# Vercy AI instruction - YAML 1.2 (JSON-compatible) { "vercy": "1.0-draft", "publication": { "status": "published", "adjudicationStatus": "reviewable-draft", "publishableCanonical": false, "generatedAt": "2026-10-06T21:14:45Z", "synthesisSha256": "492778626610b419e9a30a27b6267b6a9fb386fc367f62c7849d9485a9658b98", "providerMode": "single-provider-waiver", "providers": [ "Codex" ], "waivedProviders": [ "Claude", "Grok" ] }, "metaModel": { "id": "WM-LIV-017", "registryId": "vr.wm-liv-017", "name": "Pedigree / Biological Lineage", "version": "0.1.0", "previousVersions": [], "entryKind": "pattern", "family": "World Models", "category": "Physical world and living systems", "industry": [ "Cross-industry" ], "domain": [ "PHY.LIV.LIN" ], "tags": [ "pedigree", "biological", "lineage", "phy.liv.lin" ], "status": "published" }, "canonicalUrl": "https://ver.cy/models/wm-liv-017-pedigree-biological-lineage/", "sourceUrl": "https://github.com/ver-cy/world-models/tree/feat/mega-model-registry/research/runs/wm-liv-017", "model": { "registry_id": "vr.wm-liv-017", "model_id": "WM-LIV-017", "name": "Pedigree / Biological Lineage", "entry_kind": "pattern", "purpose": "Describe reusable, evidence-qualified biological descent graphs and their bounded lineage records across species.", "scope_statement": "A pattern for versioned lineage assertions between separately identified biological subjects, with scoped graph views, evidence and analysis references. Instances may be pedigrees maintained by a scientific, clinical, breeding or conservation steward. Cross-species reuse requires an explicit node-granularity and reproductive-mode profile. This research draft neither determines parentage nor executes genetic, clinical or breeding decisions.", "in_scope": [ "Pattern profile, graph identity, organism or explicitly typed germplasm node references and uncertain identities", "Directed descent assertions, role distinctions, unknown parents, alternate hypotheses, temporal checks and evidence", "Versioned graph coverage, externally derived analysis references, exchange losses, stewardship and protected views" ], "out_of_scope": [ "Organism, taxon, breed, cultivar, population, sample and genotype master records", "Evolutionary phylogeny, general genealogy, legal parenthood, inheritance rights and household relations as independent subjects", "Laboratory analysis, diagnosis, reproductive intervention, mating selection, autonomous discovery or disclosure of sensitive family relationships", "Detailed microbial, cell-line, horizontal-transfer and polyploid inheritance implementations; these require additional evidence and profiles" ], "boundary_notes": [ { "neighbor": "WM-LIV-002 Organism Individual", "distinction": "Registry parent_ids is a candidate placement, not biological or type inheritance. This pattern links separately mastered subjects and does not become an organism. Population or germplasm nodes require a distinct typed master binding.", "source_refs": [ "SRC-001", "SRC-005" ] }, { "neighbor": "Taxon phylogeny and breed or cultivar classifiers", "distinction": "Lineage assertions concern profiled subjects and reproductive descent; a taxonomic class or similarity cluster cannot supply an individual parentage edge.", "source_refs": [ "SRC-004", "SRC-005" ] }, { "neighbor": "Clinical family history and social or legal family relationships", "distinction": "Relative histories can remain uncertain. Social and gestational context may be referenced with explicit roles but never converted into genetic descent or legal rights.", "source_refs": [ "SRC-001", "SRC-004", "SRC-006" ] }, { "neighbor": "Biosample, assay, variant and phenotype records", "distinction": "Evidence and observations remain separately mastered, linked by scoped identifiers and versions. Matching a sample or variant is not an automatic assertion of parentage or disease.", "source_refs": [ "SRC-003", "SRC-004", "SRC-006" ] }, { "neighbor": "Record provenance and breeding programme", "distinction": "Document derivation records who produced a claim. Biological descent records the claim itself. Register acceptance and programme decisions remain externally authorized activities.", "source_refs": [ "SRC-004", "SRC-007" ] } ] }, "sources": [ { "id": "SRC-001", "title": "Pedigree Conceptual Model", "organization": "Global Alliance for Genomics and Health", "url": "https://pedigree.readthedocs.io/en/latest/pedigree-model.html", "version_or_date": "Development documentation 0.1, accessed 2026-10-07; release pin unresolved", "source_type": "schema", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:13:02Z", "relevance": "Individual, Relationship and Pedigree sections distinguish referenced members, directed relations, collection identity and partial dates. Human-family example; cross-species extension is authored here." }, { "id": "SRC-002", "title": "Using the Pedigree Standard", "organization": "Global Alliance for Genomics and Health", "url": "https://pedigree.readthedocs.io/en/latest/using-the-pedigree-model.html", "version_or_date": "Development documentation, displayed revision 0555e135", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:13:02Z", "relevance": "Conceptual model is not a standalone exchange format. Direction and reduced forms require explicit mapping. Implementation-specific privacy and ethics review remains necessary." }, { "id": "SRC-003", "title": "Phenopacket Schema Pedigree", "organization": "Global Alliance for Genomics and Health", "url": "https://phenopacket-schema.readthedocs.io/en/latest/pedigree.html", "version_or_date": "Schema 2.0 documentation, accessed 2026-10-07; latest URL not immutable", "source_type": "schema", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:13:02Z", "relevance": "PED-compatible family and individual identifiers, parent fields, unknown founder sentinels, affected status and sample alignment. The proposed adapter must account for encoding differences and information loss." }, { "id": "SRC-004", "title": "General Rules: Parentage recording methods", "organization": "International Committee for Animal Recording", "url": "https://wiki.icar.org/index.php/General_Rules%3A_Parentage_recording_methods", "version_or_date": "Living guideline accessed 2026-10-07; current revision pin unresolved", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:13:02Z", "relevance": "Selected livestock guidance distinguishes genetic and recipient dams, animal identity, recorded breeding events and parentage evidence. Visual resemblance alone is insufficient. Species-specific thresholds are not generalized." }, { "id": "SRC-005", "title": "BrAPI V2.1 Germplasm Pedigree specification", "organization": "Breeding API community", "url": "https://github.com/plantbreeding/BrAPI/tree/brapi-V2.1/Specification/BrAPI-Germplasm/Pedigree", "version_or_date": "brapi-V2.1 branch, accessed 2026-10-07; commit pin unresolved", "source_type": "schema", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:13:02Z", "relevance": "Plant germplasm parent references have contextual roles including SELF, CLONAL and POPULATION. Requested depth and omitted relatives affect completeness. Germplasm nodes must not be automatically equated to organism individuals." }, { "id": "SRC-006", "title": "FHIR R5 FamilyMemberHistory", "organization": "Health Level Seven International", "url": "https://hl7.org/fhir/R5/familymemberhistory.html", "version_or_date": "FHIR 5.0.0 R5, Trial Use resource", "source_type": "schema", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:13:02Z", "relevance": "Sections 9.4.1 and 9.4.3 cover varying accuracy of relative health histories, record status, absent reasons, approximate dates and condition references. A clinical family history is not automatically a confirmed biological pedigree." }, { "id": "SRC-007", "title": "PROV-O: The PROV Ontology", "organization": "World Wide Web Consortium", "url": "https://www.w3.org/TR/prov-o/", "version_or_date": "Recommendation 2013-04-30", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:13:02Z", "relevance": "Entity, activity, agent, revision and qualified attribution ground the evidence trail. Biological descent is distinct from document derivation; provenance alone proves no parentage." }, { "id": "SRC-008", "title": "General Data Protection Regulation", "organization": "European Union", "url": "https://eur-lex.europa.eu/eli/reg/2016/679/oj/eng", "version_or_date": "Regulation (EU) 2016/679, original act; current consolidation not verified", "source_type": "legislation", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:13:02Z", "relevance": "Selected Articles 5, 6, 9, 16 and 17 support scoped purpose, processing basis, sensitive data handling, correction and qualified erasure. Applicability and exceptions need jurisdiction review; consent is not the only possible basis." }, { "id": "SRC-009", "title": "Date and Time on the Internet: Timestamps", "organization": "Internet Engineering Task Force", "url": "https://www.rfc-editor.org/rfc/rfc3339.html", "version_or_date": "RFC 3339, July 2002, section 5.6", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:13:02Z", "relevance": "Syntax for event timestamps with seconds and offset. Partial biological dates and intervals remain separate typed values, without invented precision." } ], "structure": { "bundles": [ { "id": "liv017-b-identity", "name": "Pattern and graph identity", "description": "Proposed pattern and graph identity requirements for the lineage pattern.", "rationale": "Groups related questions so adopters can bind evidence, profile constraints and responsible roles without absorbing external subject masters.