Workbench beta 3.5", "interface_build": "EA-20260729-15", "formal_v1_candidate_label": "v1.0.0-database-resource", "canonical_bundle_identity_digest_sha256": "b435f2100badd88e81dae1afa47bff278ba97d56d84df6d5d4dd6c3d4096b256" }, "x-missing-value-semantics": "null means unavailable, not applicable or not assessed as specified by the adjacent assessment_status; false means assessed and false." }, "paths": { "/api/v1.1/genes/{gene}.json": { "get": { "summary": "Canonical typed gene record for genes listed in individual_gene_manifest.json", "description": "Individual static files are published for governed and rendered gene pages only. Use gene buckets for complete 17,921-record coverage.", "parameters": [ { "name": "gene", "in": "path", "required": true, "schema": { "type": "string", "pattern": "^[A-Z0-9-]+$" } } ], "responses": { "200": { "description": "Typed gene evidence record", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/GeneRecord" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/gene_buckets/{prefix}.json": { "get": { "summary": "Typed records keyed by official gene symbol", "responses": { "200": { "description": "Gene bucket", "content": { "application/json": { "schema": { "type": "object", "additionalProperties": { "$ref": "#/components/schemas/GeneRecord" } } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/gene_bucket_manifest.json": { "get": { "summary": "Bucket paths and record counts for all 17,921 typed records", "responses": { "200": { "description": "Gene bucket manifest", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/individual_gene_manifest.json": { "get": { "summary": "Genes with individual static JSON objects", "responses": { "200": { "description": "Individual endpoint manifest", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/identifier_mapping.json": { "get": { "summary": "Frozen HGNC alias and external-ID mapping with ambiguity preserved", "responses": { "200": { "description": "HGNC identifier mapping", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/study_card_manifest.json": { "get": { "summary": "Stable governed Study Card routes and exports", "responses": { "200": { "description": "Study Card manifest", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/study-cards/{gene}.json": { "get": { "summary": "Versioned action-specific Study Card for a governed hypothesis", "responses": { "200": { "description": "Static Study Card object", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/StudyCard" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/scientific_program.json": { "get": { "summary": "Dual-track state-transition scientific program", "responses": { "200": { "description": "Scientific program contract", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/dmd_minimum_perturbome.json": { "get": { "summary": "Draft 24-slot DMD Minimum Perturbome protocol", "responses": { "200": { "description": "Minimum Perturbome protocol", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/generalization_ladder.json": { "get": { "summary": "G0–G7 generalization and leaderboard contract", "responses": { "200": { "description": "Generalization ladder", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/registered_studies.json": { "get": { "summary": "Immutable prospective Registered Study registry", "responses": { "200": { "description": "Registered Study registry", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/experimental_outcomes.json": { "get": { "summary": "Prospective experimental outcome registry", "responses": { "200": { "description": "Experimental outcome registry", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/release_manifest.json": { "get": { "summary": "Single authoritative release identity", "responses": { "200": { "description": "Release manifest", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/ReleaseManifest" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/release_file_registry.json": { "get": { "summary": "Current object IDs, filenames, sizes and SHA-256 values", "responses": { "200": { "description": "Release file registry", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/FileRegistry" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/benchmark_summary.json": { "get": { "summary": "Typed authoritative repeated-fold benchmark summary", "responses": { "200": { "description": "Benchmark summary", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/BenchmarkSummary" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/vcc_readiness.json": { "get": { "summary": "Machine-readable VCC 2026 preparation and benchmark-gap matrix", "responses": { "200": { "description": "VCC benchmark-readiness matrix", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/vcc_evaluation_contract.json": { "get": { "summary": "Preregistered VCC evaluation template with baselines, disjoint splits, metrics and activation gates", "responses": { "200": { "description": "VCC evaluation contract", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/vcc_metric_diagnostic.json": { "get": { "summary": "Executed formula-aligned aggregate-delta metric diagnostic on 55 external perturbation targets", "responses": { "200": { "description": "VCC-style aggregate-delta metric diagnostic", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/strict_outcomes.json": { "get": { "summary": "Sixteen typed strict-outcome records", "responses": { "200": { "description": "Strict outcome collection", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/OutcomeCollection" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/dmd_coverage_reconciliation.json": { "get": { "summary": "Reconciliation of the 17,921 Atlas genes and 17,919 usable DMD-context rows", "responses": { "200": { "description": "DMD coverage reconciliation", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/DmdCoverageReconciliation" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/prior_robustness_registry.json": { "get": { "summary": "Registered five-rule DMD-prior robustness analysis; no gene grades assigned yet", "responses": { "200": { "description": "Prior robustness registry", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/PriorRobustnessRegistry" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/prediction_readiness.json": { "get": { "summary": "Machine-readable P0/P1/P2 disease-prediction claim gate", "responses": { "200": { "description": "Prediction-readiness gate", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/PredictionReadiness" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/v1_release_gate.json": { "get": { "summary": "Machine-readable formal v1.0 database-resource freeze gate", "responses": { "200": { "description": "v1 release freeze gate", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/V1ReleaseGate" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/v1_external_authorization_dossier.json": { "get": { "summary": "Machine-readable DOI, licence and maintainer authorization dossier", "responses": { "200": { "description": "v1 external authorization dossier", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/ExternalAuthorizationDossier" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/prediction_registry.json": { "get": { "summary": "Empty prospective prediction registry and unlock boundary", "responses": { "200": { "description": "Prediction