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inbred strain

vr.tr.inbred-strain · thing-q1893126

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.

Thing Registry Cross-cutting context XCT.REL

Bundle → Layer → Finding → Questions Filled

6 bundles · 11 layers · 18 findings · 28 questions

Inbred status and boundaries Establish what qualifies as an inbred strain for the organism and authority concerned.

Applicable recognition rule

Connect the classification to an explicit standard and its domain of application.

Qualification basis

Record the authority's requirements separately from the evidence that a lineage satisfies them.

  1. Which authority and version define inbred-strain status for this taxon? definition
  2. Which requirements are supported, contradicted or undocumented for this lineage? boundary

Neighbouring lineage types

Resolve confusion with closed stocks, hybrids, clones and partially inbred lines.

Classification discriminators

Use reproduction, pedigree and genetic evidence rather than appearance or naming alone.

  1. Does the record describe a maintained inbred lineage, an F1 cross, a clone or a stock still undergoing inbreeding? boundary
  2. What evidence distinguishes the claimed category from its closest alternative? provenance
Pedigree and inbreeding history Represent the descent and mating history supporting the lineage's status.

Founding and generation accounting

Identify founders and the basis of reported generation counts.

Traceable founding descent

Associate ancestral animals or stocks with pedigree records and explicitly mark gaps.

  1. Which founders or ancestral stocks are documented, and where are the supporting breeding records? provenance
  2. From which mating event are inbreeding generations counted, and which generations lack records? measurement

Mating regime continuity

Track the breeding scheme and events that may interrupt its evidential continuity.

Regime and exceptions

Record mating relationships, substitutions, outcrosses and any justification for equivalent inbreeding.

  1. Which mating relationships were used in each documented period, including any outcross or breeder substitution? provenance
  2. Under the adopted standard, how should each interruption or alternative regime affect the qualification claim? action
Genetic uniformity and authentication Evaluate genetic evidence at the level of sampled organisms and identified stocks.

Homozygosity and sampling

Keep measured heterozygosity distinct from pedigree-based expectations.

Assay-bounded uniformity

Record genomic coverage and sampling limits for both homozygosity and between-animal agreement.

  1. What residual heterozygosity and between-animal discordance were measured, using which denominators and quality filters? measurement
  2. Which animals, generations, colonies and genomic regions does the evidence cover? boundary

Reference matching and discrepancies

Assess whether sampled material supports its claimed strain and substrain identity.

Authentication interpretation

Record reference provenance and alternative explanations for a genetic mismatch.

  1. Which authenticated reference and marker set support the identity comparison? provenance
  2. What follow-up evidence would distinguish assay error, sample mix-up, contamination, residual segregation or lineage change? action
Substrains and stock continuity Connect lineage names to branches, repositories and biological material through time.

Branch identity

Represent separations and derivatives without creating unrequested registry entries.

Strain-substrain resolution

Link each designation to its parent lineage, separation history and nomenclature decision.

  1. Which exact strain or substrain designation applies, and which authority or provider supports it? provenance
  2. Does a separately maintained branch require a substrain designation under the applicable rules? boundary

Material continuity

Trace transfers, archives and recoveries that connect present stocks to earlier lineage material.

Stock and archive chain

Associate each available stock with its source generation, transfer history and authentication evidence.

  1. Which transfers, archived lots and recovery events connect this stock to the claimed lineage? provenance
  2. What identity checks are needed before recovered or newly acquired material is accepted as a working stock? action
Experimental use and comparability Assess whether evidence about a strain supports a particular experimental role or comparison.

Phenotype evidence boundaries

Tie strain-associated observations to the actual animals and conditions studied.

Contextualised strain traits

Record the scope of trait evidence before applying it to other stocks or settings.

  1. Which substrain, stock, sex, age and environmental conditions underlie the reported trait? provenance
  2. What evidence supports transferring that observation to the stock and conditions now proposed? boundary

Control and comparison decisions

Make the required genetic matching and unresolved differences explicit.

Fit for comparison

Assess a proposed control or substitute against the experiment's specific dependence on genetic background.

  1. Which strain, substrain and stock differences could confound the proposed comparison? boundary
  2. Should the agent accept the match, obtain further authentication or select another stock given those differences? action
Evidence and external alignment What the world already says about this thing, gathered so the model can be checked against it.