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005" ], "layers": [ { "id": "liv017-l-profile", "name": "Applicability profile", "description": "Select an explicit domain, reproductive mode and node granularity before interpreting the graph. A pattern version, a lineage record and a diagram rendition have different identities. Unsupported modes are retained as unresolved profile requests.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005" ], "findings": [ { "id": "liv017-f-profile", "name": "Applicability profile", "description": "Select an explicit domain, reproductive mode and node granularity before interpreting the graph. A pattern version, a lineage record and a diagram rendition have different identities. Unsupported modes are retained as unresolved profile requests.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005" ], "questions": [ { "id": "liv017-f-profile-q1", "text": "Which biological subjects and descent modes does this lineage profile cover?", "kind": "definition", "answer_data": [ "species or taxon reference", "reproductive mode", "node granularity", "profile exclusions" ] }, { "id": "liv017-f-profile-q2", "text": "Which master identifier and revision identify this pedigree independently of its focal subject?", "kind": "identity", "answer_data": [ "master namespace", "pedigree identifier", "pattern version", "record revision" ] }, { "id": "liv017-f-profile-q3", "text": "How does the profile distinguish individual organisms from germplasm, populations and samples?", "kind": "classification", "answer_data": [ "node type vocabulary", "master bindings", "conversion restrictions" ] } ], "data_elements": [ { "id": "liv017-f-profile-data-profile-ref", "name": "Profile reference", "description": "Versioned domain, mode, granularity and exclusions.", "value_kind": "reference", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-004", "SRC-005" ] }, { "id": "liv017-f-profile-data-graph-key", "name": "Graph identity", "description": "Master namespace, stable graph identifier and immutable revision.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-004", "SRC-005" ] } ], "artifacts": [ { "id": "liv017-f-profile-artifact", "name": "Applicability profile record", "description": "Proposed versioned record of the answers, supporting references, review state and access restrictions for applicability profile.", "media_or_form": [ "structured JSON record", "controlled human-readable report" ], "serial": true, "identity_strategy": "Authoritative master-system namespace and identifier first; version is distinct from identity. Use a namespaced local UUID only when no master exists. Never use a date, name or digest as the subject identity.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005" ] } ], "inline_only_rationale": null } ] }, { "id": "liv017-l-members", "name": "Member identity and reconciliation", "description": "Resolve namespaced member references without merging on a label or genotype. Unknown persons and ambiguous germplasm references get scoped provisional identity; samples and pedigree subjects retain explicit mapping evidence. An identity correction can invalidate dependent edges.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ], "findings": [ { "id": "liv017-f-members", "name": "Member identity and reconciliation", "description": "Resolve namespaced member references without merging on a label or genotype. Unknown persons and ambiguous germplasm references get scoped provisional identity; samples and pedigree subjects retain explicit mapping evidence. An identity correction can invalidate dependent edges.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ], "questions": [ { "id": "liv017-f-members-q1", "text": "How is each graph member linked to a master subject or a scoped provisional identifier?", "kind": "identity", "answer_data": [ "member reference", "namespace", "provisional state", "resolution evidence" ] }, { "id": "liv017-f-members-q2", "text": "Which evidence connects a sample identifier or germplasm accession to this member?", "kind": "relationship", "answer_data": [ "mapping assertion", "sample or accession master", "mapping scope", "reviewer" ] }, { "id": "liv017-f-members-q3", "text": "How are duplicate labels and disputed identity merges represented without losing competing histories?", "kind": "exception", "answer_data": [ "candidate identity matches", "merge decision reference", "superseded references", "unresolved conflicts" ] } ], "data_elements": [ { "id": "liv017-f-members-data-members", "name": "Member index", "description": "Typed namespaced references with provisional state, aliases and source mappings.", "value_kind": "collection", "cardinality": "1..n", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ] }, { "id": "liv017-f-members-data-identity-review", "name": "Identity review", "description": "Evidence-backed proposed merge or split with dependent assertion impact.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ] } ], "artifacts": [ { "id": "liv017-f-members-artifact", "name": "Member identity and reconciliation record", "description": "Proposed versioned record of the answers, supporting references, review state and access restrictions for member identity and reconciliation.", "media_or_form": [ "structured JSON record", "controlled human-readable report" ], "serial": true, "identity_strategy": "Authoritative master-system namespace and identifier first; version is distinct from identity. Use a namespaced local UUID only when no master exists. Never use a date, name or digest as the subject identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "liv017-b-descent", "name": "Descent assertions", "description": "Proposed descent assertions requirements for the lineage pattern.", "rationale": "Groups related questions so adopters can bind evidence, profile constraints and responsible roles without absorbing external subject masters.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007" ], "layers": [ { "id": "liv017-l-edges", "name": "Directed and role-qualified parentage", "description": "Represent each assertion with subject, predicate, object, role, source and assertion state. Genetic contribution, gestation and social context remain distinct. Selfing links an earlier biological subject to a distinct offspring; it does not justify a self-loop caused by collapsed accession identifiers.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ], "findings": [ { "id": "liv017-f-edges", "name": "Directed and role-qualified parentage", "description": "Represent each assertion with subject, predicate, object, role, source and assertion state. Genetic contribution, gestation and social context remain distinct. Selfing links an earlier biological subject to a distinct offspring; it does not justify a self-loop caused by collapsed accession identifiers.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ], "questions": [ { "id": "liv017-f-edges-q1", "text": "Which parent-to-offspring direction and contribution role does each descent assertion express?", "kind": "relationship", "answer_data": [ "parent reference", "offspring reference", "role code and vocabulary version", "assertion identifier" ] }, { "id": "liv017-f-edges-q2", "text": "How are genetic contributors, gestational recipients and contextual family relations kept separate?", "kind": "composition", "answer_data": [ "edge category", "contribution context", "external social relation reference", "profile cardinality" ] }, { "id": "liv017-f-edges-q3", "text": "How does the selected profile encode selfing, clonal propagation or unresolved multiple parent candidates?", "kind": "constraint", "answer_data": [ "reproductive mode", "distinct generation identities", "candidate set semantics", "unsupported case disposition" ] } ], "data_elements": [ { "id": "liv017-f-edges-data-assertions", "name": "Descent assertions", "description": "Parent and offspring references, role and vocabulary, profile, source and review state per assertion.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ] }, { "id": "liv017-f-edges-data-context-links", "name": "Contextual relations", "description": "Typed non-descent references excluded from biological ancestry traversal.