{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T10:27:13Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 25.7, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09527-1fa2-7943-a2a9-c7d20d155e79\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: inbred strain\nSense to describe: (none recorded)\nDomain code: XCT.REL\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001 r", "usd": 0.0, "recall": true }, "codex": { "seconds": 69.7, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09527-1faa-77f1-a8e0-17f8b0ecf8e9\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: inbred strain\nRegistry id: vr.tr.inbred-strain\nPlane / domain: XCT / XCT.REL\nRegistry definition: (none recorded)\nNames folded into this entry: (none" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-05T18:30:00Z", "ingestedAt": "2026-10-05T13:30:32+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:27+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q1893126", "registryId": "vr.tr.inbred-strain", "name": "inbred strain", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "XCT.REL" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q1893126/", "model": { "registry_id": "vr.tr.inbred-strain", "name": "inbred strain", "purpose": "Enable an agent to recognise an inbred strain, assess evidence for its genetic continuity, and decide whether particular stocks can be maintained, compared or used under that identity.", "definition": "An inbred strain is a breeding population established and maintained through repeated mating of close relatives or self-fertilization, resulting in high homozygosity and genetic similarity among its members.", "scope_statement": "This model owns the lineage identity and inbred-status claims of vr.tr.inbred-strain, provisionally understood as a sexually reproduced lineage established and maintained through systematic inbreeding; it relates that lineage to its constituent organisms, colonies, ancestral strains and derivatives without identifying it with any one stock.", "in_scope": [ "Species-specific criteria for recognising a lineage as an inbred strain", "Founding ancestry, mating history and continuity of descent", "Evidence for homozygosity and genetic consistency within the lineage", "Relationships among strain identity, substrains and separately maintained colonies", "Genetic authentication, maintenance status and suitability for specified comparisons" ], "out_of_scope": [ "Individual organism anatomy, health and life history", "General species taxonomy and population genetics theory", "Facility operations and detailed animal husbandry procedures", "Complete experimental protocols and study results", "Independent models of outbred stocks, hybrids, clones and engineered alleles" ], "distinguishing_features": [ "Require a documented inbreeding history against an applicable standard; a closed breeding population or an informal strain name alone does not establish inbred status.", "For mouse and rat recognition, test the documented pedigree against the guideline requiring at least 20 consecutive generations of sibling mating or an accepted equivalent, together with its ancestry and maintenance conditions. [MGI strain nomenclature guidelines](https://www.informatics.jax.org/mgihome/nomen/strains.shtml)", "Distinguish an inbred strain from an F1 hybrid using parental identities and breeding history; uniform appearance or similar genotypes among sampled animals cannot resolve this boundary alone.", "Distinguish a sexually maintained lineage from a clone by recording its mode of reproduction and descent.", "Resolve substrain identity before treating stocks as interchangeable: branches may be known or suspected to differ genetically. [JAX inbred mouse nomenclature](https://www.jax.org/jax-mice-and-services/customer-support/technical-support/genetics-and-nomenclature/inbred-mice)" ], "characteristics": [ { "name": "Taxon and recognition standard", "kind": "relation", "unit_or_values": "Species or taxon identifier linked to a named, versioned inbred-strain standard", "why_it_matters": "Prevents a criterion established for one organism group from being silently applied to another." }, { "name": "Inbred qualification", "kind": "state", "unit_or_values": "Unassessed | supported under named standard | disputed | insufficient evidence", "why_it_matters": "Separates a strain label from an evaluated claim." }, { "name": "Mating regime", "kind": "category", "unit_or_values": "Sibling mating | parent-offspring mating | other documented regime | mixed history | unknown", "why_it_matters": "Makes the route to inbreeding and any claimed equivalence assessable." }, { "name": "Documented inbreeding generations", "kind": "measurement", "unit_or_values": "Generations, with counting origin, pedigree coverage and interruptions", "why_it_matters": "A generation count is interpretable only with its breeding history." }, { "name": "Observed residual heterozygosity", "kind": "measurement", "unit_or_values": "Fraction or percentage of eligible callable loci, with assay, genomic regions, sample and date", "why_it_matters": "Provides measured evidence without treating unobserved regions as homozygous." }, { "name": "Within-stock genotype discordance", "kind": "measurement", "unit_or_values": "Discordant genotype comparisons divided by eligible comparisons, with loci, animals and method", "why_it_matters": "Distinguishes homozygosity within an animal from agreement among animals." }, { "name": "Strain and substrain identity", "kind": "relation", "unit_or_values": "Accepted designation, aliases, parent lineage and applicable nomenclature authority", "why_it_matters": "Connects names to the precise lineage represented." }, { "name": "Stock authentication status", "kind": "state", "unit_or_values": "Not assessed | matches specified reference | unresolved discrepancy | inconsistent with claimed identity", "why_it_matters": "Supports decisions