{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.wm-liv-017","code":"wm-liv-017-pedigree-biological-lineage","url":"https://ver.cy/models/wm-liv-017-pedigree-biological-lineage/","name":"Pedigree / Biological Lineage","alternateNames":[],"kind":"world-model","status":"published","version":"0.1.0","language":"en","classifiers":{"family":"World Models","category":"Physical world and living systems","entryKind":"pattern","plane":"","domain":["PHY.LIV.LIN"],"industry":["Cross-industry"],"navPath":"NAV.PHY.LIV.LIN","tags":["pedigree","biological","lineage","phy.liv.lin"],"facets":{}},"whatItIs":"A pedigree or biological lineage is the recorded line of descent among organisms, across generations, with the parent-offspring links and the inheritance patterns traced through them, for animals, plants, microbes or people. The single organism, the breed or cultivar as a class and the evolutionary phylogeny of taxa are separate subjects.","purpose":"Describe reusable, evidence-qualified biological descent graphs and their bounded lineage records across species.","scope":{"in":["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":["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"],"boundaries":[{"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."},{"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."},{"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."},{"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."},{"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."}]},"distinguishingFeatures":["Records actual descent among individual organisms, while a phylogeny relates taxa.","A structure linking many individuals, not the record of one organism.","Spans species: livestock herd books, plant breeding lines, laboratory strains and human family pedigrees.","Distinct from a breed or cultivar, which is a class defined partly by pedigree."],"structure":{"bundles":[{"id":"LIV017-B1","name":"Descent links","description":"Who descends from whom.","layers":[{"id":"LIV017-B1-L1","name":"Parentage","description":"Parent-offspring links with their evidence.","findings":[{"id":"LIV017-F01","name":"Recorded parents","description":"The sire and dam, or seed and pollen parents, recorded for an individual.","questions":[{"text":"Which individuals are recorded as parents of this organism?","id":"LIV017-Q01"},{"text":"Is parentage verified by genotyping or only declared?","id":"LIV017-Q02"}]},{"id":"LIV017-F02","name":"Generations covered","description":"How many ancestral generations the record covers and how complete they are.","questions":[{"text":"How many generations back is the lineage recorded?","id":"LIV017-Q03"},{"text":"Which ancestors are unknown or missing?","id":"LIV017-Q04"}]}]}]},{"id":"LIV017-B2","name":"Inheritance analysis","description":"What the lineage says about traits and relatedness.","layers":[{"id":"LIV017-B2-L1","name":"Relatedness and traits","description":"Coefficients and trait segregation computed from the lineage.","findings":[{"id":"LIV017-F03","name":"Relatedness","description":"Inbreeding and relationship coefficients computed from the pedigree.","questions":[{"text":"What inbreeding coefficient does the individual have, and from how many generations?","id":"LIV017-Q05"},{"text":"How closely related are two given individuals?","id":"LIV017-Q06"}]},{"id":"LIV017-F04","name":"Trait inheritance","description":"The pattern of a trait or variant through the lineage.","questions":[{"text":"Which trait or variant is traced, and with which inheritance pattern?","id":"LIV017-Q07"},{"text":"Which relatives are carriers or affected according to the record?","id":"LIV017-Q08"}]}]}]},{"id":"LIV017-B3","name":"Registry and consent","description":"Who keeps the lineage and on what basis.","layers":[{"id":"LIV017-B3-L1","name":"Register and rights","description":"The herd book, studbook or study holding the record.","findings":[{"id":"LIV017-F05","name":"Keeping register","description":"The register or study that holds the lineage.","questions":[{"text":"Which herd book, studbook, breeding programme or study holds the record?","id":"LIV017-Q09"},{"text":"Under which rules are entries accepted and corrected?","id":"LIV017-Q10"}]},{"id":"LIV017-F06","name":"Consent for human pedigrees","description":"The basis for recording human family members.","questions":[{"text":"For a human pedigree, which family members consented to be recorded?","id":"LIV017-Q11"}]}]}]}]},"agentConduct":{"may":["Compute inbreeding and relationship coefficients from recorded pedigrees.","Flag inconsistent parentage, such as impossible dates or conflicting genotypes.","Trace a trait or variant through a non-human lineage for breeding decisions.","Report the completeness of a pedigree."],"mustNot":["Disclose human family pedigrees or carrier status to anyone outside the consented purpose.","Infer and reveal non-paternity or undisclosed relationships.","Alter registered parentage without the register's correction procedure.","Present declared parentage as genetically verified."],"requiresHuman":["Registering or correcting parentage in an official herd book or studbook.","Communicating inherited disease risk to family members.","Approving matings in conservation breeding programmes."]},"ethics":{"considerations":["Human pedigrees reveal health risks and family secrets that affect relatives who never consented.","Breeding on narrow lineages raises inbreeding and animal welfare problems.","Pedigree records carry economic value and can be falsified for gain."],"affectedParties":["Family members in human pedigrees","Breeders and owners of animals and plants","Animals bred under the lineage decisions","Genetic counsellors and researchers"]},"owners":{"steward":"The breed society, breeding programme, studbook keeper or research team that maintains the lineage record.","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."]}],"masterSystems":["Herd book or studbook","Plant breeding database","Zoo and conservation studbook","Clinical genetics family record"]},"relations":[{"target":"WM-LIV-002","type":"references","note":"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."