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ] } ], "artifacts": [ { "id": "liv017-f-edges-artifact", "name": "Directed and role-qualified parentage record", "description": "Proposed versioned record of the answers, supporting references, review state and access restrictions for directed and role-qualified parentage.", "media_or_form": [ "structured JSON record", "controlled human-readable report" ], "serial": true, "identity_strategy": "Authoritative master-system namespace and identifier first; version is distinct from identity. Use a namespaced local UUID only when no master exists. Never use a date, name or digest as the subject identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ] } ], "inline_only_rationale": null } ] }, { "id": "liv017-l-uncertainty", "name": "Unknown and competing ancestry", "description": "Keep absent, withheld, not requested and disputed parentage distinct. A founder is relative to a dataset boundary and is not proof of no ancestors. Competing hypotheses remain separate claim sets; any numerical confidence must name its method and scale, without a default probability.", "source_refs": [ "SRC-003", "SRC-005", "SRC-006", "SRC-007" ], "findings": [ { "id": "liv017-f-uncertainty", "name": "Unknown and competing ancestry", "description": "Keep absent, withheld, not requested and disputed parentage distinct. A founder is relative to a dataset boundary and is not proof of no ancestors. Competing hypotheses remain separate claim sets; any numerical confidence must name its method and scale, without a default probability.", "source_refs": [ "SRC-003", "SRC-005", "SRC-006", "SRC-007" ], "questions": [ { "id": "liv017-f-uncertainty-q1", "text": "What explains each missing or unavailable parent reference in this graph view?", "kind": "state", "answer_data": [ "absence reason", "visibility restriction", "query inclusion settings", "unresolved reference" ] }, { "id": "liv017-f-uncertainty-q2", "text": "Which alternative parentage hypotheses remain supported or contradicted by the recorded evidence?", "kind": "evidence", "answer_data": [ "hypothesis identifiers", "supporting and contrary evidence", "review states", "method-qualified confidence" ] }, { "id": "liv017-f-uncertainty-q3", "text": "Which founder assumptions and truncated branches limit conclusions drawn from the pedigree?", "kind": "quality", "answer_data": [ "dataset boundary", "unobserved ancestry", "founder assumptions", "analysis restrictions" ] } ], "data_elements": [ { "id": "liv017-f-uncertainty-data-absence", "name": "Parentage absence", "description": "Reason-coded absence with view context; restricted reasons may also require redaction.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-003", "SRC-005", "SRC-006", "SRC-007" ] }, { "id": "liv017-f-uncertainty-data-hypotheses", "name": "Competing claims", "description": "Alternative assertion sets with separate support, challenge and disposition records.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-003", "SRC-005", "SRC-006", "SRC-007" ] } ], "artifacts": [ { "id": "liv017-f-uncertainty-artifact", "name": "Unknown and competing ancestry record", "description": "Proposed versioned record of the answers, supporting references, review state and access restrictions for unknown and competing ancestry.", "media_or_form": [ "structured JSON record", "controlled human-readable report" ], "serial": true, "identity_strategy": "Authoritative master-system namespace and identifier first; version is distinct from identity. Use a namespaced local UUID only when no master exists. Never use a date, name or digest as the subject identity.", "source_refs": [ "SRC-003", "SRC-005", "SRC-006", "SRC-007" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "liv017-b-evidence", "name": "Evidence and temporal checks", "description": "Proposed evidence and temporal checks requirements for the lineage pattern.", "rationale": "Groups related questions so adopters can bind evidence, profile constraints and responsible roles without absorbing external subject masters.", "source_refs": [ "SRC-002", "SRC-004", "SRC-006", "SRC-007", "SRC-009" ], "layers": [ { "id": "liv017-l-support", "name": "Evidence chain and acceptance", "description": "Link reports and declarations to exactly the assertion they support or challenge. Preserve collector, sample mapping, method and interpretation references. Reported, evidence-supported and officially accepted are separate states; this pattern never promotes one into another automatically.", "source_refs": [ "SRC-004", "SRC-006", "SRC-007" ], "findings": [ { "id": "liv017-f-support", "name": "Evidence chain and acceptance", "description": "Link reports and declarations to exactly the assertion they support or challenge. Preserve collector, sample mapping, method and interpretation references. Reported, evidence-supported and officially accepted are separate states; this pattern never promotes one into another automatically.", "source_refs": [ "SRC-004", "SRC-006", "SRC-007" ], "questions": [ { "id": "liv017-f-support-q1", "text": "Who supplied, interpreted and accepted the evidence for this parentage claim?", "kind": "provenance", "answer_data": [ "reporter", "collector or laboratory reference", "interpreter", "accepting authority and scope" ] }, { "id": "liv017-f-support-q2", "text": "Which record, assay or declaration supports or contradicts the claim and what limitations apply?", "kind": "evidence", "answer_data": [ "versioned evidence reference", "sample chain reference", "method", "limitations", "contrary evidence" ] }, { "id": "liv017-f-support-q3", "text": "What register procedure authorizes acceptance or correction of this recorded parentage?", "kind": "authority", "answer_data": [ "register reference", "acceptance rule version", "authorized decision reference", "decision date" ] } ], "data_elements": [ { "id": "liv017-f-support-data-support", "name": "Assertion evidence index", "description": "Versioned evidence links with support direction, provenance and restrictions.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-004", "SRC-006", "SRC-007" ] }, { "id": "liv017-f-support-data-acceptance", "name": "Acceptance record", "description": "External register decision and authorized scope, distinct from local evidence review.", "value_kind": "reference", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-004", "SRC-006", "SRC-007" ] } ], "artifacts": [ { "id": "liv017-f-support-artifact", "name": "Evidence chain and acceptance record", "description": "Proposed versioned record of the answers, supporting references, review state and access restrictions for evidence chain and acceptance.", "media_or_form": [ "structured JSON record", "controlled human-readable report" ], "serial": true, "identity_strategy": "Authoritative master-system namespace and identifier first; version is distinct from identity. Use a namespaced local UUID only when no master exists. Never use a date, name or digest as the subject identity.", "source_refs": [ "SRC-004", "SRC-006", "SRC-007" ] } ], "inline_only_rationale": null } ] }, { "id": "liv017-l-time", "name": "Dates and graph consistency", "description": "Separate reproductive-event time, uncertain biological dates, recording time and correction time. Proposed checks reject self-ancestry in a resolved organism descent graph, flag cycles and unresolved references, and apply only documented profile chronology rules. Shared ancestors are valid repeated paths, not cycles.", "source_refs": [ "SRC-002", "SRC-004", "SRC-007", "SRC-009" ], "findings": [ { "id": "liv017-f-time", "name": "Dates and graph consistency", "description": "Separate reproductive-event time, uncertain biological dates, recording time and correction time. Proposed checks reject self-ancestry in a resolved organism descent graph, flag cycles and unresolved references, and apply only documented profile chronology rules. Shared ancestors are valid repeated paths, not cycles.", "source_refs": [ "SRC-002", "SRC-004", "SRC-007", "SRC-009" ], "questions": [ { "id": "liv017-f-time-q1", "text": "Which event dates, intervals and record timestamps constrain this descent assertion?", "kind": "temporal", "answer_data": [ "event type", "date precision", "uncertainty interval", "recorded timestamp", "source" ] }, { "id": "liv017-f-time-q2", "text": "Which profile-specific chronology and ancestry checks passed, failed or could not run?", "kind": "validation", "answer_data": [ "profile rule identifier", "validation result", "cycle or reference diagnostics", "indeterminate reason" ] }, { "id": "liv017-f-time-q3", "text": "How are stored reproductive material, uncertain dates and accession identity reuse handled before a chronology alarm is accepted?", "kind": "exception", "answer_data": [ "exception evidence", "material or event reference", "identity granularity", "qualified review" ] } ], "data_elements": [ { "id": "liv017-f-time-data-times", "name": "Temporal assertions", "description": "Typed biological date or interval plus precision and separate RFC 3339 record timestamps.