{ "openapi": "3.1.0", "info": { "title": "biosingularity API", "version": "0.4.0", "description": "Policy-driven biomedical evidence linter. The typed proposition contract returns ALLOW/REVIEW/BLOCK with exact evidence receipts; experimental free-text discovery is conservatively capped at REVIEW. No model is in the decision path.", "x-cardinal-rule": "A false 'pass' is the only unforgivable failure; unverifiable \u2192 review." }, "servers": [ { "url": "https://biosingularity.netlify.app", "description": "public demo subset (open, per-IP rate-limited, no key)" }, { "url": "https://", "description": "metered hosted API \u2014 full datalake depth (x-api-key)" } ], "paths": { "/api/verify": { "get": { "operationId": "verify", "summary": "Verify a whole free-text answer \u2014 the full ground() verdict.", "parameters": [ { "name": "q", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "demo+hosted" } }, "/api/repair": { "get": { "operationId": "repair", "summary": "Verify then REPAIR an answer into a shippable one \u2014 retracted citations deleted, contradicted sentences struck, sourced warnings appended. Never rewrites a claim.", "parameters": [ { "name": "q", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "demo+hosted" } }, "/api/discovery": { "get": { "operationId": "discovery", "summary": "Trust-gate an AI-generated discovery (publish/review/reject).", "parameters": [ { "name": "q", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [ { "apiKey": [] } ], "x-runs-on": "hosted" } }, "/api/audit": { "get": { "operationId": "audit", "summary": "Audit cited DOIs for retraction / erratum.", "parameters": [ { "name": "q", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "demo+hosted" } }, "/api/target": { "get": { "operationId": "target", "summary": "Gene\u2013disease corroboration (add &disease=).", "parameters": [ { "name": "gene", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "demo+hosted" } }, "/api/entities": { "get": { "operationId": "entities", "summary": "Drug / trial verifier (drug= and/or nct=). Trials include ICMJE prospective-registration and FDAAA results-reporting compliance.", "parameters": [ { "name": "drug", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "demo+hosted" } }, "/api/cellline": { "get": { "operationId": "cellline", "summary": "Cell-line authentication vs the Cellosaurus problematic register (or ?q= to scan prose). Offline, bundled register.", "parameters": [ { "name": "name", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "demo+hosted" } }, "/api/label": { "get": { "operationId": "label", "summary": "FDA structured product label facts \u2014 boxed warning, contraindications, dosage.", "parameters": [ { "name": "drug", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "demo+hosted" } }, "/api/decompose": { "get": { "operationId": "decompose", "summary": "Extract checkable entities from a claim.", "parameters": [ { "name": "q", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "demo+hosted" } }, "/api/evidence/search": { "get": { "operationId": "evidence_search", "summary": "Find candidate papers through OpenAlex + SemOpenAlex. Discovery only; never a verification verdict.", "parameters": [ { "name": "q", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" }, { "name": "limit", "in": "query", "schema": { "type": "integer", "minimum": 1, "maximum": 50, "default": 20 } }, { "name": "published_after", "in": "query", "schema": { "type": "string", "format": "date" } }, { "name": "open_access", "in": "query", "schema": { "type": "boolean" } }, { "name": "sources", "in": "query", "schema": { "type": "string" }, "description": "comma-separated allow-list: openalex_api,semopenalex" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "demo+hosted" } }, "/api/evidence/neighbourhood": { "get": { "operationId": "evidence_neighbourhood", "summary": "Expand one bounded citation hop around an OpenAlex work. Discovery only.", "parameters": [ { "name": "work_id", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" }, { "name": "direction", "in": "query", "schema": { "type": "string", "enum": [ "references", "citations", "both" ], "default": "both" } }, { "name": "limit", "in": "query", "schema": { "type": "integer", "minimum": 1, "maximum": 50, "default": 20 } }, { "name": "sources", "in": "query", "schema": { "type": "string" } } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "demo+hosted" } }, "/api/evidence/resolve": { "get": { "operationId": "evidence_resolve", "summary": "Resolve