},{"target":"External germplasm or population master","type":"references","note":"Use only in a declared plant or population profile; bind node granularity explicitly and never coerce into organism identity."},{"target":"External biosample, assay and phenotype masters","type":"references","note":"Versioned evidence and observation links with controlled access; no copying of raw genomic or health records is required."},{"target":"External register or research authorization record","type":"references","note":"Acceptance, stewardship, processing basis and approved use remain externally governed references."},{"target":"GA4GH pedigree, Phenopackets, FHIR and BrAPI profiles","type":"aligned","note":"Conceptual alignments only. Exact versioned adapters, vocabularies and executable conformance require future profile work."},{"target":"PROV-O","type":"aligned","note":"Record-level attribution and derivation alignment; never interpret document derivation as biological parentage."},{"target":"WM-LIV-002 Organism Individual","type":"neighbor","note":"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."},{"target":"Taxon phylogeny and breed or cultivar classifiers","type":"neighbor","note":"Lineage assertions concern profiled subjects and reproductive descent; a taxonomic class or similarity cluster cannot supply an individual parentage edge."},{"target":"Clinical family history and social or legal family relationships","type":"neighbor","note":"Relative histories can remain uncertain. Social and gestational context may be referenced with explicit roles but never converted into genetic descent or legal rights."},{"target":"Biosample, assay, variant and phenotype records","type":"neighbor","note":"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."},{"target":"Record provenance and breeding programme","type":"neighbor","note":"Document derivation records who produced a claim. Biological descent records the claim itself. Register acceptance and programme decisions remain externally authorized activities."},{"target":"WM-LIV-002","type":"parent"}],"interaction":{"identity":{"applicability":"required","items":["Each individual in the lineage is identified by its registration number in the keeping register.","A lineage record is identified by the register together with the focal individual or family identifier."]},"properties":{"applicability":"not-applicable","items":[]},"recognition":{"applicability":"optional","items":["A pedigree shows individuals linked by parent-offspring relations over generations.","Often confused with a phylogenetic tree, a breed standard or a single genotype result."]},"capabilities":{"applicability":"required","items":["Supports computation of inbreeding and relationship coefficients.","Supports genetic evaluation and mating decisions in breeding.","Supports tracing inherited variants in families and populations."]},"hazards":{"applicability":"required","items":["Disclosure of inherited disease risk or non-paternity.","Hidden inbreeding from incomplete or falsified records.","Fraud with registration papers of valuable animals."]},"interfaces":{"applicability":"required","items":["ICAR guidelines for animal identification and recording.","GA4GH Pedigree standard for human pedigrees in genomic medicine.","Standardized pedigree nomenclature used in clinical genetics."]},"context":{"applicability":"required","items":["Kept by breed societies, breeding companies, zoos, plant breeders and clinical genetics services.","Human pedigrees are health data under data protection law."]}},"sources":[{"title":"Pedigree Conceptual Model","url":"https://pedigree.readthedocs.io/en/latest/pedigree-model.html","note":"Global Alliance for Genomics and Health"},{"title":"Using the Pedigree Standard","url":"https://pedigree.readthedocs.io/en/latest/using-the-pedigree-model.html","note":"Global Alliance for Genomics and Health"},{"title":"Phenopacket Schema Pedigree","url":"https://phenopacket-schema.readthedocs.io/en/latest/pedigree.html","note":"Global Alliance for Genomics and Health"},{"title":"General Rules: Parentage recording methods","url":"https://wiki.icar.org/index.php/General_Rules%3A_Parentage_recording_methods","note":"International Committee for Animal Recording"},{"title":"BrAPI V2.1 Germplasm Pedigree specification","url":"https://github.com/plantbreeding/BrAPI/tree/brapi-V2.1/Specification/BrAPI-Germplasm/Pedigree","note":"Breeding API community"},{"title":"FHIR R5 FamilyMemberHistory","url":"https://hl7.org/fhir/R5/familymemberhistory.html","note":"Health Level Seven International"},{"title":"PROV-O: The PROV Ontology","url":"https://www.w3.org/TR/prov-o/","note":"World Wide Web Consortium"},{"title":"General Data Protection Regulation","url":"https://eur-lex.europa.eu/eli/reg/2016/679/oj/eng","note":"European Union"},{"title":"Date and Time on the Internet: Timestamps","url":"https://www.rfc-editor.org/rfc/rfc3339.html","note":"Internet Engineering Task Force"},{"title":"ICAR Guidelines for animal recording, International Committee for Animal Recording"},{"title":"Recommendations for standardized human pedigree nomenclature, National Society of Genetic Counselors"}],"openQuestions":["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.","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."],"resources":{"spec":"/models/wm-liv-017-pedigree-biological-lineage/spec.yaml","agents":"/models/wm-liv-017-pedigree-biological-lineage/AGENTS.md","source":"https://github.com/ver-cy/world-models/tree/feat/mega-model-registry/research/runs/wm-liv-017"},"provenance":{"origin":"world-models research","builtFrom":["models/wm-liv-017-pedigree-biological-lineage/spec.yaml","ver-cy/world-models/card-supplements/wm-liv-017-pedigree-biological-lineage.json"],"providers":["Codex"],"researchStatus":"reviewable-draft","generatedAt":"2026-10-06T21:14:45Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"not-applicable","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"interaction.properties":"A lineage is a record of relations between organisms; coefficients are computed, not physically measured.","_supplement":"Sections authored in card supplement 1.0.0 by Claude (Opus 5.5) (2026-10-06, unreviewed). Written from the card's existing content and established practice in the field; no new sources were read. Unreviewed."},"score":1.0}}