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-004", "SRC-007", "SRC-009" ] }, { "id": "liv017-f-time-data-checks", "name": "Consistency report", "description": "Rule version, inputs, diagnostics, blocked checks and reviewer disposition.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-004", "SRC-007", "SRC-009" ] } ], "artifacts": [ { "id": "liv017-f-time-artifact", "name": "Dates and graph consistency record", "description": "Proposed versioned record of the answers, supporting references, review state and access restrictions for dates and graph consistency.", "media_or_form": [ "structured JSON record", "controlled human-readable report" ], "serial": true, "identity_strategy": "Authoritative master-system namespace and identifier first; version is distinct from identity. Use a namespaced local UUID only when no master exists. Never use a date, name or digest as the subject identity.", "source_refs": [ "SRC-002", "SRC-004", "SRC-007", "SRC-009" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "liv017-b-analysis", "name": "Coverage and analysis context", "description": "Proposed coverage and analysis context requirements for the lineage pattern.", "rationale": "Groups related questions so adopters can bind evidence, profile constraints and responsible roles without absorbing external subject masters.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005", "SRC-006", "SRC-007" ], "layers": [ { "id": "liv017-l-extent", "name": "Graph extent and completeness", "description": "A lineage view records its focus, permitted depth, edge filter and retrieval limitations. Coverage counts refer to a declared snapshot and denominator. A privacy-filtered or depth-limited graph cannot be presented as a complete family or used silently as the full analysis input.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ], "findings": [ { "id": "liv017-f-extent", "name": "Graph extent and completeness", "description": "A lineage view records its focus, permitted depth, edge filter and retrieval limitations. Coverage counts refer to a declared snapshot and denominator. A privacy-filtered or depth-limited graph cannot be presented as a complete family or used silently as the full analysis input.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ], "questions": [ { "id": "liv017-f-extent-q1", "text": "Which focal members, edge categories and depth limits define this lineage view?", "kind": "composition", "answer_data": [ "focus references", "edge filter", "ancestor and descendant depth", "snapshot revision" ] }, { "id": "liv017-f-extent-q2", "text": "How is the reported coverage measured and which denominator or expected slots does it use?", "kind": "measurement", "answer_data": [ "metric definition", "count", "denominator", "profile assumptions", "not-computable reason" ] }, { "id": "liv017-f-extent-q3", "text": "Which missing branches reflect access filtering, incomplete retrieval or biological uncertainty?", "kind": "access", "answer_data": [ "view-specific omission categories", "pagination completion", "redaction-safe disclosure", "uncertainty distinction" ] } ], "data_elements": [ { "id": "liv017-f-extent-data-view", "name": "View definition", "description": "Snapshot, focus, filters, depth, pagination state and authorized recipient scope.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ] }, { "id": "liv017-f-extent-data-coverage-metrics", "name": "Coverage metrics", "description": "Method-qualified counts and denominator with truncation and disclosure limits.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ] } ], "artifacts": [ { "id": "liv017-f-extent-artifact", "name": "Graph extent and completeness record", "description": "Proposed versioned record of the answers, supporting references, review state and access restrictions for graph extent and completeness.", "media_or_form": [ "structured JSON record", "controlled human-readable report" ], "serial": true, "identity_strategy": "Authoritative master-system namespace and identifier first; version is distinct from identity. Use a namespaced local UUID only when no master exists. Never use a date, name or digest as the subject identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ] } ], "inline_only_rationale": null } ] }, { "id": "liv017-l-interpretations", "name": "Derived relatedness and inheritance references", "description": "Record an externally produced analysis as a separate, revisable interpretation tied to the exact input graph and observation set. The pattern does not supply coefficient algorithms or infer carrier status, disease, genetic certainty or mating suitability. Different definitions and assumptions are not interchangeable.", "source_refs": [ "SRC-003", "SRC-006", "SRC-007" ], "findings": [ { "id": "liv017-f-interpretations", "name": "Derived relatedness and inheritance references", "description": "Record an externally produced analysis as a separate, revisable interpretation tied to the exact input graph and observation set. The pattern does not supply coefficient algorithms or infer carrier status, disease, genetic certainty or mating suitability. Different definitions and assumptions are not interchangeable.", "source_refs": [ "SRC-003", "SRC-006", "SRC-007" ], "questions": [ { "id": "liv017-f-interpretations-q1", "text": "Which relatedness or inbreeding result is reported, under which definition and input assumptions?", "kind": "measurement", "answer_data": [ "external result reference", "metric definition", "dimensionless scale or unit", "algorithm version", "founder and ploidy assumptions", "uncertainty" ] }, { "id": "liv017-f-interpretations-q2", "text": "Which trait, variant or condition observations are linked to an inheritance interpretation?", "kind": "relationship", "answer_data": [ "observation references", "subject links", "assessment time", "interpretation author", "unknown or untested state" ] }, { "id": "liv017-f-interpretations-q3", "text": "What review and permitted purpose constrain use of the analysis result?", "kind": "decision", "answer_data": [ "qualified reviewer", "purpose restrictions", "input revision", "clinical or breeding decision boundary", "stale flag" ] } ], "data_elements": [ { "id": "liv017-f-interpretations-data-analysis-ref", "name": "Analysis reference", "description": "Versioned external result with method, inputs, assumptions, uncertainty and permitted use.", "value_kind": "reference", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-003", "SRC-006", "SRC-007" ] }, { "id": "liv017-f-interpretations-data-observations", "name": "Observation references", "description": "Separately mastered phenotype or variant evidence; missing is not negative.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-003", "SRC-006", "SRC-007" ] } ], "artifacts": [ { "id": "liv017-f-interpretations-artifact", "name": "Derived relatedness and inheritance references record", "description": "Proposed versioned record of the answers, supporting references, review state and access restrictions for derived relatedness and inheritance references.", "media_or_form": [ "structured JSON record", "controlled human-readable report" ], "serial": true, "identity_strategy": "Authoritative master-system namespace and identifier first; version is distinct from identity. Use a namespaced local UUID only when no master exists. Never use a date, name or digest as the subject identity.", "source_refs": [ "SRC-003", "SRC-006", "SRC-007" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "liv017-b-exchange", "name": "Revision and exchange", "description": "Proposed revision and exchange requirements for the lineage pattern.", "rationale": "Groups related questions so adopters can bind evidence, profile constraints and responsible roles without absorbing external subject masters.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008" ], "layers": [ { "id": "liv017-l-revision", "name": "Correction and supersession", "description": "Corrections create a traceable local revision and mark affected exports or interpretations stale. Withdrawal of a claim, entered-in-error status and erasure of protected payload have different effects. Preserve only the history permitted by applicable retention rules.", "source_refs": [ "SRC-006", "SRC-007", "SRC-008" ], "findings": [ { "id": "liv017-f-revision", "name": "Correction and supersession", "description": "Corrections create a traceable local revision and mark affected exports or interpretations stale. Withdrawal of a claim, entered-in-error status and erasure of protected payload have different effects. Preserve only the history permitted by applicable retention rules.", "source_refs": [ "SRC-006", "SRC-007", "SRC-008" ], "questions": [ { "id": "liv017-f-revision-q1", "text": "What state and supersession links describe the current pedigree revision and its disputed assertions?", "kind": "lifecycle", "answer_data": [ "revision state", "supersedes link", "assertion status", "review event" ] }, { "id": "liv017-f-revision-q2", "text": "Which dependent views, analyses and recipients require reassessment after a parentage or identity correction?", "kind": "process", "answer_data": [ "dependency index", "stale outputs", "controlled notification task", "recalculation eligibility" ] }, { "id": "liv017-f-revision-q3", "text": "What correction history may remain after lawful deletion or restricted retention expires?", "kind": "retention", "answer_data": [ "retention authority", "payload disposal scope", "minimal lawful tombstone", "hold review" ] } ], "data_elements": [ { "id": "liv017-f-revision-data-revision-log", "name": "Revision decisions", "description": "Revision, reason, actor, affected claims and permitted retained history.", "value_kind": "collection", "cardinality": "1..n", "required": true, "source_refs": [ "SRC-006", "SRC-007", "SRC-008" ] }, { "id": "liv017-f-revision-data-impact", "name": "Dependency impact", "description": "Local stale marks and proposed follow-up tasks; no external notification is executed.