an exact DOI or OpenAlex work id to a provenance-stamped discovery record.", "parameters": [ { "name": "id", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "demo+hosted" } }, "/api/evidence/context": { "get": { "operationId": "evidence_context", "summary": "Return non-deciding OA, topic, citation, and retraction-screening context.", "parameters": [ { "name": "id", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "demo+hosted" } }, "/api/contested": { "get": { "operationId": "contested", "summary": "Is this reference DISPUTED in the citing literature? (scite Smart Citations \u2014 contested is not retracted, so the verdict is amber.)", "parameters": [ { "name": "doi", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "hosted" } }, "/api/resolve": { "get": { "operationId": "resolve", "summary": "Resolve a gene name to its HGNC approved symbol, ABSTAINING when the name matches several genes with no single approved symbol.", "parameters": [ { "name": "gene", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [], "x-runs-on": "hosted" } }, "/api/provenance": { "get": { "operationId": "provenance", "summary": "Durable receipt lookup for a prior verdict.", "parameters": [ { "name": "ref", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [ { "apiKey": [] } ], "x-runs-on": "hosted" } }, "/api/evidence-base": { "get": { "operationId": "evidence-base", "summary": "Integrity score for a systematic review's INCLUDED studies. The denominator is the explicit included list, never a bibliography; add &bibliography= to have background citations partitioned out.", "parameters": [ { "name": "included", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [ { "apiKey": [] } ], "x-runs-on": "hosted" } }, "/api/desk": { "get": { "operationId": "desk", "summary": "Editor's desk screen over manuscript TEXT: retracted/disputed references, misidentified cell lines, trial-registry compliance, uncheckable prose \u2014 with an extraction-quality gate, so a document we could not fully read can never read clean.", "parameters": [ { "name": "q", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [ { "apiKey": [] } ], "x-runs-on": "hosted" } }, "/api/portfolio": { "get": { "operationId": "portfolio", "summary": "Funder portfolio integrity exposure for comma-separated NIH core project numbers. A portfolio report, never a scoreboard of people.", "parameters": [ { "name": "grants", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [ { "apiKey": [] } ], "x-runs-on": "hosted" } }, "/api/repro": { "get": { "operationId": "repro", "summary": "Does the paper's DECLARED evidence resolve? Data accessions (GEO/ENA/SRA/BioProject/ArrayExpress/dbGaP/PDB/PRIDE/DataCite) + the data-availability statement. Cannot return red: a dead accession is not evidence the paper is wrong.", "parameters": [ { "name": "doi", "in": "query", "required": true, "schema": { "type": "string" }, "description": "URL-encoded input" } ], "responses": { "200": { "description": "verdict", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Verdict" } } } }, "429": { "description": "rate limit / quota exhausted (reserved before work)" } }, "security": [ { "apiKey": [] } ], "x-runs-on": "hosted" } }, "/api/health": { "get": { "operationId": "health", "summary": "Datalake reachability (hosted, no auth).", "responses": { "200": { "description": "health" } } } }, "/api/capabilities": { "get": { "operationId": "capabilities", "summary": "Machine-readable capability manifest (public, no auth).", "responses": { "200": { "description": "capabilities" } } } }, "/api/v2/verify": { "post": { "operationId": "verifyProposition", "summary": "Verify one typed proposition under a declared policy \u2014 the automatable gate.", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/VerificationRequestV2" } } } }, "responses": { "200": { "description": "typed verification decision", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/VerificationResponseV2" } } } }, "400": { "description": "malformed contract" }, "429": { "description": "rate limit / quota exhausted" } }, "security": [], "x-runs-on": "demo+hosted" } }, "/api/scientific-review": { "post": { "operationId": "reviewScientificManuscript", "summary": "Extract claims/issues, audit methods/statistics, bind discovery candidates, and compare