Reported evidence

Findings from the breadth pass, kept separate from the structural claims.

Check these first

Recalled without web access and unsourced; every item is a lead to verify.

  1. Which of these check these first hold for the sense of inbred strain this model covers, and on what evidence? provenance

Kinds and varieties

Recalled without web access and unsourced; every item is a lead to verify.

  1. Which of these kinds and varieties hold for the sense of inbred strain this model covers, and on what evidence? provenance

Identifiers and schemes

Recalled without web access and unsourced; every item is a lead to verify.

  1. Which of these identifiers and schemes hold for the sense of inbred strain this model covers, and on what evidence? provenance

Standards and regulation

Recalled without web access and unsourced; every item is a lead to verify.

  1. Which of these standards and regulation hold for the sense of inbred strain this model covers, and on what evidence? provenance

Real-world use

Recalled without web access and unsourced; every item is a lead to verify.

  1. Which of these real-world use hold for the sense of inbred strain this model covers, and on what evidence? provenance

Typical measurements

Recalled without web access and unsourced; every item is a lead to verify.

  1. Which of these typical measurements hold for the sense of inbred strain this model covers, and on what evidence? provenance

Failure modes and hazards

Recalled without web access and unsourced; every item is a lead to verify.

  1. Which of these failure modes and hazards hold for the sense of inbred strain this model covers, and on what evidence? provenance

Neighbouring kinds and how to tell them apart

Recalled without web access and unsourced; every item is a lead to verify.

  1. 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? provenance

Classifiers Filled

Family
Thing Registry
Category
Cross-cutting context
Entry kind
thing
Plane
XCT
Domain
XCT.REL
Other names and narrower kinds
inbred strain of mice, congenic animals

What it is Filled

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.

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

Why it exists Filled

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.

Distinguishing features Filled

  • 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)

What robots and AI may and may not do Filled

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.

Only with a human decision

  • Any decision to breed, cull or transfer animals in a colony.
  • Starting experiments that use animals of the strain.

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.

Moral aspects Filled

  • 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.

Who is affected

  • The animals themselves
  • Researchers and people relying on their results
  • Animal care staff

Owners Filled

Steward

The breeding facility or repository that maintains the strain; the licensed establishment answers for animal welfare.

Master systems

  • Strain repository and nomenclature databases

Links to other meta-models Filled

parent

  • Q1647200 - registry parent class

What else AI and robots need to interact with it Filled

Identity and identifiers required Filled

  • Vercy registry: vr.tr.inbred-strain
  • Wikidata: Q1893126 (https://www.wikidata.org/wiki/Q1893126)

Direct properties not applicable Not applicable

  • Taxon and recognition standard: Species or taxon identifier linked to a named, versioned inbred-strain standard
  • Inbred qualification: Unassessed | supported under named standard | disputed | insufficient evidence
  • Mating regime: Sibling mating | parent-offspring mating | other documented regime | mixed history | unknown
  • Documented inbreeding generations: Generations, with counting origin, pedigree coverage and interruptions
  • Observed residual heterozygosity: Fraction or percentage of eligible callable loci, with assay, genomic regions, sample and date
  • Within-stock genotype discordance: Discordant genotype comparisons divided by eligible comparisons, with loci, animals and method
  • Strain and substrain identity: Accepted designation, aliases, parent lineage and applicable nomenclature authority
  • Stock authentication status: Not assessed | matches specified reference | unresolved discrepancy | inconsistent with claimed identity
  • Lineage availability: Live stock documented | archived material documented | both documented | no recoverable material known | unknown

Plane XCT: no invented physical properties.

Recognition optional Filled

  • 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.

Capabilities and actions required Filled

  • 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

Hazards and failure modes required Filled

  • 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 interfaces required Filled

  • 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.

Context of use required Filled

  • 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 Filled

  1. Wikidata item Q1893126: inbred strain - identity and sense of the item
  2. Wikipedia: Inbred strain - general description of the item

Open questions

  • 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?

Machine files

Provenance

thing registry research (pass 2) · unreviewed

Built from: models/things/publications/thing-q1893126/spec.json