about a particular stock without invalidating every stock of the strain." }, { "name": "Lineage availability", "kind": "state", "unit_or_values": "Live stock documented | archived material documented | both documented | no recoverable material known | unknown", "why_it_matters": "Separates persistence of the strain concept from access to biological material." } ], "affordances": [ "Assess an inbred-status claim against a named standard and identify missing pedigree evidence", "Resolve strain names to precise substrain and stock identities before acquisition or comparison", "Compare genetic assays with a documented reference and flag discrepancies for investigation", "Evaluate whether a breeding change, separation or outcross requires reassessment of lineage identity", "Select a documented stock or archived source whose evidence supports a specified experimental use" ], "agent_conduct": { "may": [ "Report a strain's designation, origin and characteristics from the holding facility's records.", "Track breeding records and genetic monitoring results for a colony it is authorized to manage." ], "must_not": [ "Record or present an animal as belonging to a strain it has not been confirmed to belong to.", "Mix breeding lines in ways that contaminate a strain without recording it.", "Neglect the welfare of animals in a breeding colony or hide signs of suffering.", "Use or supply animals for research outside an approved and licensed project." ], "requires_human": [ "Any decision to breed, cull or transfer animals in a colony.", "Starting experiments that use animals of the strain." ] }, "ethics": { "considerations": [ "Inbred animals are bred for research and can suffer from inherited conditions caused by inbreeding.", "Wrongly identified strains waste animals and undermine the reproducibility of research." ], "affected_parties": [ "The animals themselves", "Researchers and people relying on their results", "Animal care staff" ] }, "owners": { "steward": "The breeding facility or repository that maintains the strain; the licensed establishment answers for animal welfare.", "master_systems": [ "Strain repository and nomenclature databases" ] }, "visual_identification": [ "A strain designation following standard nomenclature on cage cards and records.", "Uniform coat colour and body type across members of the colony.", "Individual ear tags, tattoos or microchips linked to breeding records." ], "failure_modes_and_hazards": [ "Genetic contamination from accidental crossing with another strain.", "Genetic drift that makes sub-lines diverge from the original strain.", "Inherited disease and reduced fertility caused by inbreeding depression." ], "standards_and_regulation": [ "Guidelines for Nomenclature of Mouse and Rat Strains, International Committee on Standardized Genetic Nomenclature for Mice.", "Directive 2010/63/EU on the protection of animals used for scientific purposes, European Parliament and Council of the European Union." ], "what_it_is_for": [ "Inbred strains are maintained in experimental biology and agricultural research where genetic consistency supports comparisons between individuals or studies.", "They help researchers investigate inherited traits, responses to experimental conditions and interactions between genotype and environment.", "Breeding histories and genetic evidence are used to assess whether a stock retains the identity of the named strain." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q1893126: inbred strain", "url": "https://www.wikidata.org/wiki/Q1893126", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Inbred strain", "url": "https://en.wikipedia.org/wiki/Inbred_strain", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "inbred-status-and-boundaries", "name": "Inbred status and boundaries", "description": "Establish what qualifies as an inbred strain for the organism and authority concerned.", "rationale": "The registry supplies no definition, so the agent must expose the adopted criterion and its limits.", "layers": [ { "id": "applicable-recognition-rule", "name": "Applicable recognition rule", "description": "Connect the classification to an explicit standard and its domain of application.", "findings": [ { "id": "qualification-basis", "name": "Qualification basis", "description": "Record the authority's requirements separately from the evidence that a lineage satisfies them.", "questions": [ { "text": "Which authority and version define inbred-strain status for this taxon?", "kind": "definition", "id": "qualification-basis-q01" }, { "text": "Which requirements are supported, contradicted or undocumented for this lineage?", "kind": "boundary", "id": "qualification-basis-q02" } ] } ] }, { "id": "neighbouring-lineage-types", "name": "Neighbouring lineage types", "description": "Resolve confusion with closed stocks, hybrids, clones and partially inbred lines.", "findings": [ { "id": "classification-discriminators", "name": "Classification discriminators", "description": "Use reproduction, pedigree and genetic evidence rather than appearance or naming alone.", "questions": [ { "text": "Does the record describe a maintained inbred lineage, an F1 cross, a clone or a stock still undergoing inbreeding?", "kind": "boundary", "id": "classification-discriminators-q01" }, { "text": "What evidence distinguishes the claimed category from its closest alternative?", "kind": "provenance", "id": "classification-discriminators-q02" } ] } ] } ] }, { "id": "pedigree-and-inbreeding-history", "name": "Pedigree and inbreeding history", "description": "Represent the descent and mating history supporting the lineage's status.", "rationale": "Genetic measurements alone cannot reconstruct whether the claimed breeding history occurred.", "layers": [ { "id": "founding-and-generation-accounting", "name": "Founding and generation accounting", "description": "Identify founders and the basis of reported generation counts.", "findings": [ { "id": "traceable-founding-descent", "name": "Traceable founding descent", "description": "Associate ancestral animals or stocks with pedigree records and explicitly mark gaps.", "questions": [ { "text": "Which founders or ancestral stocks are documented, and where are the supporting breeding records?", "kind": "provenance", "id": "traceable-founding-descent-q01" }, { "text": "From which mating event are inbreeding generations counted, and which generations lack records?", "kind": "measurement", "id": "traceable-founding-descent-q02" } ] } ] }, { "id": "mating-regime-continuity", "name": "Mating regime continuity", "description": "Track the breeding scheme and events that may interrupt its evidential continuity.", "findings": [ { "id": "regime-and-exceptions", "name": "Regime and exceptions", "description": "Record mating relationships, substitutions, outcrosses and any justification for equivalent inbreeding.", "questions": [ { "text": "Which mating relationships were used in each documented period, including any outcross or breeder substitution?", "kind": "provenance", "id": "regime-and-exceptions-q01" }, { "text": "Under the adopted standard, how should each interruption or alternative regime affect the qualification claim?", "kind": "action", "id": "regime-and-exceptions-q02" } ] } ] } ] }, { "id": "genetic-uniformity-and-authentication", "name": "Genetic uniformity and authentication", "description": "Evaluate genetic evidence at the level of sampled organisms and identified stocks.", "rationale": "An inbred designation must not be translated into an unsupported claim of complete genetic identity.", "layers": [ { "id": "homozygosity-and-sampling", "name": "Homozygosity and sampling", "description": "Keep measured heterozygosity distinct from pedigree-based expectations.", "findings": [ { "id": "assay-bounded-uniformity", "name": "Assay-bounded uniformity", "description": "Record genomic coverage and sampling limits for both homozygosity and between-animal agreement.", "questions": [ { "text": "What residual heterozygosity and between-animal discordance were measured, using which denominators and quality filters?", "kind": "measurement", "id": "assay-bounded-uniformity-q01" }, { "text": "Which animals, generations, colonies and genomic regions does the evidence cover?", "kind": "boundary", "id": "assay-bounded-uniformity-q02" } ] } ] }, { "id": "reference-matching-and-discrepancies", "name": "Reference matching and discrepancies", "description": "Assess whether sampled material supports its claimed strain and substrain identity.", "findings": [ { "id": "authentication-interpretation", "name": "Authentication interpretation", "description": "Record reference provenance and alternative explanations for a genetic mismatch.", "questions": [ { "text": "Which authenticated reference and marker set support the identity comparison?", "kind": "provenance", "id": "authentication-interpretation-q01" }, { "text": "What follow-up evidence would distinguish assay error, sample mix-up, contamination, residual segregation or lineage change?", "kind": "action", "id": "authentication-interpretation-q02" } ] } ] } ] }, { "id": "substrains-and-stock-continuity", "name": "Substrains and stock continuity", "description": "Connect lineage names to branches, repositories and biological material through time.", "rationale": "A shared root name does not provide enough information to establish continuity between separately maintained stocks.", "layers": [ { "id": "branch-identity", "name": "Branch identity", "description": "Represent separations and derivatives without creating unrequested registry entries.", "findings": [ { "id": "strain-substrain-resolution", "name": "Strain-substrain resolution", "description": "Link each designation to its parent lineage, separation history and nomenclature decision.", "questions": [ { "text": "Which exact strain or substrain designation applies, and which authority or provider supports it?", "kind": "provenance", "id": "strain-substrain-resolution-q01" }, { "text": "Does a separately maintained branch require a substrain designation under the applicable rules?", "kind": "boundary", "id": "strain-substrain-resolution-q02" } ] } ] }, { "id": "material-continuity", "name": "Material continuity", "description": "Trace transfers, archives and recoveries that connect present stocks to earlier lineage material.", "findings": [ { "id": "stock-and-archive-chain", "name": "Stock and archive chain", "description": "Associate each available stock with its source generation, transfer history and authentication evidence.", "questions": [ { "text": "Which transfers, archived lots and recovery events connect this stock to the claimed lineage?", "kind": "provenance", "id": "stock-and-archive-chain-q01" }, { "text": "What identity checks are needed before recovered or newly acquired material is accepted as a working stock?", "kind": "action", "id": "stock-and-archive-chain-q02" } ] } ] } ] }, { "id": "experimental-use-and-comparability", "name": "Experimental use and comparability", "description": "Assess whether evidence about a strain supports a particular experimental role or comparison.", "rationale": "Recognition as inbred does not by itself establish phenotype consistency or suitability as a control.", "layers": [ { "id": "phenotype-evidence-boundaries", "name": "Phenotype evidence boundaries", "description": "Tie strain-associated observations to the actual animals and conditions studied.", "findings": [ { "id": "contextualised-strain-traits", "name": "Contextualised strain traits", "description": "Record the scope of trait evidence before applying it to other stocks or settings.", "questions": [ { "text": "Which substrain, stock, sex, age and environmental conditions underlie the reported trait?", "kind": "provenance", "id": "contextualised-strain-traits-q01" }, { "text": "What evidence supports transferring that