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-006", "SRC-007", "SRC-008" ] } ], "artifacts": [ { "id": "liv017-f-revision-artifact", "name": "Correction and supersession record", "description": "Proposed versioned record of the answers, supporting references, review state and access restrictions for correction and supersession.", "media_or_form": [ "structured JSON record", "controlled human-readable report" ], "serial": true, "identity_strategy": "Authoritative master-system namespace and identifier first; version is distinct from identity. Use a namespaced local UUID only when no master exists. Never use a date, name or digest as the subject identity.", "source_refs": [ "SRC-006", "SRC-007", "SRC-008" ] } ], "inline_only_rationale": null } ] }, { "id": "liv017-l-bindings", "name": "Typed exchange and loss accounting", "description": "Every adapter declares target version, identifier mapping, relationship orientation, missing-value rules and losses. Human PED-oriented fields and plant germplasm structures cannot represent every profile. Export must refuse unsupported meanings or provide an authorized loss report; a picture is not the graph master.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006" ], "findings": [ { "id": "liv017-f-bindings", "name": "Typed exchange and loss accounting", "description": "Every adapter declares target version, identifier mapping, relationship orientation, missing-value rules and losses. Human PED-oriented fields and plant germplasm structures cannot represent every profile. Export must refuse unsupported meanings or provide an authorized loss report; a picture is not the graph master.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006" ], "questions": [ { "id": "liv017-f-bindings-q1", "text": "Which versioned binding maps this profile to a target pedigree or family-history format?", "kind": "interoperability", "answer_data": [ "target schema and version", "field and code mappings", "node granularity", "direction rules" ] }, { "id": "liv017-f-bindings-q2", "text": "What information would be lost or misrepresented by the target format?", "kind": "constraint", "answer_data": [ "unrepresentable roles", "uncertainty loss", "identity collisions", "withheld-data exposure", "refusal policy" ] }, { "id": "liv017-f-bindings-q3", "text": "Which round-trip fixtures check unknown-parent sentinels, enum meanings and partial graph exports?", "kind": "validation", "answer_data": [ "fixture identifiers", "expected semantics", "round-trip result", "unmapped values", "conformance limitation" ] } ], "data_elements": [ { "id": "liv017-f-bindings-data-binding", "name": "Exchange binding", "description": "Versioned target mapping proposal with vocabulary pins and refusal rules.", "value_kind": "reference", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006" ] }, { "id": "liv017-f-bindings-data-loss-report", "name": "Export assessment", "description": "Recipient-scoped loss list, redactions, test results and release decision.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006" ] } ], "artifacts": [ { "id": "liv017-f-bindings-artifact", "name": "Typed exchange and loss accounting record", "description": "Proposed versioned record of the answers, supporting references, review state and access restrictions for typed exchange and loss accounting.", "media_or_form": [ "structured JSON record", "controlled human-readable report" ], "serial": true, "identity_strategy": "Authoritative master-system namespace and identifier first; version is distinct from identity. Use a namespaced local UUID only when no master exists. Never use a date, name or digest as the subject identity.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "liv017-b-governance", "name": "Stewardship and permitted use", "description": "Proposed stewardship and permitted use requirements for the lineage pattern.", "rationale": "Groups related questions so adopters can bind evidence, profile constraints and responsible roles without absorbing external subject masters.", "source_refs": [ "SRC-002", "SRC-004", "SRC-006", "SRC-008" ], "layers": [ { "id": "liv017-l-responsibility", "name": "Authority and processing basis", "description": "Identify accountable roles without assigning ownership of people or biological truth. Record the register mandate or research purpose and the applicable processing basis for every sensitive use. A focal participant cannot authorize every use of data about relatives merely by supplying a pedigree.", "source_refs": [ "SRC-004", "SRC-008" ], "findings": [ { "id": "liv017-f-responsibility", "name": "Authority and processing basis", "description": "Identify accountable roles without assigning ownership of people or biological truth. Record the register mandate or research purpose and the applicable processing basis for every sensitive use. A focal participant cannot authorize every use of data about relatives merely by supplying a pedigree.", "source_refs": [ "SRC-004", "SRC-008" ], "questions": [ { "id": "liv017-f-responsibility-q1", "text": "Which steward maintains the graph and which masters retain authority over subjects and evidence?", "kind": "ownership", "answer_data": [ "steward role", "master responsibilities", "delegation limits", "register mandate" ] }, { "id": "liv017-f-responsibility-q2", "text": "What purpose and applicable processing basis cover each human pedigree use and affected relative?", "kind": "privacy", "answer_data": [ "purpose", "jurisdiction", "basis determination", "sensitive-data condition", "consent scope when applicable" ] }, { "id": "liv017-f-responsibility-q3", "text": "Which ethics, welfare or register approvals constrain this profile before operational use?", "kind": "requirement", "answer_data": [ "approval references", "scope and expiry", "responsible reviewer", "unresolved adoption requirements" ] } ], "data_elements": [ { "id": "liv017-f-responsibility-data-stewardship", "name": "Stewardship assignment", "description": "Accountable roles, mandates, master boundaries and delegation expiry.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-004", "SRC-008" ] }, { "id": "liv017-f-responsibility-data-use-basis", "name": "Use authorization", "description": "Purpose, jurisdiction, legal or ethical review and restrictions; no blanket consent assumption.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-004", "SRC-008" ] } ], "artifacts": [ { "id": "liv017-f-responsibility-artifact", "name": "Authority and processing basis record", "description": "Proposed versioned record of the answers, supporting references, review state and access restrictions for authority and processing basis.", "media_or_form": [ "structured JSON record", "controlled human-readable report" ], "serial": true, "identity_strategy": "Authoritative master-system namespace and identifier first; version is distinct from identity. Use a namespaced local UUID only when no master exists. Never use a date, name or digest as the subject identity.", "source_refs": [ "SRC-004", "SRC-008" ] } ], "inline_only_rationale": null } ] }, { "id": "liv017-l-disclosure", "name": "Protected views and return of results", "description": "Access covers graph topology, member attributes, evidence and derived outputs. Suppressing a name alone is not a sufficient release decision. Unexpected relationship or health implications require restricted professional review; this model supplies no automated discovery, disclosure or re-identification operation.", "source_refs": [ "SRC-002", "SRC-006", "SRC-008" ], "findings": [ { "id": "liv017-f-disclosure", "name": "Protected views and return of results", "description": "Access covers graph topology, member attributes, evidence and derived outputs. Suppressing a name alone is not a sufficient release decision. Unexpected relationship or health implications require restricted professional review; this model supplies no automated discovery, disclosure or re-identification operation.", "source_refs": [ "SRC-002", "SRC-006", "SRC-008" ], "questions": [ { "id": "liv017-f-disclosure-q1", "text": "Which access controls protect graph edges, indirect relationship clues and derived outputs for this recipient?", "kind": "security", "answer_data": [ "recipient role", "purpose", "node and edge policy", "derived-output restrictions", "release review" ] }, { "id": "liv017-f-disclosure-q2", "text": "How are unexpected parentage or health implications contained and routed for qualified review?", "kind": "privacy", "answer_data": [ "restricted case reference", "authorized reviewer", "communication policy", "no automatic disclosure" ] }, { "id": "liv017-f-disclosure-q3", "text": "What audit and withdrawal process governs an approved view or export?", "kind": "access", "answer_data": [ "release scope", "access log", "expiry", "withdrawal action", "downstream copy limitations" ] } ], "data_elements": [ { "id": "liv017-f-disclosure-data-access-view", "name": "Access view policy", "description": "Recipient-purpose policy over nodes, edges, evidence and derived outputs.