revisions. Heuristics are REVIEW-only.", "requestBody": { "required": true, "content": { "application/json": { "schema": { "type": "object", "required": [ "text" ], "additionalProperties": false, "properties": { "text": { "type": "string", "minLength": 1, "maxLength": 2000000 }, "manuscript_id": { "type": "string", "maxLength": 500 }, "previous_text": { "type": "string", "maxLength": 2000000 }, "review_issues": { "type": "array", "maxItems": 500, "items": { "anyOf": [ { "type": "string", "minLength": 1, "maxLength": 20000 }, { "type": "object", "minProperties": 1 } ] } }, "discover": { "type": "boolean", "default": false } } } } } }, "responses": { "200": { "description": "four-stage candidate review packet", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/ScientificReviewV1" } } } }, "400": { "description": "malformed request" }, "413": { "description": "request exceeds text bound" }, "429": { "description": "rate limit / quota exhausted" } }, "security": [], "x-runs-on": "demo+hosted" } } }, "components": { "schemas": { "Verdict": { "type": "object", "properties": { "recommend": { "type": "string", "enum": [ "pass", "review", "reject" ] }, "overall_severity": { "type": "string", "enum": [ "red", "amber", "info", "green" ] }, "coverage_confidence": { "type": [ "number", "null" ], "description": "grounded/total \u2014 COVERAGE, not a probability" }, "verdict_certainty": { "type": [ "string", "null" ], "enum": [ "high", "moderate", "low", null ], "description": "how firm the verdict is \u2014 threshold retry-vs-surface on this" }, "confidence": { "type": [ "number", "null" ], "description": "back-compat alias of coverage_confidence" }, "summary": { "type": "string" }, "counts": { "type": "object" }, "coverage": { "type": "object" }, "claims": { "type": "array", "items": { "type": "object", "properties": { "kind": { "type": "string" }, "ref": { "type": "string" }, "severity": { "type": "string", "enum": [ "red", "amber", "info", "green" ] }, "detail": { "type": "string" }, "receipt": { "type": [ "string", "null" ] }, "grounded": { "type": "boolean" }, "code": { "type": [ "string", "null" ], "description": "stable reason code \u2014 branch on this" }, "remediation": { "type": "object", "description": "{action, instruction, target?} on red/amber claims" } } } }, "graph": { "type": "object" } }, "required": [ "recommend", "overall_severity", "claims" ] }, "VerificationRequestV2": { "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://biosingularity.example/schemas/verification-request-v2.schema.json", "title": "biosingularity Verification Contract v2 request", "type": "object", "additionalProperties": false, "required": [ "subject", "predicate", "object" ], "properties": { "schema_version": { "const": "2.0" }, "subject": { "type": "object", "additionalProperties": false, "required": [ "type", "id" ], "properties": { "type": { "type": "string", "minLength": 1, "maxLength": 100 }, "id": { "type": "string", "minLength": 1, "maxLength": 1000 }, "identifiers": { "type": "object", "additionalProperties": { "type": "string" } } } }, "predicate": { "type": "string", "minLength": 1, "maxLength": 200 }, "object": { "type": "object", "additionalProperties": false, "required": [ "value" ], "properties": { "value": { "type": "string", "minLength": 1, "maxLength": 500 } } }, "polarity": { "enum": [ "affirmed", "denied" ], "default": "affirmed" }, "qualifiers": { "type": "object" }, "citations": { "type": "array", "maxItems": 50, "items": { "type": "string", "maxLength": 1000 } }, "policy": { "type": "string", "minLength": 1, "maxLength": 200, "default": "research-ai-core/0.1" } } }, "VerificationResponseV2": { "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://biosingularity.example/schemas/verification-response-v2.schema.json", "title": "biosingularity Verification Contract v2 response", "type": "object", "additionalProperties": false, "required": [ "schema_version", "decision", "recommendation", "reason", "subject", "predicate", "object", "polarity", "resolution", "evidence", "policy", "receipt" ], "properties": { "schema_version": { "const": "2.0" }, "decision": { "enum": [ "SUPPORTED", "CONTRADICTED", "UNRESOLVED", "OUT_OF_SCOPE" ] }, "recommendation": { "enum": [ "ALLOW", "REVIEW", "BLOCK" ] }, "reason": { "type": "string" }, "subject": { "type": "object" }, "predicate": { "type": "string" }, "object": { "type": "object" }, "polarity": { "enum": [ "affirmed", "denied" ] }, "resolution": { "type": "object" }, "evidence": { "type": "array", "items": { "type": "object", "additionalProperties": false, "required": [ "source", "source_name", "source_class", "commercial_status", "record_id", "url", "detail", "data_as_of" ], "properties": { "source": { "type": "string" }, "source_name": { "type": [ "string", "null" ] }, "source_class": { "type": [ "string", "null" ] }, "commercial_status": { "type": [ "string", "null" ] }, "record_id": { "type": [ "string", "null" ] }, "url": { "type": [ "string", "null" ] }, "detail": { "type": [ "string", "null" ] }, "data_as_of": { "type": [ "string", "null" ] } } } }, "policy": { "type": "object" }, "receipt": { "type": "object", "required": [ "issued_at", "request_sha256", "snapshot_id", "predicate_registry_version", "source_registry_version", "hash_covers", "result_sha256", "receipt_id" ] } } }, "ScientificReviewV1": { "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://biosingularity.ai/schemas/scientific-review-v1.schema.json", "title": "biosingularity scientific review packet", "type": "object", "required": [ "schema_version", "generated_at", "manuscript", "status", "recommendation", "stages", "counts", "safety", "receipt" ], "properties": { "schema_version": { "const": "scientific-review/1" }, "generated_at": { "type": "string", "format": "date-time" }, "manuscript": { "$ref": "#/$defs/manuscript" }, "status": { "enum": [ "review_required", "incomplete" ] }, "recommendation": { "const": "REVIEW" }, "stages": { "type": "object", "required": [ "claims", "methods", "evidence", "revision" ], "properties": { "claims": { "$ref": "#/$defs/claimsStage" }, "methods": { "$ref": "#/$defs/methodsStage" }, "evidence": { "$ref": "#/$defs/evidenceStage" }, "revision": { "anyOf": [ { "type": "null" }, { "$ref": "#/$defs/revisionStage" } ] } }, "additionalProperties": false }, "counts": { "type": "object" }, "safety": { "type": "object", "required": [ "maximum_heuristic_recommendation", "discovery_decision_eligible", "empty_claims_can_be_clean", "human_confirmation_required" ], "properties": { "maximum_heuristic_recommendation": { "const": "REVIEW" }, "discovery_decision_eligible": { "const": false }, "empty_claims_can_be_clean": { "const": false }, "human_confirmation_required": { "const": true } }, "additionalProperties": false }, "limitations": { "type": "array", "items": { "type": "string" } }, "receipt": { "$ref": "#/$defs/receipt" }, "annotation_scaffold": { "type": "object" } }, "additionalProperties": false, "$defs": { "manuscript": { "type": "object", "required": [ "id", "sha256", "chars" ], "properties": { "id": { "type": [ "string", "null" ] }, "sha256": { "type": "string", "pattern": "^[a-f0-9]{64}$" }, "chars": { "type": "integer", "minimum": 1 } }, "additionalProperties": false }, "locator": { "type": "object", "required": [ "section", "paragraph", "sentence", "char_start", "char_end", "source_sha256" ], "properties": { "section": { "type": "string" }, "paragraph": { "type": "integer", "minimum": 1 }, "sentence": { "type": "integer", "minimum": 1 }, "char_start": { "type": "integer", "minimum": 0 }, "char_end": { "type": "integer", "minimum": 1 }, "source_sha256": { "type": "string", "pattern": "^[a-f0-9]{64}$" } }, "additionalProperties": false }, "claim": { "type": "object", "required": [ "claim_id", "source_quote", "source_quote_sha256", "locator", "claim_type", "subject", "predicate", "object", "polarity", "qualifiers", "extraction_confidence", "priority_score", "review_priority", "uncertainties", "status", "decision", "human_confirmation_required", "receipt" ], "properties": { "claim_id": { "type": "string", "pattern": "^clm_[a-f0-9]{16}$" }, "source_quote": { "type": "string", "minLength": 1 }, "source_quote_sha256": { "type": "string", "pattern": "^[a-f0-9]{64}$" }, "locator": { "$ref": "#/$defs/locator" }, "claim_type": { "enum": [ "causal", "safety", "comparative", "association", "quantitative", "methodological", "interpretive", "descriptive" ] }, "subject": { "type": "object", "required": [ "type", "id" ] }, "predicate": { "type": "string" }, "object": { "type": "object", "required": [ "type", "value" ] }, "polarity": { "enum": [ "affirmed", "denied" ] }, "qualifiers": { "type": "object" }, "extraction_confidence": { "type": "number", "minimum": 0, "maximum": 1 }, "priority_score": { "type": "number", "minimum": 