registry", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/PredictionRegistry" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/prospective_predictions.json": { "get": { "summary": "Prospectively registered prediction cards", "responses": { "200": { "description": "Registry; empty in this release", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/ProspectivePredictionRegistry" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/prospective_validation_board.json": { "get": { "summary": "Append-only prospective outcome board", "responses": { "200": { "description": "Board; empty in this release", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/ProspectiveOutcomeBoard" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/api/v1.1/error_catalog.json": { "get": { "summary": "Static API error codes and host-response boundary", "responses": { "200": { "description": "Error catalogue", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } }, "/comparison/{comparison_id}/json": { "get": { "summary": "Checksum-addressed, server-rendered comparison object", "parameters": [ { "name": "comparison_id", "in": "path", "required": true, "schema": { "type": "string", "pattern": "^CMP-20260726-[A-F0-9]{12}$" } }, { "name": "payload", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Deflate/base64url self-contained payload whose SHA-256 prefix must match comparison_id." } ], "responses": { "200": { "description": "Stable comparison object", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/ComparisonObject" } } } }, "400": { "$ref": "#/components/responses/BadRequest" }, "404": { "$ref": "#/components/responses/NotFound" }, "410": { "$ref": "#/components/responses/Deprecated" }, "500": { "$ref": "#/components/responses/InternalError" } } } } }, "components": { "responses": { "BadRequest": { "description": "Malformed identifier or request", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "NotFound": { "description": "Record not found; a static host may return no JSON body", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "Deprecated": { "description": "Object removed from the current schema with a versioned successor", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "InternalError": { "description": "Unexpected serving error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } }, "schemas": { "Error": { "type": "object", "additionalProperties": false, "required": [ "error_code", "message", "release" ], "properties": { "error_code": { "type": "string", "enum": [ "INVALID_IDENTIFIER", "GENE_NOT_FOUND", "OBJECT_DEPRECATED", "INTERNAL_ERROR" ] }, "message": { "type": "string" }, "release": { "type": "string", "enum": [ "v1.0.0-database-resource" ] } } }, "EvidenceLayer": { "type": "object", "additionalProperties": false, "required": [ "assessment_status" ], "properties": { "assessment_status": { "type": "string", "enum": [ "assessed", "not_assessed" ] }, "support_status": { "type": "string", "nullable": true, "enum": [ "supported", "supported_with_limits", "context_evidence_present" ] }, "evidence_level": { "type": "string", "nullable": true }, "observed_cells": { "type": "integer", "nullable": true }, "hit": { "type": "boolean", "nullable": true }, "effect_size": { "type": "number", "nullable": true }, "fdr": { "type": "number", "nullable": true }, "context": { "type": "string", "nullable": true }, "interpretation": { "type": "string", "nullable": true }, "target_specific_predictive_support": { "type": "string", "nullable": true, "enum": [ "supported", "not_supported" ] }, "ood_status": { "type": "string", "nullable": true, "enum": [ "in_domain", "out_of_domain", "not_assessed", "not_applicable" ] } } }, "IdentifierRecord": { "type": "object", "additionalProperties": false, "required": [ "approved_symbol", "symbol_status", "aliases", "previous_symbols", "species" ], "properties": { "approved_symbol": { "type": "string" }, "symbol_status": { "type": "string", "enum": [ "approved", "not_matched_to_frozen_hgnc_subset" ] }, "hgnc_id": { "type": "string", "nullable": true }, "aliases": { "type": "array", "items": { "type": "string" } }, "previous_symbols": { "type": "array", "items": { "type": "string" } }, "ensembl_gene_id": { "type": "string", "nullable": true }, "ncbi_gene_id": { "type": "integer", "nullable": true }, "species": { "type": "string", "enum": [ "Homo sapiens" ] } } }, "SourceDirectionAgreement": { "type": "object", "additionalProperties": false, "required": [ "agreeing_sources", "assessed_sources", "directional_sources", "proportion" ], "properties": { "agreeing_sources": { "type": "integer", "nullable": true }, "assessed_sources": { "type": "integer", "nullable": true }, "directional_sources": { "type": "integer", "nullable": true }, "proportion": { "type": "number", "nullable": true } } }, "GapProfile": { "type": "object", "additionalProperties": false, "required": [ "decision_blocking_gap", "highest_missing_evidence_layer", "secondary_gaps" ], "properties": { "decision_blocking_gap": { "type": "object", "additionalProperties": false, "required": [ "code", "label" ], "properties": { "code": { "type": "string", "pattern": "^GAP-[0-9]{2}$" }, "label": { "type": "string" } } }, "highest_missing_evidence_layer": { "type": "string" }, "secondary_gaps": { "type": "array", "items": { "type": "string" } } } }, "BenchmarkMetric": { "type": "object", "additionalProperties": false, "required": [ "estimator", "mean", "ci95", "n_realizations", "targets_per_realization", "bootstrap_replicates", "bootstrap_seed", "source_object", "source_table" ], "properties": { "estimator": { "type": "string" }, "mean": { "type": "number" }, "ci95": { "type": "array", "minItems": 2, "maxItems": 2, "items": { "type": "number" } }, "n_realizations": { "type": "integer" }, "targets_per_realization": { "type": "integer" }, "bootstrap_replicates": { "type": "integer" }, "bootstrap_seed": { "type": "integer" }, "source_object": { "type": "string" }, "source_table": { "type": "string" } } }, "BenchmarkSummary": { "type": "object", "additionalProperties": false, "required": [ "schema_version", "benchmark_release", "estimator_scope", "metrics", "absolute_and_relative_audit" ], "properties": { "schema_version": { "type": "string", "enum": [ "1.1" ] }, "benchmark_release": { "type": "string", "enum": [ "repeated-fold-v2.2" ] }, "estimator_scope": { "type": "string", "enum": [ "same_processed_hepg2_dataset" ] }, "metrics": { "type": "object", "additionalProperties": false, "required": [ "rmse_difference_vs_zero", "rmse_difference_vs_train_mean", "raw_cosine_difference_vs_train_mean", "perturbation_specific_residual_cosine" ], "properties": { "rmse_difference_vs_zero": { "$ref": "#/components/schemas/BenchmarkMetric" }, "rmse_difference_vs_train_mean": { "$ref": "#/components/schemas/BenchmarkMetric" }, "raw_cosine_difference_vs_train_mean": { "$ref": "#/components/schemas/BenchmarkMetric" }, "perturbation_specific_residual_cosine": { "$ref": "#/components/schemas/BenchmarkMetric" } } }, "absolute_and_relative_audit": { "type": "object", "additionalProperties": false, "required": [ "model_mean_rmse", "train_mean_rmse", "zero_rmse", "relative_improvement_vs_train_mean", "relative_improvement_vs_zero", "target_distribution" ], "properties": { "model_mean_rmse": { "type": "number" }, "train_mean_rmse": { "type": "number" }, "zero_rmse": { "type": "number" }, "relative_improvement_vs_train_mean": { "type": "number" }, "relative_improvement_vs_zero": { "type": "number" }, "target_distribution": { "type": "object", "additionalProperties": false, "required": [ "target_count", "improved_vs_train_mean", "worsened_vs_train_mean", "exactly_unchanged_vs_train_mean" ], "properties": { "target_count": { "type": "integer" }, "improved_vs_train_mean": { "type": "integer" }, "worsened_vs_train_mean": { "type": "integer" }, "exactly_unchanged_vs_train_mean": { "type": "integer" } } } } } } }, "OutcomeRecord": { "type": "object", "additionalProperties": false, "required": [ "outcome_id", "model", "split", "endpoint", "comparator", "n_genes", "model_mean_rmse", "baseline_mean_rmse", "favorable_difference", "ci95", "multiplicity_adjusted_p", "paired_rmse_support", "raw_direction_support", "strict_gate", "legacy_rmse_only_gate" ], "properties": { "outcome_id": { "type": "string", "pattern": "^STRICT-[0-9]{2}$" }, "model": { "type": "string" }, "split": { "type": "string" }, "endpoint": { "type": "string", "enum": [ "rmse_gain_vs_zero", "rmse_gain_vs_train_mean" ] }, "comparator": { "type": "string" }, "n_genes": { "type": "integer" }, "model_mean_rmse": { "type": "number" }, "baseline_mean_rmse": { "type": "number" }, "favorable_difference": { "type": "number" }, "ci95": { "type": "array", "minItems": 2, "maxItems": 2, "items": { "type": "number" } }, "multiplicity_adjusted_p": { "type": "number", "nullable": true }, "paired_rmse_support": { "type": "string", "enum": [ "supported", "not_supported" ] }, "raw_direction_support": { "type": "string", "enum": [ "supported", "not_supported" ] }, "strict_gate": { "type": "string", "enum": [ "pass", "fail" ] }, "legacy_rmse_only_gate": { "type": "string", "enum": [ "pass", "fail" ] } } }, "OutcomeCollection": { "type": "object", "additionalProperties": false, "required": [ "outcome_schema", "schema_version", "benchmark_release", "record_count", "records" ], "properties": { "outcome_schema": { "type": "string", "enum": [ "nmd-vcell-strict-outcome-collection/1.0" ] }, "schema_version": { "type": "string", "enum": [ "1.1" ] }, "benchmark_release": { "type": "string", "enum": [ "repeated-fold-v2.2" ] }, "record_count": { "type": "integer", "enum": [ 16 ] }, "records": { "type": "array", "minItems": 16, "maxItems": 16, "items": { "$ref": "#/components/schemas/OutcomeRecord" } } } }, "PredictionCard": { "type": "object", "additionalProperties": false, "required": [ "prediction_id", "registered_at", "gene", "model_release", "training_freeze", "biological_context", "perturbation", "primary_endpoint", "predicted_direction", "uncertainty_interval", "abstention_status", "prospective_holdout_id" ], "properties": { "prediction_id": { "type": "string" }, "registered_at": { "type": "string", "format": "date-time" }, "gene": { "type": "string" }, "model_release": { "type": "string" }, "training_freeze": { "type": "string", "format": "date" }, "biological_context": { "type": "string" }, "perturbation": { "type": "string" }, "primary_endpoint": { "type": "string" }, "predicted_direction": { "type": "string" }, "uncertainty_interval": { "type": "array", "minItems": 2, "maxItems": 2, "items": { "type": "number" } }, "abstention_status": { "type": "string" }, "prospective_holdout_id": { "type": "string" } } }, "V1PublicationTarget": { "type": "object", "additionalProperties": false, "required": [ "target_schema", "target_label", "candidate_status", "freeze_package_status", "formal_v1_release", "database_release_claim_boundary", "database_paper_ready_when", "permitted_v1_claim", "not_authorized_claims", "paper_package_objects" ], "properties": { "target_schema": { "type": "string", "enum": [ "nmd-vcell-v1-publication-target/1.0" ] }, "target_label": { "type": "string" }, "candidate_status": { "type": "string" }, "freeze_package_status": { "type": "string" }, "formal_v1_release": { "type": "boolean", "enum": [ false ] }, "database_release_claim_boundary": { "type": "string", "enum": [ "v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release." ] }, "database_paper_ready_when": { "type": "array", "items": { "type": "string" } }, "permitted_v1_claim": { "type": "string" }, "not_authorized_claims": { "type": "array", "items": { "type": "string" } }, "paper_package_objects": { "type": "array", "items": { "type": "string" } } } }, "V1ReleaseGate": { "type": "object", "additionalProperties": false, "required": [ "gate_schema", "resource_release", "interface_build", "formal_v1_release", "freeze_status", "database_release_claim_boundary", "candidate_status", "internal_gate_summary", "external_gate_summary", "internal_gates", "external_gates", "publication_package", "claim_boundary_enforced_on_pages", "prediction_claim_state", "unlock_rule" ], "properties": { "gate_schema": { "type": "string", "enum": [ "nmd-vcell-v1-release-gate/1.0" ] }, "resource_release": { "type": "string", "enum": [ "v1.0.0-database-resource" ] }, "interface_build": { "type": "string", "enum": [ "EA-20260729-15" ] }, "formal_v1_release": { "type": "boolean", "enum": [ false ] }, "freeze_status": { "type": "string", "enum": [ "v1_final_release_freeze_candidate" ] }, "database_release_claim_boundary": { "type": "string", "enum": [ "v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release." ] }, "candidate_status": { "type": "string" }, "internal_gate_summary": { "type": "object", "additionalProperties": false, "required": [ "pass", "total" ], "properties": { "pass": { "type": "integer" }, "total": { "type": "integer" } } }, "external_gate_summary": { "type": "object", "additionalProperties": false, "required": [ "complete", "pending", "total" ], "properties": { "complete": { "type": "integer", "enum": [ 0 ] }, "pending": { "type": "integer" }, "total": { "type": "integer" } } }, "internal_gates": { "type": "array", "items": { "type": "object", "additionalProperties": false, "required": [ "id", "status", "evidence" ], "properties": { "id": { "type": "string" }, "status": { "type": "string", "enum": [ "pass" ] }, "evidence": { "type": "string" } } } }, "external_gates": { "type": "array", "items": { "type": "object", "additionalProperties": false, "required": [ "id", "status", "required_input" ], "properties": { "id": { "type": "string" }, "status": { "type": "string" }, "required_input": { "type": "string" } } } }, "publication_package": { "type": "array", "items": { "type": "string" } }, "claim_boundary_enforced_on_pages": { "type": "array", "items": { "type": "string" } }, "prediction_claim_state": { "type": "string" }, "unlock_rule": { "type": "string" } } }, "ExternalAuthorizationDossier": { "type": "object", "additionalProperties": false, "required": [ "dossier_schema", "resource_release", "interface_build", "formal_v1_release", "dossier_status", "database_release_claim_boundary", "external_gate_summary", "required_external_inputs", "deposit_manifest", "deposit_file_list", "authorization_checklist", "input_template", "metadata_template", "validator", "handoff", "page", "privacy_boundary", "non_automated_actions", "automatic_unlock" ], "properties": { "dossier_schema": { "type": "string", "enum": [ "nmd-vcell-v1-external-authorization-dossier/1.0" ] }, "resource_release": { "type": "string", "enum": [ "v1.0.0-database-resource" ] }, "interface_build": { "type": "string", "enum": [ "EA-20260729-15" ] }, "formal_v1_release": { "type": "boolean", "enum": [ false ] }, "dossier_status": { "type": "string", "enum": [ "ready_for_author_institution_input_formal_v1_locked" ] }, "database_release_claim_boundary": { "type": "string", "enum": [ "v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release." ] }, "external_gate_summary": { "type": "object", "additionalProperties": false, "required": [ "complete", "pending", "total" ], "properties": { "complete": { "type": "integer", "enum": [ 0 ] }, "pending": { "type": "integer" }, "total": { "type": "integer" } } }, "required_external_inputs": { "type": "array", "items": { "type": "object", "additionalProperties": false, "required": [ "gate_id", "status", "required_input" ], "properties": { "gate_id": { "type": "string" }, "status": { "type": "string" }, "required_input": { "type": "string" } } } }, "deposit_manifest": { "type": "string" }, "deposit_file_list": { "type": "string" }, "authorization_checklist": { "type": "string" }, "input_template": { "type": "string" }, "metadata_template": { "type": "string" }, "validator": { "type": "string" }, "handoff": { "type": "string" }, "page": { "type": "string" }, "privacy_boundary": { "type": "string" }, "non_automated_actions": { "type": "array", "items": { "type": "string" } }, "automatic_unlock": { "type": "boolean", "enum": [ false ] }, "release_layers": { "type": "array", "items": { "type": "object" } } } }, "PredictionReadiness": { "type": "object", "additionalProperties": false, "required": [ "readiness_schema", "resource_release", "model_release", "benchmark_protocol", "current_level", "recommended_next_level", "clinical_level_status", "platform_claim_state", "allowed_current_claims", "locked_claims", "levels", "gate_summary", "p1_required_before_unlock", "p2_required_before_unlock", "minimum_validation_boundary", "reporting_alignment", "empty_registry_semantics" ], "properties": { "readiness_schema": { "type": "string", "enum": [ "nmd-vcell-disease-prediction-readiness/1.0" ] }, "resource_release": { "type": "string", "enum": [ "v1.0.0-database-resource" ] }, "model_release": { "type": "string", "enum": [ "ridge-safe-v2.3" ] }, "benchmark_protocol": { "type": "string", "enum": [ "repeated-fold-v2.2" ] }, "current_level": { "type": "string", "enum": [ "P0_prediction_infrastructure_only" ] }, "recommended_next_level": { "type": "string", "enum": [ "P1_research_use_dmd_perturbation_response_prediction" ] }, "clinical_level_status": { "type": "string", "enum": [ "P2_clinical_prediction_locked" ] }, "platform_claim_state": { "type": "string" }, "allowed_current_claims": { "type": "array", "items": { "type": "string" } }, "locked_claims": { "type": "array", "items": { "type": "string" } }, "levels": { "type": "array", "minItems": 3, "items": { "type": "object", "additionalProperties": false, "required": [ "level", "label", "status", "claim_allowed" ], "properties": { "level": { "type": "string", "enum": [ "P0", "P1", "P2" ] }, "label": { "type": "string" }, "status": { "type": "string" }, "claim_allowed": { "type": "string" } } } }, "gate_summary": { "type": "object", "additionalProperties": false, "required": [ "governed_hypotheses", "observed_hepg2_perturbation", "external_myoblast_context_assessed", "independent_muscle_or_dmd_perturbation_replication", "therapeutic_or_clinical_validation", "prediction_registered", "outcome_measured" ], "properties": { "governed_hypotheses": { "type": "integer" }, "observed_hepg2_perturbation": { "type": "integer" }, "external_myoblast_context_assessed": { "type": "integer" }, "independent_muscle_or_dmd_perturbation_replication": { "type": "integer", "enum": [ 0 ] }, "therapeutic_or_clinical_validation": { "type": "integer", "enum": [ 0 ] }, "prediction_registered": { "type": "integer", "enum": [ 0 ] }, "outcome_measured": { "type": "integer", "enum": [ 0 ] } } }, "p1_required_before_unlock": { "type": "array", "items": { "type": "string" } }, "p2_required_before_unlock": { "type": "array", "items": { "type": "string" } }, "minimum_validation_boundary": { "type": "string" }, "reporting_alignment": { "type": "array", "items": { "type": "string" } }, "empty_registry_semantics": { "type": "string" } } }, "PredictionRegistry": { "type": "object", "additionalProperties": false, "required": [ "registry_schema", "resource_release", "interface_build", "registry_status", "claim_state", "counts", "schemas", "records", "outcomes", "empty_registry_semantics", "p1_unlock_requires", "p2_unlock_requires", "not_authorized_claims" ], "properties": { "registry_schema": { "type": "string", "enum": [ "nmd-vcell-prediction-registry/1.0" ] }, "resource_release": { "type": "string", "enum": [ "v1.0.0-database-resource" ] }, "interface_build": { "type": "string", "enum": [ "EA-20260729-15" ] }, "registry_status": { "type": "string", "enum": [ "empty_scaffold_no_predictions_registered" ] }, "claim_state": { "type": "string" }, "counts": { "type": "object", "additionalProperties": false, "required": [ "prediction_registered", "outcome_measured", "abstained_predictions", "failed_predictions", "passed_predictions" ], "properties": { "prediction_registered": { "type": "integer", "enum": [ 0 ] }, "outcome_measured": { "type": "integer", "enum": [ 0 ] }, "abstained_predictions": { "type": "integer", "enum": [ 0 ] }, "failed_predictions": { "type": "integer", "enum": [ 0 ] }, "passed_predictions": { "type": "integer", "enum": [ 0 ] } } }, "schemas": { "type": "object", "additionalProperties": false, "required": [ "prediction_card", "outcome_board", "external_validation_import_template" ], "properties": { "prediction_card": { "type": "string" }, "outcome_board": { "type": "string" }, "external_validation_import_template": { "type": "string" } } }, "records": { "type": "array", "maxItems": 0, "items": { "$ref": "#/components/schemas/PredictionCard" } }, "outcomes": { "type": "array", "maxItems": 0, "items": { "$ref": "#/components/schemas/ProspectiveOutcomeRecord" } }, "empty_registry_semantics": { "type": "string" }, "p1_unlock_requires": { "type": "array", "items": { "type": "string" } }, "p2_unlock_requires": { "type": "array", "items": { "type": "string" } }, "not_authorized_claims": { "type": "array", "items": { "type": "string" } } } }, "ProspectivePredictionRegistry": { "type": "object", "additionalProperties": false, "required": [ "schema_version", "registry_status", "records", "note" ], "properties": { "schema_version": { "type": "string", "enum": [ "1.1" ] }, "registry_status": { "type": "string", "enum": [ "open_for_future_registration_no_predictions_registered" ] }, "records": { "type": "array", "items": { "$ref": "#/components/schemas/PredictionCard" } }, "note": { "type": "string" } } }, "ProspectiveOutcomeRecord": { "type": "object", "additionalProperties": false, "required": [ "prediction_id", "outcome_locked_at", "observed_effect", "observed_interval", "primary_endpoint_met" ], "properties": { "prediction_id": { "type": "string" }, "outcome_locked_at": { "type": "string", "format": "date-time" }, "observed_effect": { "type": "number" }, "observed_interval": { "type": "array", "minItems": 2, "maxItems": 2, "items": { "type": "number" } }, "primary_endpoint_met": { "type": "boolean" } } }, "ProspectiveOutcomeBoard": { "type": "object", "additionalProperties": false, "required": [ "schema_version", "board_status", "records", "claim_boundary" ], "properties": { "schema_version": { "type": "string", "enum": [ "1.1" ] }, "board_status": { "type": "string", "enum": [ "scaffold_only_no_prospective_outcomes" ] }, "records": { "type": "array", "items": { "$ref": "#/components/schemas/ProspectiveOutcomeRecord" } }, "claim_boundary": { "type": "string", "enum": [ "v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release." ] } } }, "StudyCard": { "type": "object", "additionalProperties": false, "required": [ "object_id", "card_schema", "card_version", "resource_release", "evidence_freeze", "interface_build", "gene", "card_type", "current_action_code", "current_action", "lifecycle", "decision_blocking_gap", "highest_missing_evidence_layer", "secondary_gaps", "frozen_evidence_snapshot", "unresolved_question", "biological_context", "perturbation_modality", "comparator_and_controls", "primary_endpoint", "secondary_endpoints", "primary_estimand", "state_transition_design", "perturbation_direction_rationale", "minimally_important_effect", "negligible_effect_margin", "suggested_sample_size_range", "randomisation_unit", "blocking_factors", "statistical_model", "multiple_testing_family", "missing_data_rule", "assay_qc_thresholds", "guide_concordance_rule", "donor_replication_rule", "estimated_time_band", "estimated_cost_band", "preregistration_status", "inferential_unit", "evidence_import_requirements", "planning_fields_not_applicable", "stop_rules", "escalation_rule", "evidence_transition", "data_release_plan", "boundary", "stable_url", "exports" ], "properties": { "object_id": { "type": "string", "pattern": "^SC:" }, "card_schema": { "type": "string", "enum": [ "nmd-vcell-study-card/1.5" ] }, "card_version": { "type": "string", "enum": [ "1.5" ] }, "resource_release": { "type": "string", "enum": [ "v1.0.0-database-resource" ] }, "evidence_freeze": { "type": "string", "format": "date" }, "interface_build": { "type": "string", "enum": [ "EA-20260729-15" ] }, "gene": { "type": "string" }, "card_type": { "type": "string", "enum": [ "expression_verification", "muscle_perturbation", "risk_context_review", "computational_replication", "evidence_import_audit" ] }, "current_action_code": { "type": "string", "nullable": true }, "current_action": { "type": "string" }, "lifecycle": { "type": "object", "additionalProperties": false, "required": [ "state", "revision", "immutable", "registered_at", "supersedes", "immutable_after_registration" ], "properties": { "state": { "type": "string", "enum": [ "DRAFT" ] }, "revision": { "type": "integer", "minimum": 1 }, "immutable": { "type": "boolean", "enum": [ false ] }, "registered_at": { "type": "string", "nullable": true }, "supersedes": { "type": "string", "nullable": true }, "immutable_after_registration": { "type": "boolean", "enum": [ true ] } } }, "decision_blocking_gap": { "type": "object", "additionalProperties": false, "required": [ "code", "label" ], "properties": { "code": { "type": "string" }, "label": { "type": "string" } } }, "highest_missing_evidence_layer": { "type": "string" }, "secondary_gaps": { "type": "array", "items": { "type": "string" } }, "frozen_evidence_snapshot": { "type": "object", "additionalProperties": false, "required": [ "snapshot_schema", "source_record", "highest_supported_level", "highest_assessed_level", "observed_hepg2_perturbation", "external_context_screen", "dmd_prior", "context_metrics", "visual_boundary" ], "properties": { "snapshot_schema": { "type": "string", "enum": [ "nmd-vcell-study-card-frozen-evidence-snapshot/1.0" ] }, "source_record": { "type": "string" }, "highest_supported_level": { "type": "string" }, "highest_assessed_level": { "type": "string" }, "observed_hepg2_perturbation": { "type": "object", "additionalProperties": false, "required": [ "assessment_status", "support_status", "observed_cells" ], "properties": { "assessment_status": { "type": "string" }, "support_status": { "type": "string", "nullable": true }, "observed_cells": { "type": "number", "nullable": true } } }, "external_context_screen": { "type": "object", "additionalProperties": false, "required": [ "assessment_status", "support_status", "hit", "effect_size", "fdr", "interpretation" ], "properties": { "assessment_status": { "type": "string" }, "support_status": { "type": "string", "nullable": true }, "hit": { "type": "boolean", "nullable": true }, "effect_size": { "type": "number", "nullable": true }, "fdr": { "type": "number", "nullable": true }, "interpretation": { "type": "string", "nullable": true } } }, "dmd_prior": { "type": "object", "additionalProperties": false, "required": [ "integrated_prior_direction", "source_direction_state", "source_agreement_proportion", "agreeing_sources", "assessed_sources", "coverage_state", "uncertainty_state" ], "properties": { "integrated_prior_direction": { "type": "string", "nullable": true }, "source_direction_state": { "type": "string", "nullable": true }, "source_agreement_proportion": { "type": "number", "nullable": true }, "agreeing_sources": { "type": "integer", "nullable": true }, "assessed_sources": { "type": "integer", "nullable": true }, "coverage_state": { "type": "string", "nullable": true }, "uncertainty_state": { "type": "string", "nullable": true } } }, "context_metrics": { "type": "object", "additionalProperties": false, "required": [ "skeletal_muscle_median_tpm", "depmap_median_gene_effect", "moderate_dependency_flag" ], "properties": { "skeletal_muscle_median_tpm": { "type": "number", "nullable": true }, "depmap_median_gene_effect": { "type": "number", "nullable": true }, "moderate_dependency_flag": { "type": "boolean", "nullable": true } } }, "visual_boundary": { "type": "string" } } }, "unresolved_question": { "type": "string" }, "biological_context": { "type": "string" }, "perturbation_modality": { "type": "string" }, "comparator_and_controls": { "type": "array", "items": { "type": "string" } }, "primary_endpoint": { "type": "string" }, "secondary_endpoints": { "type": "array", "items": { "type": "string" } }, "primary_estimand": { "type": "string" }, "state_transition_design": { "type": "object", "additionalProperties": false, "required": [ "scientific_object", "mechanism_hypothesis", "cell_context_fields", "timepoint_plan", "endpoint_domains", "cell_cell_consequence", "response_archetype" ], "properties": { "scientific_object": { "type": "string" }, "mechanism_hypothesis": { "type": "string" }, "cell_context_fields": { "type": "object" }, "timepoint_plan": { "type": "array", "items": { "type": "object", "required": [ "window", "role", "status" ], "properties": { "window": { "type": "string" }, "role": { "type": "string" }, "status": { "type": "string" } } } }, "endpoint_domains": { "type": "object" }, "cell_cell_consequence": { "type": "object" }, "response_archetype": { "type": "object" } } }, "perturbation_direction_rationale": { "type": "object", "additionalProperties": false, "required": [ "selected_hypothesis", "allowed_hypotheses", "required_justification" ], "properties": { "selected_hypothesis": { "type": "string" }, "allowed_hypotheses": { "type": "array", "items": { "type": "string" } }, "required_justification": { "type": "string" } } }, "minimally_important_effect": { "type": "string", "nullable": true }, "negligible_effect_margin": { "type": "string", "nullable": true }, "suggested_sample_size_range": { "type": "string", "nullable": true }, "randomisation_unit": { "type": "string", "nullable": true }, "blocking_factors": { "type": "array", "items": { "type": "string" } }, "statistical_model": { "type": "string" }, "multiple_testing_family": { "type": "string" }, "missing_data_rule": { "type": "string" }, "assay_qc_thresholds": { "type": "array", "items": { "type": "string" } }, "guide_concordance_rule": { "type": "string" }, "donor_replication_rule": { "type": "string" }, "estimated_time_band": { "type": "string" }, "estimated_cost_band": { "type": "string" }, "preregistration_status": { "type": "string" }, "inferential_unit": { "type": "string" }, "evidence_import_requirements": { "type": "array", "items": { "type": "string" } }, "planning_fields_not_applicable": { "type": "array", "items": { "type": "string" } }, "stop_rules": { "type": "array", "items": { "type": "string" } }, "escalation_rule": { "type": "string" }, "evidence_transition": { "type": "string" }, "data_release_plan": { "type": "string" }, "boundary": { "type": "string" }, "stable_url": { "type": "string" }, "exports": { "type": "object", "additionalProperties": false, "required": [ "json", "yaml", "tsv" ], "properties": { "json": { "type": "string" }, "yaml": { "type": "string" }, "tsv": { "type": "string" } } } } }, "FileObject": { "type": "object", "additionalProperties": false, "required": [ "object_id", "filename", "size_bytes", "sha256" ], "properties": { "object_id": { "type": "string" }, "filename": { "type": "string" }, "size_bytes": { "type": "integer" }, "sha256": { "type": "string", "pattern": "^[a-f0-9]{64}$" }, "role": { "type": "string" }, "layer_release": { "type": "string" }, "coverage": { "type": "string" }, "total_table_count": { "type": "integer" }, "nonempty_table_count": { "type": "integer" }, "hosting_path": { "type": "string" }, "parts_manifest": { "type": "string" }, "hosting_status": { "type": "string" }, "scope_manifest_inside_archive": { "type": "string" } } }, "FileRegistry": { "type": "object", "additionalProperties": false, "required": [ "registry_schema", "resource_release", "identity_rule", "current_release", "archived_release_policy" ], "properties": { "registry_schema": { "type": "string" }, "resource_release": { "type": "string", "enum": [ "v1.0.0-database-resource" ] }, "identity_rule": { "type": "string" }, "current_release": { "type": "array", "items": { "$ref": "#/components/schemas/FileObject" } }, "archived_release_policy": { "type": "string" } } }, "ReleaseManifest": { "type": "object", "additionalProperties": false, "required": [ "manifest_schema", "resource", "release_config", "resource_release", "evidence_freeze", "gene_schema_version", "research_object_schema_version", "interface_label", "interface_build", "model_release", "benchmark_protocol", "prior_algorithm_version", "version_axes", "canonical_archive", "release_layers", "composite_release_requires_both_layers", "sqlite", "benchmark_summary", "object_counts", "candidate_coverage", "v1_publication_target", "disease_prediction_readiness", "v1_release_gate", "v1_external_authorization_dossier", "prediction_registry", "claim_boundary", "formal_v1_release", "release_readiness", "external_release_gates", "external_release_gate_status", "overlay_archive" ], "properties": { "manifest_schema": { "type": "string" }, "resource": { "type": "string" }, "release_config": { "type": "string" }, "resource_release": { "type": "string", "enum": [ "v1.0.0-database-resource" ] }, "evidence_freeze": { "type": "string", "format": "date" }, "gene_schema_version": { "type": "string", "enum": [ "1.1" ] }, "research_object_schema_version": { "type": "string", "enum": [ "1.3" ] }, "interface_label": { "type": "string", "enum": [ "Research Workbench beta 3.5" ] }, "interface_build": { "type": "string", "enum": [ "EA-20260729-15" ] }, "model_release": { "type": "string", "enum": [ "ridge-safe-v2.3" ] }, "benchmark_protocol": { "type": "string", "enum": [ "repeated-fold-v2.2" ] }, "prior_algorithm_version": { "type": "string" }, "version_axes": { "type": "object", "additionalProperties": false, "required": [ "resource_release", "evidence_freeze", "schema_version", "model_release", "benchmark_release", "interface_label", "interface_build" ], "properties": { "resource_release": { "type": "string", "enum": [ "v1.0.0-database-resource" ] }, "evidence_freeze": { "type": "string", "format": "date" }, "schema_version": { "type": "string", "enum": [ "1.1" ] }, "model_release": { "type": "string", "enum": [ "ridge-safe-v2.3" ] }, "benchmark_release": { "type": "string", "enum": [ "repeated-fold-v2.2" ] }, "interface_label": { "type": "string", "enum": [ "Research Workbench beta 3.5" ] }, "interface_build": { "type": "string", "enum": [ "EA-20260729-15" ] } } }, "canonical_archive": { "$ref": "#/components/schemas/FileObject" }, "release_layers": { "type": "array", "items": { "type": "object", "additionalProperties": false, "required": [ "layer", "required_for_composite_release", "archive" ], "properties": { "layer": { "type": "string" }, "required_for_composite_release": { "type": "boolean" }, "archive": { "$ref": "#/components/schemas/FileObject" } } } }, "composite_release_requires_both_layers": { "type": "boolean" }, "sqlite": { "$ref": "#/components/schemas/FileObject" }, "object_counts": { "type": "object", "additionalProperties": { "type": "integer" } }, "benchmark_summary": { "type": "object", "additionalProperties": false, "required": [ "rmse_difference_vs_zero", "rmse_difference_vs_train_mean", "raw_cosine_difference_vs_train_mean", "perturbation_specific_residual_cosine" ], "properties": { "rmse_difference_vs_zero": { "$ref": "#/components/schemas/BenchmarkMetric" }, "rmse_difference_vs_train_mean": { "$ref": "#/components/schemas/BenchmarkMetric" }, "raw_cosine_difference_vs_train_mean": { "$ref": "#/components/schemas/BenchmarkMetric" }, "perturbation_specific_residual_cosine": { "$ref": "#/components/schemas/BenchmarkMetric" } } }, "candidate_coverage": { "type": "object", "additionalProperties": false, "required": [ "governed_hypotheses", "observed_hepg2_perturbation", "external_myoblast_context_assessed", "independent_muscle_or_dmd_perturbation_replication", "therapeutic_or_clinical_validation" ], "properties": { "governed_hypotheses": { "type": "integer" }, "observed_hepg2_perturbation": { "type": "integer" }, "external_myoblast_context_assessed": { "type": "integer" }, "independent_muscle_or_dmd_perturbation_replication": { "type": "integer" }, "therapeutic_or_clinical_validation": { "type": "integer" } } }, "v1_publication_target": { "$ref": "#/components/schemas/V1PublicationTarget" }, "disease_prediction_readiness": { "$ref": "#/components/schemas/PredictionReadiness" }, "v1_release_gate": { "$ref": "#/components/schemas/V1ReleaseGate" }, "v1_external_authorization_dossier": { "$ref": "#/components/schemas/ExternalAuthorizationDossier" }, "prediction_registry": { "$ref": "#/components/schemas/PredictionRegistry" }, "claim_boundary": { "type": "string" }, "formal_v1_release": { "type": "boolean", "enum": [ false ] }, "release_readiness": { "type": "object", "additionalProperties": false, "required": [ "status", "formal_v1_ready", "freeze_package_status", "database_release_claim_boundary", "external_gate_input_contract", "internal_gates", "external_gates" ], "properties": { "status": { "type": "string" }, "formal_v1_ready": { "type": "boolean", "enum": [ false ] }, "freeze_package_status": { "type": "string" }, "database_release_claim_boundary": { "type": "string", "enum": [ "v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release." ] }, "external_gate_input_contract": { "type": "object", "additionalProperties": false, "required": [ "template", "validator", "instructions", "automatic_formal_release" ], "properties": { "template": { "type": "string" }, "validator": { "type": "string" }, "instructions": { "type": "string" }, "automatic_formal_release": { "type": "boolean", "enum": [ false ] } } }, "internal_gates": { "type": "array", "items": { "type": "object", "additionalProperties": false, "required": [ "id", "status", "evidence" ], "properties": { "id": { "type": "string" }, "status": { "type": "string", "enum": [ "pass" ] }, "evidence": { "type": "string" } } } }, "external_gates": { "type": "array", "items": { "type": "object", "additionalProperties": false, "required": [ "id", "status", "required_input" ], "properties": { "id": { "type": "string" }, "status": { "type": "string" }, "required_input": { "type": "string" } } } } } }, "external_release_gates": { "type": "array", "items": { "type": "string" } }, "external_release_gate_status": { "type": "object", "additionalProperties": { "type": "string" } }, "overlay_archive": { "$ref": "#/components/schemas/FileObject" } } }, "DmdCoverageReconciliation": { "type": "object", "additionalProperties": false, "required": [ "reconciliation_schema", "resource_release", "evidence_freeze", "atlas_gene_count", "source_audit_gene_count", "dmd_context_gene_count", "no_usable_dmd_context_count", "records", "interpretation" ], "properties": { "reconciliation_schema": { "type": "string" }, "resource_release": { "type": "string", "enum": [ "v1.0.0-database-resource" ] }, "evidence_freeze": { "type": "string", "format": "date" }, "atlas_gene_count": { "type": "integer", "enum": [ 17921 ] }, "source_audit_gene_count": { "type": "integer", "enum": [ 17920 ] }, "dmd_context_gene_count": { "type": "integer", "enum": [ 17919 ] }, "no_usable_dmd_context_count": { "type": "integer", "enum": [ 2 ] }, "records": { "type": "array", "minItems": 2, "maxItems": 2, "items": { "type": "object", "additionalProperties": false, "required": [ "gene", "reason", "source_audit_assessment_status", "source_audit_source_count", "dmd_context_assessment_status" ], "properties": { "gene": { "type": "string", "enum": [ "GARS1", "NEFL" ] }, "reason": { "type": "string" }, "source_audit_assessment_status": { "type": "string", "enum": [ "assessed", "not_assessed" ] }, "source_audit_source_count": { "type": "integer", "enum": [ 0, 2 ] }, "dmd_context_assessment_status": { "type": "string", "enum": [ "not_assessed" ] } } } }, "interpretation": { "type": "string" } } }, "PriorRobustnessRegistry": { "type": "object", "additionalProperties": false, "required": [ "registry_schema", "resource_release", "registry_status", "grades", "registered_prior_variants", "ancillary_source_sensitivity", "records", "note" ], "properties": { "registry_schema": { "type": "string" }, "resource_release": { "type": "string", "enum": [ "v1.0.0-database-resource" ] }, "registry_status": { "type": "string", "enum": [ "method_registered_analysis_not_yet_run" ] }, "grades": { "type": "object", "additionalProperties": false, "required": [ "R1", "R2", "R3", "R4", "R5" ], "properties": { "R1": { "type": "string" }, "R2": { "type": "string" }, "R3": { "type": "string" }, "R4": { "type": "string" }, "R5": { "type": "string" } } }, "registered_prior_variants": { "type": "array", "minItems": 5, "maxItems": 5, "items": { "type": "string" } }, "ancillary_source_sensitivity": { "type": "string", "enum": [ "leave_one_source_out" ] }, "records": { "type": "array", "maxItems": 0, "items": { "type": "object" } }, "note": { "type": "string" } } }, "ComparisonGeneCore": { "type": "object", "additionalProperties": false, "required": [ "gene", "identifiers", "decision", "highest_supported_level", "highest_assessed_level", "dmd_context", "evidence_status", "context_metrics", "evidence_gaps", "has_detailed_audit_record" ], "properties": { "gene": { "type": "string" }, "identifiers": { "type": "object", "additionalProperties": false, "required": [ "hgnc_id", "ensembl_gene_id", "ncbi_gene_id" ], "properties": { "hgnc_id": { "type": "string", "nullable": true }, "ensembl_gene_id": { "type": "string", "nullable": true }, "ncbi_gene_id": { "type": "integer", "nullable": true } } }, "decision": { "type": "object", "additionalProperties": false, "required": [ "current_action", "current_display_label", "formal_deprioritization" ], "properties": { "current_action": { "type": "string", "nullable": true }, "current_display_label": { "type": "string", "nullable": true }, "formal_deprioritization": { "type": "boolean" } } }, "highest_supported_level": { "type": "string" }, "highest_assessed_level": { "type": "string" }, "dmd_context": { "type": "object", "additionalProperties": false, "required": [ "integrated_prior_direction", "source_direction_state", "source_direction_agreement", "variant_stability_state", "evidence_module_memberships", "statistical_support_state", "coverage_state", "uncertainty_state" ], "properties": { "integrated_prior_direction": { "type": "string", "nullable": true }, "source_direction_state": { "type": "string" }, "source_direction_agreement": { "$ref": "#/components/schemas/SourceDirectionAgreement" }, "variant_stability_state": { "type": "string" }, "evidence_module_memberships": { "type": "array", "items": { "type": "string" } }, "statistical_support_state": { "type": "string" }, "coverage_state": { "type": "string" }, "uncertainty_state": { "type": "string" } } }, "evidence_status": { "type": "object", "additionalProperties": false, "required": [ "observed_hepg2_perturbation", "external_context_screen" ], "properties": { "observed_hepg2_perturbation": { "type": "object", "additionalProperties": false, "required": [ "assessment_status", "observed_cells" ], "properties": { "assessment_status": { "type": "string" }, "observed_cells": { "type": "integer", "nullable": true } } }, "external_context_screen": { "type": "object", "additionalProperties": false, "required": [ "assessment_status", "hit" ], "properties": { "assessment_status": { "type": "string" }, "hit": { "type": "boolean", "nullable": true } } } } }, "context_metrics": { "type": "object", "additionalProperties": false, "required": [ "skeletal_muscle_median_tpm", "moderate_dependency_flag" ], "properties": { "skeletal_muscle_median_tpm": { "type": "number", "nullable": true }, "moderate_dependency_flag": { "type": "boolean", "nullable": true } } }, "evidence_gaps": { "type": "object", "additionalProperties": false, "required": [ "decision_blocking_gap", "highest_missing_evidence_layer" ], "properties": { "decision_blocking_gap": { "type": "object", "additionalProperties": false, "required": [ "code", "label" ], "properties": { "code": { "type": "string" }, "label": { "type": "string" } } }, "highest_missing_evidence_layer": { "type": "string" } } }, "has_detailed_audit_record": { "type": "boolean" } } }, "ComparisonObject": { "type": "object", "additionalProperties": false, "required": [ "comparison_schema", "comparison_id", "payload_sha256", "resource_release", "schema_version", "evidence_freeze", "interface_build", "generated_at", "original_input_identifiers", "identifier_mapping", "ranking_generated", "rows", "claim_boundary" ], "properties": { "comparison_schema": { "type": "string", "enum": [ "nmd-vcell-comparison-object/1.0" ] }, "comparison_id": { "type": "string", "pattern": "^CMP-20260726-[A-F0-9]{12}$" }, "payload_sha256": { "type": "string", "pattern": "^[a-f0-9]{64}$" }, "resource_release": { "type": "string", "enum": [ "v1.0.0-database-resource" ] }, "schema_version": { "type": "string", "enum": [ "1.1" ] }, "evidence_freeze": { "type": "string", "format": "date" }, "interface_build": { "type": "string", "enum": [ "EA-20260729-15" ] }, "generated_at": { "type": "string", "format": "date-time" }, "original_input_identifiers": { "type": "array", "items": { "type": "string" } }, "identifier_mapping": { "type": "object", "additionalProperties": false, "required": [ "source", "retrieved_at" ], "properties": { "source": { "type": "string" }, "retrieved_at": { "type": "string", "format": "date" } } }, "ranking_generated": { "type": "boolean", "enum": [ false ] }, "rows": { "type": "array", "items": { "type": "object", "additionalProperties": false, "required": [ "input_identifiers", "normalized_symbol", "mapping_status", "mapping_source", "mapping_candidates", "gene", "record" ], "properties": { "input_identifiers": { "type": "array", "items": { "type": "string" } }, "normalized_symbol": { "type": "string", "nullable": true }, "mapping_status": { "type": "string" }, "mapping_source": { "type": "string" }, "mapping_candidates": { "type": "array", "items": { "type": "string" } }, "gene": { "type": "string" }, "record": { "allOf": [ { "$ref": "#/components/schemas/ComparisonGeneCore" } ], "nullable": true } } } }, "claim_boundary": { "type": "string" } } }, "GeneRecord": { "type": "object", "additionalProperties": false, "required": [ "schema_version", "resource_release", "gene", "identifiers", "highest_supported_level", "highest_assessed_level", "evidence_status", "decision", "evidence_gaps" ], "properties": { "schema_version": { "type": "string", "enum": [ "1.1" ] }, "resource_release": { "type": "string", "enum": [ "v1.0.0-database-resource" ] }, "evidence_freeze": { "type": "string", "format": "date" }, "gene": { "type": "string" }, "identifiers": { "$ref": "#/components/schemas/IdentifierRecord" }, "highest_supported_level": { "type": "string", "enum": [ "L1_resource_record", "L2_observed_same_context_perturbation" ] }, "highest_assessed_level": { "type": "string", "enum": [ "L1_resource_record", "L2_observed_same_context_perturbation", "L3a_external_context_screen" ] }, "evidence_status": { "type": "object", "additionalProperties": false, "required": [ "resource_record", "observed_hepg2_perturbation", "internal_model_support", "external_context_screen", "independent_perturbation_replication", "dmd_muscle_validation", "functional_validation", "therapeutic_utility" ], "properties": { "resource_record": { "$ref": "#/components/schemas/EvidenceLayer" }, "observed_hepg2_perturbation": { "$ref": "#/components/schemas/EvidenceLayer" }, "internal_model_support": { "$ref": "#/components/schemas/EvidenceLayer" }, "external_context_screen": { "$ref": "#/components/schemas/EvidenceLayer" }, "independent_perturbation_replication": { "$ref": "#/components/schemas/EvidenceLayer" }, "dmd_muscle_validation": { "$ref": "#/components/schemas/EvidenceLayer" }, "functional_validation": { "$ref": "#/components/schemas/EvidenceLayer" }, "therapeutic_utility": { "$ref": "#/components/schemas/EvidenceLayer" } } }, "decision": { "type": "object", "additionalProperties": false, "required": [ "current_numeric_rank", "formal_deprioritization", "historical_rank_is_current" ], "properties": { "current_action": { "type": "string", "nullable": true, "enum": [ "verify_expression", "muscle_assay", "risk_review", "computational_replication", "hold_pending_external_audit" ] }, "current_display_label": { "type": "string", "nullable": true }, "current_numeric_rank": { "type": "integer", "nullable": true }, "formal_deprioritization": { "type": "boolean" }, "external_evidence_status": { "type": "string", "nullable": true, "enum": [ "author_report_pending_import" ] }, "historical_rank": { "type": "integer", "nullable": true }, "historical_rank_is_current": { "type": "boolean" } } }, "evidence_gaps": { "$ref": "#/components/schemas/GapProfile" }, "dmd_context": { "type": "object", "additionalProperties": false, "required": [ "integrated_prior_direction", "source_direction_state", "source_direction_agreement", "variant_stability_state", "evidence_module_memberships", "statistical_support_state", "coverage_state", "integration_method", "uncertainty_state", "conflict_reason", "integrated_direction_is_prior_not_ground_truth" ], "properties": { "integrated_prior_direction": { "type": "string", "nullable": true, "enum": [ "up", "down", "mixed_or_zero" ] }, "source_direction_state": { "type": "string", "enum": [ "consistent_up", "consistent_down", "conflicted", "not_assessed" ] }, "source_direction_agreement": { "$ref": "#/components/schemas/SourceDirectionAgreement" }, "variant_stability_state": { "type": "string", "enum": [ "same_sign_across_variants", "sign_varied_across_variants", "all_zero_across_variants", "not_assessed" ] }, "variant_count": { "type": "integer", "nullable": true }, "evidence_module_memberships": { "type": "array", "items": { "type": "string", "enum": [ "source_limited", "direction_conflicted", "exploratory_multisource_core", "multisource_direction_consistent", "insufficient_direction_evidence" ] } }, "statistical_support_state": { "type": "string", "enum": [ "context_level_significant_rows_present", "direction_only_no_significant_context_rows", "not_assessed" ] }, "coverage_state": { "type": "string", "pattern": "^(?:[1-4]_of_4_sources|not_assessed)$" }, "integration_method": { "type": "string" }, "uncertainty_state": { "type": "string", "enum": [ "direction_conflict_retained", "incomplete_source_coverage", "direction_consistent_not_formal_meta_analysis" ] }, "conflict_reason": { "type": "string", "nullable": true }, "integrated_direction_is_prior_not_ground_truth": { "type": "boolean" }, "consensus_direction": { "type": "string", "nullable": true, "deprecated": true, "description": "Deprecated legacy name; use integrated_prior_direction." }, "consensus_direction_deprecation": { "type": "object", "additionalProperties": false, "properties": { "deprecated": { "type": "boolean", "enum": [ true ] }, "replacement": { "type": "string", "enum": [ "integrated_prior_direction" ] }, "policy": { "type": "string" } } } } }, "context_metrics": { "type": "object", "additionalProperties": false, "properties": { "skeletal_muscle_median_tpm": { "type": "number", "nullable": true }, "depmap_median_gene_effect": { "type": "number", "nullable": true }, "moderate_dependency_flag": { "type": "boolean", "nullable": true }, "observed_counteralignment": { "type": "number", "nullable": true } } }, "summary": { "type": "string", "nullable": true }, "links": { "type": "object", "additionalProperties": false, "properties": { "research_record": { "type": "string" }, "detailed_audit_record": { "type": "string", "nullable": true }, "legacy_api_record": { "type": "string", "nullable": true }, "release_manifest": { "type": "string" } } } } } } } }