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-002", "SRC-006", "SRC-008" ] }, { "id": "liv017-f-disclosure-data-release-log", "name": "Disclosure decisions", "description": "Qualified review, release or refusal, scope, expiry and withdrawal limits.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-006", "SRC-008" ] } ], "artifacts": [ { "id": "liv017-f-disclosure-artifact", "name": "Protected views and return of results record", "description": "Proposed versioned record of the answers, supporting references, review state and access restrictions for protected views and return of results.", "media_or_form": [ "structured JSON record", "controlled human-readable report" ], "serial": true, "identity_strategy": "Authoritative master-system namespace and identifier first; version is distinct from identity. Use a namespaced local UUID only when no master exists. Never use a date, name or digest as the subject identity.", "source_refs": [ "SRC-002", "SRC-006", "SRC-008" ] } ], "inline_only_rationale": null } ] } ] } ] }, "functions": [ { "id": "liv017-fn-register", "name": "Register a local graph revision", "description": "Proposed local operation to bind a pedigree to a profile and member references.", "inputs": [ "profile version", "graph master identifier", "typed member references" ], "outputs": [ "draft revision or refusal diagnostics" ], "preconditions": [ "Authorized steward role and purpose-scoped access to all referenced material", "Expected revision matches; profile, evidence and master bindings are available or explicitly unresolved", "Applicable privacy and adoption review permits this operation; no independent runtime implementation is claimed" ], "effects": [ "Create a local draft only; unresolved node types block ready status." ], "source_refs": [ "SRC-001", "SRC-005", "SRC-007" ] }, { "id": "liv017-fn-assert", "name": "Record a qualified descent claim", "description": "Proposed local operation to attach an attributed assertion without certifying biological truth.", "inputs": [ "current graph revision", "typed endpoints and role", "support and contrary evidence" ], "outputs": [ "recorded claim or refusal" ], "preconditions": [ "Authorized steward role and purpose-scoped access to all referenced material", "Expected revision matches; profile, evidence and master bindings are available or explicitly unresolved", "Applicable privacy and adoption review permits this operation; no independent runtime implementation is claimed" ], "effects": [ "Retain alternative claims; separate local recording from external register acceptance." ], "source_refs": [ "SRC-001", "SRC-004", "SRC-007" ] }, { "id": "liv017-fn-check", "name": "Assess profile consistency", "description": "Proposed local validation operation; no genotype inference or clinical assessment.", "inputs": [ "graph snapshot", "pinned rule profile", "authorized date and identity evidence" ], "outputs": [ "pass, fail or indeterminate diagnostics" ], "preconditions": [ "Authorized steward role and purpose-scoped access to all referenced material", "Expected revision matches; profile, evidence and master bindings are available or explicitly unresolved", "Applicable privacy and adoption review permits this operation; no independent runtime implementation is claimed" ], "effects": [ "Report reference, direction, cycle and qualified chronology issues without silently repairing claims." ], "source_refs": [ "SRC-002", "SRC-004", "SRC-005" ] }, { "id": "liv017-fn-view", "name": "Prepare a restricted lineage view", "description": "Proposed local view preparation with bounded traversal and disclosure review.", "inputs": [ "recipient and purpose", "authorized graph revision", "depth and edge filters" ], "outputs": [ "restricted preview and loss report or refusal" ], "preconditions": [ "Authorized steward role and purpose-scoped access to all referenced material", "Expected revision matches; profile, evidence and master bindings are available or explicitly unresolved", "Applicable privacy and adoption review permits this operation; no independent runtime implementation is claimed" ], "effects": [ "Record truncation and redaction; no external transmission or sensitive inference is authorized." ], "source_refs": [ "SRC-002", "SRC-005", "SRC-008" ] }, { "id": "liv017-fn-revise", "name": "Supersede a disputed assertion", "description": "Proposed local correction operation with explicit dependency impact.", "inputs": [ "expected revision", "authorized correction evidence", "retention assessment" ], "outputs": [ "new revision and stale-output list or refusal" ], "preconditions": [ "Authorized steward role and purpose-scoped access to all referenced material", "Expected revision matches; profile, evidence and master bindings are available or explicitly unresolved", "Applicable privacy and adoption review permits this operation; no independent runtime implementation is claimed" ], "effects": [ "Preserve permitted history; do not alter a master register or contact recipients." ], "source_refs": [ "SRC-006", "SRC-007", "SRC-008" ] }, { "id": "liv017-fn-attach", "name": "Attach a reviewed analysis reference", "description": "Proposed local indexing operation for externally produced interpretation.", "inputs": [ "analysis result reference", "exact input graph revision", "method and assumptions", "qualified review" ], "outputs": [ "analysis link with use restrictions or refusal" ], "preconditions": [ "Authorized steward role and purpose-scoped access to all referenced material", "Expected revision matches; profile, evidence and master bindings are available or explicitly unresolved", "Applicable privacy and adoption review permits this operation; no independent runtime implementation is claimed" ], "effects": [ "Reject missing provenance; mark stale inputs; compute no coefficient and issue no health or breeding advice." ], "source_refs": [ "SRC-003", "SRC-006", "SRC-007" ] } ], "composition": [ { "target": "WM-LIV-002", "relation": "REFERENCE", "purpose": "Candidate binding to Organism Individual masters; registry parent placement is not type inheritance. A profile must supply valid typed subject identities even if this candidate package is unavailable.", "required": false, "source_refs": [ "SRC-001", "SRC-004" ] }, { "target": "External germplasm or population master", "relation": "REFERENCE", "purpose": "Use only in a declared plant or population profile; bind node granularity explicitly and never coerce into organism identity.", "required": false, "source_refs": [ "SRC-005" ] }, { "target": "External biosample, assay and phenotype masters", "relation": "REFERENCE", "purpose": "Versioned evidence and observation links with controlled access; no copying of raw genomic or health records is required.", "required": false, "source_refs": [ "SRC-003", "SRC-004", "SRC-006" ] }, { "target": "External register or research authorization record", "relation": "REFERENCE", "purpose": "Acceptance, stewardship, processing basis and approved use remain externally governed references.", "required": false, "source_refs": [ "SRC-004", "SRC-008" ] }, { "target": "GA4GH pedigree, Phenopackets, FHIR and BrAPI profiles", "relation": "ALIGN", "purpose": "Conceptual alignments only. Exact versioned adapters, vocabularies and executable conformance require future profile work.", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-005", "SRC-006" ] }, { "target": "PROV-O", "relation": "ALIGN", "purpose": "Record-level attribution and derivation alignment; never interpret document derivation as biological parentage.", "required": false, "source_refs": [ "SRC-007" ] } ], "serviceLayers": { "dimension": { "owner_package_requirements": [ "Name accountable scientific, clinical, breeding or conservation stewardship roles and their limited mandate.", "Pin pattern version, profile, node types, subject masters and permitted uses.", "Bind namespace, storage, interface, process references, evidence retention and access policy before use." ], "namespace_guidance": "Use an owner-controlled namespace