{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.wm-liv-012","code":"wm-liv-012-genomic-sequence-variant","url":"https://ver.cy/models/wm-liv-012-genomic-sequence-variant/","name":"Genomic Sequence / Variant","alternateNames":[],"kind":"world-model","status":"published","version":"0.3.0-research.1","language":"en","classifiers":{"family":"World Models","category":"Physical world and living systems","entryKind":"aggregate","plane":"","domain":["PHY.LIV.MOL"],"industry":["Cross-industry"],"navPath":"NAV.PHY.LIV.MOL","tags":["genomic","sequence","variant","phy.liv.mol"],"facets":{}},"whatItIs":"Owns a sequence, molecular-variant or combined-package discriminator; authoritative and computed identity; molecule, alphabet, residues, length, topology, strandedness and digest; sequence collection, assembly and reference bindings; coordinate and location semantics; reference and alternate state; normalized variation, allele, phased and structural composition; HGVS, SPDI, VCF and VRS expressions; external mappings and lift-over assertions; provenance, validation, lifecycle, access, retention and loss-aware projections. Organisms, specimens, persons, consent records, assays, reads, alignments, calls, genotypes, population frequencies, genes, phenotypes, diseases, interpretations and clinical decisions remain external.","purpose":"Represent governed biological sequence identity and computable molecular variation relative to explicit reference and coordinate context.","scope":{"in":["Sequence content identity, accession and version, digest, collection and coordinate context","Molecular variation definition, normalization, composition, expressions, mappings, validation and lifecycle","Provenance, quality, access, consent bindings, retention and loss-aware interoperability"],"out":["Owning organism, specimen, person, consent, assay, read, alignment, call, genotype, frequency, phenotype, disease, clinical interpretation or decision lifecycles","Inferring pathogenicity, functional effect or clinical action from molecular existence or predicted consequence","Protected disclosure, clinical classification, external archive mutation, identity merge or irreversible deletion without authority"],"boundaries":[{"neighbor":"WM-LIV-011","distinction":"The registered parent is retained as a reference pending boundary review; this model does not own its organism, genome, chromosome, gene or other biological-container master."},{"neighbor":"Specimen, person and consent","distinction":"A sequence or variant may be observed from a specimen linked to a person under consent. Those identities, authorization and lifecycle remain external and protected."},{"neighbor":"Assay, read, alignment, call and genotype","distinction":"Observed evidence and computational calls support a variation assertion but do not define the molecular variant or become its identity."},{"neighbor":"Gene, transcript, protein and consequence","distinction":"Feature and consequence annotations are versioned projections on external reference annotations and remain distinct from sequence state and measured functional effects."},{"neighbor":"Disease and clinical interpretation","distinction":"Condition-specific classification, evidence assessment, patient interpretation and treatment decision are independent assertions with their own actors, dates, criteria and provenance."},{"neighbor":"Archive accession and textual expression","distinction":"RefSNP, ClinVar, EVA, HGVS, SPDI and VCF records identify or express source-specific objects; mappings require pinned releases and do not silently replace computed molecular identity."}]},"distinguishingFeatures":["Describes a molecular sequence or variation in reference terms, not a call observed in a specimen or a person's genotype.","The same variant has different textual expressions; equivalence needs normalisation against an exact reference.","A reference needs an accession and version or digest; an assembly nickname alone is ambiguous.","Molecular existence or predicted consequence does not establish pathogenicity or clinical action."],"structure":{"bundles":[{"id":"subject-boundary-identity-and-biological-class","name":"Subject boundary, identity and biological class","description":"Groups the governed Resource Consumption concern for subject boundary, identity and biological class.","layers":[{"id":"root-kind-authoritative-identity-and-mastership","name":"Root kind, authoritative identity and mastership","description":"Groups Resource Consumption context for root kind, authoritative identity and mastership without importing neighboring master lifecycles.","findings":[{"id":"sequence-variant-combined-package-discriminator-and-root-identity","name":"Sequence, variant or combined-package discriminator and root identity","description":"Records sequence, variant or combined-package discriminator and root identity as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish sequence, variant or combined-package discriminator and root identity?","id":"sequence-variant-combined-package-discriminator-and-root-identity-q01","kind":"identity"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify sequence, variant or combined-package discriminator and root identity?","id":"sequence-variant-combined-package-discriminator-and-root-identity-q02","kind":"authority"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect sequence, variant or combined-package discriminator and root identity?","id":"sequence-variant-combined-package-discriminator-and-root-identity-q03","kind":"security"}]},{"id":"accession-version-computed-identifier-alias-registry-and-master-system","name":"Accession, version, computed identifier, alias, registry and master system","description":"Records accession, version, computed identifier, alias, registry and master system as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish accession, version, computed identifier, alias, registry and master system?","id":"accession-version-computed-identifier-alias-registry-and-master-system-q01","kind":"identity"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify accession, version, computed identifier, alias, registry and master system?","id":"accession-version-computed-identifier-alias-registry-and-master-system-q02","kind":"requirement"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect accession, version, computed identifier, alias, registry and master system?","id":"accession-version-computed-identifier-alias-registry-and-master-system-q03","kind":"privacy"}]}]},{"id":"molecule-alphabet-organism-and-reference-class","name":"Molecule, alphabet, organism and reference class","description":"Groups Resource Consumption context for molecule, alphabet, organism and reference class without importing neighboring master lifecycles.","findings":[{"id":"dna-rna-protein-alphabet-residue-length-topology-and-strandedness","name":"DNA, RNA, protein, alphabet, residue, length, topology and strandedness","description":"Records dna, rna, protein, alphabet, residue, length, topology and strandedness as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish dna, rna, protein, alphabet, residue, length, topology and strandedness?","id":"dna-rna-protein-alphabet-residue-length-topology-and-strandedness-q01","kind":"classification"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify dna, rna, protein, alphabet, residue, length, topology and strandedness?","id":"dna-rna-protein-alphabet-residue-length-topology-and-strandedness-q02","kind":"constraint"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect dna, rna, protein, alphabet, residue, length, topology and strandedness?","id":"dna-rna-protein-alphabet-residue-length-topology-and-strandedness-q03","kind":"retention"}]},{"id":"taxon-reference-status-assembly-collection-and-biological-scope","name":"Taxon, reference status, assembly, collection and biological scope","description":"Records taxon, reference status, assembly, collection and biological scope as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish taxon, reference status, assembly, collection and biological scope?","id":"taxon-reference-status-assembly-collection-and-biological-scope-q01","kind":"classification"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify taxon, reference status, assembly, collection and biological scope?","id":"taxon-reference-status-assembly-collection-and-biological-scope-q02","kind":"process"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect taxon, reference status, assembly, collection and biological scope?","id":"taxon-reference-status-assembly-collection-and-biological-scope-q03","kind":"access"}]}]}]},{"id":"sequence-content-collection-coordinate-and-location","name":"Sequence content, collection, coordinate and location","description":"Groups the governed Resource Consumption concern for sequence content, collection, coordinate and location.","layers":[{"id":"sequence-content-canonicalization-digest-and-collection-membership","name":"Sequence content, canonicalization, digest and collection membership","description":"Groups Resource Consumption context for sequence content, canonicalization, digest and collection membership without importing neighboring master lifecycles.","findings":[{"id":"residue-content-normalization-length-digest-algorithm-and-retrieval","name":"Residue content, normalization, length, digest algorithm and retrieval","description":"Records residue content, normalization, length, digest algorithm and retrieval as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish residue content, normalization, length, digest algorithm and retrieval?","id":"residue-content-normalization-length-digest-algorithm-and-retrieval-q01","kind":"measurement"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify residue content, normalization, length, digest algorithm and retrieval?","id":"residue-content-normalization-length-digest-algorithm-and-retrieval-q02","kind":"event"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect residue content, normalization, length, digest algorithm and retrieval?","id":"residue-content-normalization-length-digest-algorithm-and-retrieval-q03","kind":"exception"}]},{"id":"sequence-collection-names-lengths-topologies-digest-level-and-compatibility","name":"Sequence collection