observation to the stock and conditions now proposed?", "kind": "boundary", "id": "contextualised-strain-traits-q02" } ] } ] }, { "id": "control-and-comparison-decisions", "name": "Control and comparison decisions", "description": "Make the required genetic matching and unresolved differences explicit.", "findings": [ { "id": "fit-for-comparison", "name": "Fit for comparison", "description": "Assess a proposed control or substitute against the experiment's specific dependence on genetic background.", "questions": [ { "text": "Which strain, substrain and stock differences could confound the proposed comparison?", "kind": "boundary", "id": "fit-for-comparison-q01" }, { "text": "Should the agent accept the match, obtain further authentication or select another stock given those differences?", "kind": "action", "id": "fit-for-comparison-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "The unqualified term spans laboratory animals and plant breeding; the 20-generation convention is specific to laboratory-animal practice and should not be applied universally.", "Homozygosity estimates depend on breeding design and assumptions; strain recognition does not establish complete genomic identity.", "The supplied domain code has not been interpreted as evidence for a different sense; this description uses the biological breeding sense." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of inbred strain this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Classical inbred strains", "Recombinant inbred strains", "Congenic inbred strains", "Consomic inbred strains" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of inbred strain this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "scheme": "Standardized mouse strain nomenclature", "value_or_pattern": "C57BL/6J", "note": "An example identifying a particular inbred mouse strain and substrain; laboratory suffixes distinguish breeding histories." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of inbred strain this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-standards-and-regulation", "name": "Standards and regulation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "International Committee on Standardized Genetic Nomenclature for Mice: mouse strain nomenclature conventions, including recognition of inbred strains established through at least 20 consecutive generations of brother-sister mating or an equivalent breeding system." ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of inbred strain this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Providing genetically reproducible backgrounds for laboratory experiments.", "Mapping genetic influences on traits using crosses and recombinant inbred panels.", "Comparing disease susceptibility and treatment responses across genetic backgrounds.", "Studying introduced alleles or chromosome segments on controlled genetic backgrounds.", "Producing genetically consistent parental lines for plant breeding and hybrid production." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of inbred strain this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Consecutive generations of close inbreeding", "typical_range": "At least 20 for conventional laboratory mouse strain recognition", "unit": "generation" }, { "quantity": "Genomic homozygosity", "typical_range": "Expected to exceed approximately 98% after 20 generations of brother-sister mating under the conventional model", "unit": "percent" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of inbred strain this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Inbreeding depression can reduce fertility, viability or other fitness traits through increased expression of recessive deleterious alleles.", "Mutation and genetic drift can cause separated colonies to diverge into substrains.", "Accidental outcrossing, contamination or misidentification can compromise genetic consistency.", "Findings from one strain may not generalize to other strains or genetically diverse populations.", "Environmental and microbiome differences can produce phenotypic variation despite similar genetic backgrounds." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of inbred strain this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "Outbred stock", "difference": "Maintained to preserve genetic diversity rather than extensive homozygosity and within-strain genetic uniformity." }, { "name": "Clone", "difference": "Defined by descent through copying or asexual reproduction; an inbred strain usually reproduces sexually and need not be genetically identical at every locus." }, { "name": "F1 hybrid", "difference": "Offspring of two distinct inbred strains can be genetically uniform while remaining heterozygous at loci where the parents differ." }, { "name": "Substrain", "difference": "A separately maintained branch of a strain with a distinguishable breeding history or genetic divergence." }, { "name": "Breed", "difference": "A breed is maintained around ancestry and characteristic traits but need not meet an inbred strain's degree of homozygosity." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of inbred strain this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry intend laboratory animal strains specifically, or also sexually maintained inbred lineages in plants and other taxa?", "Which authoritative definitions should govern taxa outside the mouse and rat guidance consulted here, and where do their criteria differ?", "How should interrupted pedigrees and alternative breeding schemes be evaluated when no applicable authority specifies equivalence?", "Which assay coverage, sampling design and acceptance thresholds are sufficient for each proposed authentication or comparability decision?", "Does an existing Vercy world model already own this lineage concept, requiring this registry entry to link to it?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 18, "questions": 28 } }