for graph, assertion, member and artifact identifiers; keep source master namespaces intact. No company or product is assigned ownership.", "registry_links": [ "vr.wm-liv-017", "WM-LIV-002 candidate reference; version unresolved" ] }, "canon_and_patch": { "canonicalization_rules": [ "Normalize parent-to-offspring direction using a pinned role vocabulary while preserving original assertion and source direction.", "Do not merge members by name, shared genotype or accession label; do not remove contrary claims to produce a simpler graph.", "Graph normalization does not promote this reviewable research draft to canonical status." ], "patch_rules": [ "Use explicit base revision, actor, reason and affected assertion IDs; reject stale concurrent changes.", "Identity or role corrections create new revisions and mark dependent views and interpretations stale." ], "compatibility_rules": [ "Role, missing-value, node-granularity or reproductive-mode changes require an explicit migration and reviewed mapping.", "Adapters must declare unsupported cases and loss; never silently flatten uncertain or non-genetic relationships into parent fields." ] }, "artifact_rules": { "identity_priority": [ "Authoritative master-system namespace and identifier", "Owner-assigned stable accession or UUID when a master identifier is absent", "Content digest for integrity and rendition comparison only" ], "timestamp_rule": "Record event timestamps using RFC 3339 with seconds and explicit UTC offset or Z. Keep biological date-only, partial-date and interval values separate with precision and uncertainty; never invent a midnight timestamp.", "serial_naming_rule": "Use stable artifact identity plus a separate revision and rendition. Filenames and dates do not identify organisms, pedigrees or claims.", "integrity_rule": "Hash retained artifact bytes and record algorithm, provenance and access scope. A matching digest proves byte integrity, not parentage, authenticity of assertions or permission to disclose." }, "policies": [ "All structures and operations are proposals; reviewed human, livestock and plant sources do not establish a universal biological schema.", "Apply purpose limitation, sensitive-data controls and jurisdiction-specific processing bases; consent from one informant is not blanket permission for relatives.", "No automatic discovery or disclosure of unexpected family relationships, health risks or re-identification. Route implications to restricted qualified review.", "Physical properties of organisms and laboratory measurements are delegated; graph extent, revision and uncertainty are direct nonphysical properties.", "Retain typed context for gestation, social links and population ancestry without traversing them as individual genetic descent." ], "crud": { "read": [ "Check recipient, purpose, node, edge, finding and evidence permissions; treat topology and analysis as potentially sensitive." ], "create": [ "Create draft assertions with namespaced IDs, profile, reporter and evidence state; acceptance is a separate authorized decision." ], "update": [ "Require expected revision and correction authority; log support, contrary evidence and downstream stale state." ], "delete": [ "Apply lawful retention, erasure and hold review to each protected payload and derived copy; preserve only minimal permitted tombstones.", "Retiring a lineage claim does not delete an organism master or undo an external register decision; do not promise recall of all external copies." ] }, "roles": [ { "name": "Lineage steward", "responsibilities": [ "Maintain profile, graph identity, revisions and permitted master bindings." ] }, { "name": "Evidence curator", "responsibilities": [ "Preserve report attribution, sample mappings and contradictory evidence without certifying truth." ] }, { "name": "Domain reviewer", "responsibilities": [ "Assess role semantics, identity disputes, chronology exceptions and analysis-use limitations." ] }, { "name": "Privacy and ethics reviewer", "responsibilities": [ "Determine scoped use, disclosure, retention and return-of-results handling under applicable rules." ] }, { "name": "Exchange maintainer", "responsibilities": [ "Pin mappings, report losses and test semantic round trips before any operational claim." ] } ], "access": { "default_rule": "Deny access unless role and purpose authorize the exact graph view and evidence; human pedigree data and sensitive nonhuman records require explicit scoped release review.", "scopes": [ "bundle", "layer", "finding", "artifact" ], "exceptions": [ "A documented exception must name authority, purpose, recipient, scope and expiry; no emergency or research bypass is assumed.", "Redacted views must avoid exposing restricted existence, topology or unexpected findings through logs, counts or derived outputs." ], "audit_requirements": [ "Log authorized access and export decisions, relevant policy revision, actor, purpose and outcome without duplicating protected payload.", "Review failed access, correction impact and expired grants under a bounded retention policy." ] }, "agents_bootstrap": { "filename": "AGENTS.md", "required_fields": [ "Name", "Type", "Specification URL", "Storage type URL", "Interface URL", "Processes URL", "Profile version", "Owner role", "Source and review holds" ], "read_order": [ "AGENTS.md and applicable owner policies", "spec.yaml and publication holds", "Profile, master bindings and permitted-use references", "Authorized graph revision, evidence and mapping diagnostics" ] } }, "coverage": { "claim": "Source-grounded reviewable proposal for a reusable biological lineage pattern with selected human, livestock and plant examples. A separate frozen local Codex no-tools self-audit found no critical conflict. Independent review, source/version verification, adoption profiles and executable conformance remain holds; no universal inheritance or operational analysis capability is claimed.", "confidence": "medium", "checklist": [ { "dimension": "identity", "status": "covered", "notes": "Distinct pattern, graph, revision, member, assertion and artifact identity." }, { "dimension": "lifecycle", "status": "covered", "notes": "Draft, reviewed, disputed, superseded and retired claims remain separate from organism life status." }, { "dimension": "relationships", "status": "covered", "notes": "Typed directed descent, role separation and competing assertions." }, { "dimension": "temporal", "status": "covered", "notes": "Biological uncertainty and profile chronology separate from event timestamps." }, { "dimension": "provenance", "status": "covered", "notes": "Evidence and interpretation attribution without a truth guarantee." }, { "dimension": "ownership", "status": "covered", "notes": "Role-based stewardship and external master authority; no ownership of persons." }, { "dimension": "validation", "status": "gap", "notes": "Research schema validates; instance schemas, graph checks and conformance fixtures are proposed only." }, { "dimension": "access", "status": "covered", "notes": "Purpose-scoped view, edge, evidence and derived-output restrictions." }, { "dimension": "interoperability", "status": "gap", "notes": "Conceptual mappings identified; release pins and executable adapters not implemented." }, { "dimension": "direct properties", "status": "covered", "notes": "Extent, revision and uncertainty are graph properties; physical measurements delegated." }, { "dimension": "recognition and observation", "status": "covered", "notes": "Documented graph membership and assertion evidence are distinct from visual recognition or inference." }, { "dimension": "capabilities and actions", "status": "covered", "notes": "Six bounded local proposals; no operational inference, clinical advice or register mutation." }, { "dimension": "cross-species reach", "status": "gap", "notes": "Human, livestock and plant evidence only; microbial and specialized inheritance profiles deferred." }, { "dimension": "independent review", "status": "gap", "notes": "Claude and Grok skipped; separate Codex no-tools self-audit required, not independent review." }, { "dimension": "source verification", "status": "gap", "notes": "Browser-selected content reviewed; direct HTTP not attempted under owner-reported sandbox block. Current version and applicability checks remain open." } ], "known_omissions": [ "Independent external review and current source/version verification.", "Nested instance schemas, terminology release pins, executable adapters, graph validators and adversarial fixtures.", "Validated coefficient algorithms, ploidy-specific inheritance, microbial and cell-line profiles, horizontal transfer and specialized conservation practice.", "Jurisdiction-specific legal and ethics determinations, consent capacity, deceased-relative treatment, animal welfare and register acceptance procedures." ], "conflicts": [], "regional_assumptions": [ "GDPR is a selected EU legal example, not a universal privacy rule or an applicability determination.", "Human family-history