names, lengths, topologies, digest level and compatibility","description":"Records sequence collection names, lengths, topologies, digest level and compatibility as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish sequence collection names, lengths, topologies, digest level and compatibility?","id":"sequence-collection-names-lengths-topologies-digest-level-and-compatibility-q01","kind":"composition"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify sequence collection names, lengths, topologies, digest level and compatibility?","id":"sequence-collection-names-lengths-topologies-digest-level-and-compatibility-q02","kind":"measurement"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect sequence collection names, lengths, topologies, digest level and compatibility?","id":"sequence-collection-names-lengths-topologies-digest-level-and-compatibility-q03","kind":"interoperability"}]}]},{"id":"coordinate-system-interval-orientation-and-imprecision","name":"Coordinate system, interval, orientation and imprecision","description":"Groups Resource Consumption context for coordinate system, interval, orientation and imprecision without importing neighboring master lifecycles.","findings":[{"id":"reference-context-coordinate-base-boundary-convention-start-end-and-strand","name":"Reference context, coordinate base, boundary convention, start, end and strand","description":"Records reference context, coordinate base, boundary convention, start, end and strand as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish reference context, coordinate base, boundary convention, start, end and strand?","id":"reference-context-coordinate-base-boundary-convention-start-end-and-strand-q01","kind":"spatial"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify reference context, coordinate base, boundary convention, start, end and strand?","id":"reference-context-coordinate-base-boundary-convention-start-end-and-strand-q02","kind":"evidence"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect reference context, coordinate base, boundary convention, start, end and strand?","id":"reference-context-coordinate-base-boundary-convention-start-end-and-strand-q03","kind":"decision"}]},{"id":"sequence-location-circular-wrap-imprecise-range-breakend-and-adjacency","name":"Sequence location, circular wrap, imprecise range, breakend and adjacency","description":"Records sequence location, circular wrap, imprecise range, breakend and adjacency as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish sequence location, circular wrap, imprecise range, breakend and adjacency?","id":"sequence-location-circular-wrap-imprecise-range-breakend-and-adjacency-q01","kind":"spatial"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify sequence location, circular wrap, imprecise range, breakend and adjacency?","id":"sequence-location-circular-wrap-imprecise-range-breakend-and-adjacency-q02","kind":"quality"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect sequence location, circular wrap, imprecise range, breakend and adjacency?","id":"sequence-location-circular-wrap-imprecise-range-breakend-and-adjacency-q03","kind":"identity"}]}]}]},{"id":"molecular-variation-state-normalization-and-composition","name":"Molecular variation state, normalization and composition","description":"Groups the governed Resource Consumption concern for molecular variation state, normalization and composition.","layers":[{"id":"reference-alternate-state-class-and-computed-identity","name":"Reference, alternate state, class and computed identity","description":"Groups Resource Consumption context for reference, alternate state, class and computed identity without importing neighboring master lifecycles.","findings":[{"id":"reference-state-alternate-state-substitution-insertion-deletion-indel-and-repeat","name":"Reference state, alternate state, substitution, insertion, deletion, indel and repeat","description":"Records reference state, alternate state, substitution, insertion, deletion, indel and repeat as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish reference state, alternate state, substitution, insertion, deletion, indel and repeat?","id":"reference-state-alternate-state-substitution-insertion-deletion-indel-and-repeat-q01","kind":"state"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify reference state, alternate state, substitution, insertion, deletion, indel and repeat?","id":"reference-state-alternate-state-substitution-insertion-deletion-indel-and-repeat-q02","kind":"validation"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect reference state, alternate state, substitution, insertion, deletion, indel and repeat?","id":"reference-state-alternate-state-substitution-insertion-deletion-indel-and-repeat-q03","kind":"classification"}]},{"id":"normalization-canonical-form-defining-fields-digest-prefix-and-algorithm-version","name":"Normalization, canonical form, defining fields, digest prefix and algorithm version","description":"Records normalization, canonical form, defining fields, digest prefix and algorithm version as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish normalization, canonical form, defining fields, digest prefix and algorithm version?","id":"normalization-canonical-form-defining-fields-digest-prefix-and-algorithm-version-q01","kind":"identity"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify normalization, canonical form, defining fields, digest prefix and algorithm version?","id":"normalization-canonical-form-defining-fields-digest-prefix-and-algorithm-version-q02","kind":"security"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect normalization, canonical form, defining fields, digest prefix and algorithm version?","id":"normalization-canonical-form-defining-fields-digest-prefix-and-algorithm-version-q03","kind":"composition"}]}]},{"id":"allele-haplotype-copy-number-and-structural-composition","name":"Allele, haplotype, copy number and structural composition","description":"Groups Resource Consumption context for allele, haplotype, copy number and structural composition without importing neighboring master lifecycles.","findings":[{"id":"allele-cis-phased-block-haplotype-variation-set-membership-and-order","name":"Allele, cis-phased block, haplotype, variation-set membership and order","description":"Records allele, cis-phased block, haplotype, variation-set membership and order as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish allele, cis-phased block, haplotype, variation-set membership and order?","id":"allele-cis-phased-block-haplotype-variation-set-membership-and-order-q01","kind":"composition"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify allele, cis-phased block, haplotype, variation-set membership and order?","id":"allele-cis-phased-block-haplotype-variation-set-membership-and-order-q02","kind":"privacy"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect allele, cis-phased block, haplotype, variation-set membership and order?","id":"allele-cis-phased-block-haplotype-variation-set-membership-and-order-q03","kind":"relationship"}]},{"id":"copy-number-count-copy-number-change-adjacency-derivative-and-structural-profile","name":"Copy-number count, copy-number change, adjacency, derivative and structural profile","description":"Records copy-number count, copy-number change, adjacency, derivative and structural profile as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish copy-number count, copy-number change, adjacency, derivative and structural profile?","id":"copy-number-count-copy-number-change-adjacency-derivative-and-structural-profile-q01","kind":"classification"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify copy-number count, copy-number change, adjacency, derivative and structural profile?","id":"copy-number-count-copy-number-change-adjacency-derivative-and-structural-profile-q02","kind":"retention"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect copy-number count, copy-number change, adjacency, derivative and structural profile?","id":"copy-number-count-copy-number-change-adjacency-derivative-and-structural-profile-q03","kind":"state"}]}]}]},{"id":"expressions-mappings-projections-and-equivalence","name":"Expressions, mappings, projections and equivalence","description":"Groups the governed Resource Consumption concern for expressions, mappings, projections and equivalence.","layers":[{"id":"hgvs-spdi-vcf-and-other-expressions","name":"HGVS, SPDI, VCF and other expressions","description":"Groups Resource Consumption context for hgvs, spdi, vcf and other expressions without importing neighboring master lifecycles.","findings":[{"id":"hgvs-reference-coordinate-type-expression-rule-version-and-prediction-marker","name":"HGVS reference, coordinate type, expression, rule version and prediction marker","description":"Records hgvs reference, coordinate type, expression, rule version and prediction marker as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish hgvs reference, coordinate type, expression, rule version and prediction marker?","id":"hgvs-reference-coordinate-type-expression-rule-version-and-prediction-marker-q01","kind":"interoperability"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify hgvs reference, coordinate type, expression, rule version and prediction marker?","id":"hgvs-reference-coordinate-type-expression-rule-version-and-prediction-marker-q02","kind":"access"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect hgvs reference, coordinate type, expression, rule version and prediction marker?","id":"hgvs-reference-coordinate-type-expression-rule-version-and-prediction-marker-q03","kind":"lifecycle"}]},{"id":"spdi-vcf-record-allele-decomposition-multiallelic-symbolic-and-file-context","name":"SPDI, VCF record, allele decomposition, multiallelic, symbolic and file context","description":"Records spdi, vcf record, allele decomposition, multiallelic, symbolic and file context as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish spdi, vcf record, allele decomposition, multiallelic, symbolic and file context?","id":"spdi-vcf-record-allele-decomposition-multiallelic-symbolic-and-file-context-q01","kind":"interoperability"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify spdi, vcf record, allele