0, "maximum": 5 }, "review_priority": { "enum": [ "high", "medium", "standard" ] }, "uncertainties": { "type": "array", "items": { "type": "string" } }, "status": { "const": "candidate" }, "decision": { "const": "REVIEW" }, "human_confirmation_required": { "const": true }, "receipt": { "type": "object" } }, "additionalProperties": false }, "issue": { "type": "object", "required": [ "issue_id", "taxonomy", "severity", "status", "decision", "source_quote", "locator", "rationale", "remediation", "human_confirmation_required" ], "properties": { "issue_id": { "type": "string" }, "taxonomy": { "type": "string" }, "severity": { "enum": [ "low", "moderate", "high", "critical" ] }, "status": { "type": "string" }, "decision": { "const": "REVIEW" }, "claim_id": { "type": [ "string", "null" ] }, "source_quote": { "type": "string" }, "locator": { "$ref": "#/$defs/locator" }, "rationale": { "type": "string" }, "remediation": { "type": "string" }, "confidence": { "type": "number", "minimum": 0, "maximum": 1 }, "human_confirmation_required": { "const": true } }, "additionalProperties": false }, "claimsStage": { "type": "object", "required": [ "schema_version", "manuscript", "status", "recommendation", "claims", "issue_candidates", "review_queue", "coverage", "receipt" ], "properties": { "schema_version": { "const": "scientific-claims/1" }, "generated_at": { "type": "string" }, "manuscript": { "$ref": "#/$defs/manuscript" }, "status": { "enum": [ "complete", "partial", "incomplete" ] }, "recommendation": { "const": "REVIEW" }, "claims": { "type": "array", "items": { "$ref": "#/$defs/claim" } }, "issue_candidates": { "type": "array", "items": { "$ref": "#/$defs/issue" } }, "review_queue": { "type": "array", "maxItems": 50, "items": { "type": "string" } }, "coverage": { "type": "object" }, "limitations": { "type": "array", "items": { "type": "string" } }, "receipt": { "$ref": "#/$defs/receipt" } }, "additionalProperties": false }, "methodsStage": { "type": "object", "required": [ "schema_version", "status", "recommendation", "checks", "findings", "receipt" ], "properties": { "schema_version": { "const": "methods-validity/1" }, "generated_at": { "type": "string" }, "manuscript": { "type": "object" }, "status": { "const": "review_required" }, "recommendation": { "const": "REVIEW" }, "design_profile": { "type": "object" }, "checks": { "type": "array", "items": { "type": "object" } }, "findings": { "type": "array", "items": { "type": "object" } }, "counts": { "type": "object" }, "limitations": { "type": "array", "items": { "type": "string" } }, "receipt": { "$ref": "#/$defs/receipt" } }, "additionalProperties": false }, "evidenceStage": { "type": "object", "required": [ "schema_version", "status", "claims", "counts", "receipt" ], "properties": { "schema_version": { "const": "claim-evidence/1" }, "generated_at": { "type": "string" }, "manuscript": { "type": "object" }, "status": { "enum": [ "complete", "partial" ] }, "claims": { "type": "array", "items": { "type": "object" } }, "counts": { "type": "object" }, "limitations": { "type": "array", "items": { "type": "string" } }, "receipt": { "$ref": "#/$defs/receipt" } }, "additionalProperties": false }, "revisionStage": { "type": "object", "required": [ "schema_version", "status", "recommendation", "claim_changes", "issue_resolutions", "counts", "receipt" ], "properties": { "schema_version": { "const": "review-resolution/1" }, "generated_at": { "type": "string" }, "manuscript": { "type": "object" }, "status": { "const": "review_required" }, "recommendation": { "const": "REVIEW" }, "claim_changes": { "type": "array", "items": { "type": "object" } }, "issue_resolutions": { "type": "array", "items": { "type": "object" } }, "counts": { "type": "object" }, "limitations": { "type": "array", "items": { "type": "string" } }, "receipt": { "$ref": "#/$defs/receipt" } }, "additionalProperties": false }, "receipt": { "type": "object", "required": [ "result_sha256", "receipt_id" ], "properties": { "subject_sha256": { "type": "string" }, "result_sha256": { "type": "string", "pattern": "^[a-f0-9]{64}$" }, "receipt_id": { "type": "string" } }, "additionalProperties": false } } } }, "securitySchemes": { "apiKey": { "type": "apiKey", "in": "header", "name": "x-api-key" } } }, "x-mcp": { "command": "biosingularity-mcp", "install": "pip install 'biosingularity[mcp,store]'", "tools": "/tools/anthropic.json" } }