and livestock guidance retain their original scope; plant germplasm semantics need separate node types." ], "adversarial_checks": [ "Challenge self-loops caused by accession reuse separately from legitimate selfing across generations.", "Challenge the assumption that all pedigrees have exactly two known genetic parents.", "Challenge identity merges from names or genotype equality and founder status as proof of unrelatedness.", "Challenge a negative or absent phenotype as proof of no variant or future disease.", "Challenge unrestricted exports, topology leaks, stale analysis and blanket consent from a proband.", "Challenge any implication that a recorded claim, provenance chain or register acceptance establishes biological truth." ] }, "researchAdjudication": { "providerMode": "single-provider-waiver", "activeProviders": [ "codex" ], "waivedProviders": [ "claude", "grok" ], "providerPolicy": { "contract_version": "1.0.0", "mode": "single-provider-waiver", "effective_at": "2026-09-06T00:00:00Z", "scope": "Canonical single-stream subject-model research after the six-workstream consolidation", "active_providers": [ "codex" ], "waived_providers": [ { "provider": "claude", "authorized_by": "repository owner", "authorized_at": "2026-09-06T00:00:00Z", "reason": "Claude produced no result on prior 1800-second and 900-second attempts and again timed out on bounded 600-second Sonnet and 300-second Haiku passes. The owner prioritized completion over provider availability." }, { "provider": "grok", "authorized_by": "repository owner", "authorized_at": "2026-09-06T00:00:00Z", "reason": "The repository owner authorized completion without Grok when Grok is unavailable, slow or schema-invalid. Grok may still be attempted as a bounded supplemental reviewer, but its failure never blocks a valid Claude plus no-tools result." } ], "review_rule": "Codex may complete source-grounded fallback research after bounded Claude and Grok attempts fail. It requires a separate no-tools adversarial audit and remains reviewable-draft with a visible absence-of-external-review hold.", "supplemental_provider_attempts": [ { "provider": "claude", "required": false, "maximum_attempts": 1, "failure_policy": "record-and-continue", "admission_rule": "Use only a locally schema-valid result whose sources and boundaries survive adjudication." }, { "provider": "grok", "required": false, "maximum_attempts": 1, "failure_policy": "record-and-continue", "admission_rule": "Use only a locally schema-valid result whose sources and boundaries survive adjudication." } ] }, "boundaryDecision": { "entry_kind": "pattern", "status": "accepted", "rationale": "The root describes reusable graph and assertion requirements rather than one organism, relationship or pedigree instance. Concrete graphs retain their own identity and revisions. The registry Organism Individual parent is qualified as a candidate reference, not type inheritance; external subject and evidence masters remain separate." }, "decisions": [ { "concept": "Pattern boundary", "disposition": "accepted", "rationale": "The reusable root and separately identified graph instances are coherent; a collection of assertions does not force the research root to be an aggregate." }, { "concept": "Organism Individual registry parent", "disposition": "qualified", "rationale": "The parent candidate cannot establish inheritance because a lineage graph is not an organism. Optional master references preserve the intended subject boundary." }, { "concept": "Cross-species node granularity", "disposition": "accepted with limits", "rationale": "Human, livestock and plant examples are separated by explicit profiles. Germplasm and population nodes cannot be silently equated with individual organisms." }, { "concept": "Descent roles and selfing", "disposition": "accepted", "rationale": "Genetic, gestational and contextual relations remain distinct. Selfing across generations does not justify an individual self-loop or collapsing accession identities." }, { "concept": "Unknown and conflicting parents", "disposition": "accepted", "rationale": "Missing, withheld, unrequested and disputed ancestry retain distinct reasons and competing claims. Dataset founders do not prove absent ancestors or unrelatedness." }, { "concept": "Evidence and official acceptance", "disposition": "separated", "rationale": "Source attribution, sample mappings and register decisions have separate authority and state. The model does not certify biological truth from a record or digest." }, { "concept": "Chronology and graph checks", "disposition": "qualified", "rationale": "Proposed checks require profile rules and uncertain dates. Shared ancestors and stored material challenge simplistic cycle or age assumptions; indeterminate results remain available." }, { "concept": "Analysis and inheritance interpretation", "disposition": "bounded", "rationale": "Only external reviewed results and input assumptions are indexed. No coefficient algorithm, genotype inference, health-risk determination or mating decision is supplied." }, { "concept": "Revision and disposal", "disposition": "accepted with policy dependency", "rationale": "Corrections mark dependent outputs stale while history retention remains limited by lawful deletion and minimal permitted tombstones. External registers remain authoritative." }, { "concept": "Privacy and affected relatives", "disposition": "accepted with adoption hold", "rationale": "Purpose-scoped access includes graph topology and derived outputs. One participant does not authorize all relatives' data, and consent is not assumed to be the sole processing basis." }, { "concept": "Exchange conformance", "disposition": "deferred", "rationale": "Direction, sentinel, enum, granularity and information-loss questions are substantive, but nested schemas, release pins and executable adapters still require implementation and testing." }, { "concept": "Supplement and legacy inputs", "disposition": "reconciled", "rationale": "Supplement identity, property and capability claims were qualified against primary sources. No legacy alias is registered, and no supplement provider attribution is treated as an external pass." }, { "concept": "Source verification", "disposition": "held", "rationale": "Selected browser content supports the proposed concepts. Direct HTTP was unattempted under the owner-reported sandbox block; no measured status, immutable source pin or universal applicability is claimed." }, { "concept": "Independent review", "disposition": "waived and held", "rationale": "Claude and Grok were skipped with zero attempts under the owner instruction. A local Codex no-tools self-audit is a separate phase but not an independent provider review." } ], "publicationHolds": [ "Independent external review is absent under the owner-authorized single-provider waiver. Claude and Grok were skipped with zero attempts; the separate local Codex no-tools self-audit is not independent review.", "Source and version verification remains incomplete. Direct HTTP checks were not attempted under the owner-reported sandbox restriction; all nine statuses are unmeasured and zero HTTP 200 responses were measured. Selected browser evidence is recorded in source-review.md. The coordinator must run check_sources.py and verify current versions, redirects, claim support and reuse rights.", "Operational adoption requires qualified species, register, clinical, legal, privacy, ethics and welfare review. Human data processing bases, affected-relative permissions, return of results, retention and jurisdiction-specific duties are not certified by this draft.", "Nested instance schemas, exact neighbor and vocabulary pins, executable graph checks, target-format adapters and semantic round-trip fixtures remain incomplete. No runtime, exchange-conformance, register or clinical certification is claimed.", "Cross-species coverage is limited to selected human, livestock and plant examples. Specialized microbial, cell-line, horizontal-transfer and ploidy-specific profiles and validated relatedness algorithms require further evidence and review before use.", "Independent external review was explicitly waived by the repository owner; this codex-only result remains a reviewable draft." ], "deferredResearch": [ "Restore independent external review before canonical or publishable-draft promotion.", "Pin source and vocabulary releases, verify live URLs outside the sandbox and review profile-specific legal and scientific applicability.", "Build nested instance schemas and semantic fixtures for ambiguous identity, selfing, shared ancestors, uncertain parents, chronology exceptions, privacy-filtered views, corrections and lossy exchanges.", "Research specialized biological profiles and validate external analysis definitions, algorithms, assumptions and permitted use separately from this representation pattern." ] }, "statistics": { "sources": 9, "bundles": 6, "layers": 12, "findings": 12, "questions": 36, "artifacts": 12, "functions": 6 } }