decomposition, multiallelic, symbolic and file context?","id":"spdi-vcf-record-allele-decomposition-multiallelic-symbolic-and-file-context-q02","kind":"exception"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect spdi, vcf record, allele decomposition, multiallelic, symbolic and file context?","id":"spdi-vcf-record-allele-decomposition-multiallelic-symbolic-and-file-context-q03","kind":"temporal"}]}]},{"id":"cross-reference-equivalence-remapping-and-liftover","name":"Cross-reference, equivalence, remapping and lift-over","description":"Groups Resource Consumption context for cross-reference, equivalence, remapping and lift-over without importing neighboring master lifecycles.","findings":[{"id":"external-accession-mapping-relation-source-release-method-and-confidence","name":"External accession mapping, relation, source release, method and confidence","description":"Records external accession mapping, relation, source release, method and confidence as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish external accession mapping, relation, source release, method and confidence?","id":"external-accession-mapping-relation-source-release-method-and-confidence-q01","kind":"relationship"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify external accession mapping, relation, source release, method and confidence?","id":"external-accession-mapping-relation-source-release-method-and-confidence-q02","kind":"interoperability"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect external accession mapping, relation, source release, method and confidence?","id":"external-accession-mapping-relation-source-release-method-and-confidence-q03","kind":"spatial"}]},{"id":"assembly-projection-alignment-chain-orientation-normalization-and-semantic-loss","name":"Assembly projection, alignment chain, orientation, normalization and semantic loss","description":"Records assembly projection, alignment chain, orientation, normalization and semantic loss as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish assembly projection, alignment chain, orientation, normalization and semantic loss?","id":"assembly-projection-alignment-chain-orientation-normalization-and-semantic-loss-q01","kind":"process"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify assembly projection, alignment chain, orientation, normalization and semantic loss?","id":"assembly-projection-alignment-chain-orientation-normalization-and-semantic-loss-q02","kind":"decision"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect assembly projection, alignment chain, orientation, normalization and semantic loss?","id":"assembly-projection-alignment-chain-orientation-normalization-and-semantic-loss-q03","kind":"provenance"}]}]}]},{"id":"provenance-evidence-quality-validation-and-lifecycle","name":"Provenance, evidence, quality, validation and lifecycle","description":"Groups the governed Resource Consumption concern for provenance, evidence, quality, validation and lifecycle.","layers":[{"id":"source-observation-method-pipeline-and-evidence-lineage","name":"Source, observation, method, pipeline and evidence lineage","description":"Groups Resource Consumption context for source, observation, method, pipeline and evidence lineage without importing neighboring master lifecycles.","findings":[{"id":"archive-submission-study-specimen-assay-call-and-observation-references","name":"Archive, submission, study, specimen, assay, call and observation references","description":"Records archive, submission, study, specimen, assay, call and observation references as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish archive, submission, study, specimen, assay, call and observation references?","id":"archive-submission-study-specimen-assay-call-and-observation-references-q01","kind":"evidence"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify archive, submission, study, specimen, assay, call and observation references?","id":"archive-submission-study-specimen-assay-call-and-observation-references-q02","kind":"identity"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect archive, submission, study, specimen, assay, call and observation references?","id":"archive-submission-study-specimen-assay-call-and-observation-references-q03","kind":"ownership"}]},{"id":"producer-method-software-parameter-reference-release-time-and-derivation","name":"Producer, method, software, parameter, reference release, time and derivation","description":"Records producer, method, software, parameter, reference release, time and derivation as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish producer, method, software, parameter, reference release, time and derivation?","id":"producer-method-software-parameter-reference-release-time-and-derivation-q01","kind":"provenance"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify producer, method, software, parameter, reference release, time and derivation?","id":"producer-method-software-parameter-reference-release-time-and-derivation-q02","kind":"classification"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect producer, method, software, parameter, reference release, time and derivation?","id":"producer-method-software-parameter-reference-release-time-and-derivation-q03","kind":"authority"}]}]},{"id":"validation-concordance-state-change-and-retirement","name":"Validation, concordance, state change and retirement","description":"Groups Resource Consumption context for validation, concordance, state change and retirement without importing neighboring master lifecycles.","findings":[{"id":"syntax-reference-allele-coordinate-normalization-digest-round-trip-and-concordance","name":"Syntax, reference allele, coordinate, normalization, digest, round trip and concordance","description":"Records syntax, reference allele, coordinate, normalization, digest, round trip and concordance as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish syntax, reference allele, coordinate, normalization, digest, round trip and concordance?","id":"syntax-reference-allele-coordinate-normalization-digest-round-trip-and-concordance-q01","kind":"validation"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify syntax, reference allele, coordinate, normalization, digest, round trip and concordance?","id":"syntax-reference-allele-coordinate-normalization-digest-round-trip-and-concordance-q02","kind":"composition"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect syntax, reference allele, coordinate, normalization, digest, round trip and concordance?","id":"syntax-reference-allele-coordinate-normalization-digest-round-trip-and-concordance-q03","kind":"requirement"}]},{"id":"proposed-active-merged-split-deprecated-withdrawn-superseded-and-replaced-state","name":"Proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state","description":"Records proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state?","id":"proposed-active-merged-split-deprecated-withdrawn-superseded-and-replaced-state-q01","kind":"lifecycle"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state?","id":"proposed-active-merged-split-deprecated-withdrawn-superseded-and-replaced-state-q02","kind":"relationship"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state?","id":"proposed-active-merged-split-deprecated-withdrawn-superseded-and-replaced-state-q03","kind":"constraint"}]}]}]},{"id":"context-interpretation-access-retention-and-interoperability","name":"Context, interpretation, access, retention and interoperability","description":"Groups the governed Resource Consumption concern for context, interpretation, access, retention and interoperability.","layers":[{"id":"biological-clinical-and-population-context-references","name":"Biological, clinical and population context references","description":"Groups Resource Consumption context for biological, clinical and population context references without importing neighboring master lifecycles.","findings":[{"id":"gene-transcript-protein-feature-consequence-and-functional-effect-reference","name":"Gene, transcript, protein, feature, consequence and functional-effect reference","description":"Records gene, transcript, protein, feature, consequence and functional-effect reference as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish gene, transcript, protein, feature, consequence and functional-effect reference?","id":"gene-transcript-protein-feature-consequence-and-functional-effect-reference-q01","kind":"relationship"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify gene, transcript, protein, feature, consequence and functional-effect reference?","id":"gene-transcript-protein-feature-consequence-and-functional-effect-reference-q02","kind":"state"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect gene, transcript, protein, feature, consequence and functional-effect reference?","id":"gene-transcript-protein-feature-consequence-and-functional-effect-reference-q03","kind":"process"}]},{"id":"person-specimen-call-genotype-frequency-condition-interpretation-and-decision-reference","name":"Person, specimen, call, genotype, frequency, condition, interpretation and decision reference","description":"Records person, specimen, call, genotype, frequency, condition, interpretation and decision reference as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish person, specimen, call, genotype, frequency, condition, interpretation and decision reference?","id":"person-specimen-call-genotype-frequency-condition-interpretation-and-decision-reference-q01","kind":"relationship"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify person, specimen, call, genotype, frequency, condition, interpretation and decision reference?","id":"person-specimen-call-genotype-frequency-condition-interpretation-and-decision-reference-q02","kind":"lifecycle"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect person, specimen, call, genotype, frequency, condition, interpretation and decision reference?","id":"person-specimen-call-genotype-frequency-condition-interpretation-and-decision-reference-q03","kind":"event"}]}]},{"id":"sensitivity-consent-access-retention-and-loss-aware-exchange","name":"Sensitivity, consent, access, retention and loss-aware exchange","description":"Groups Resource Consumption context for sensitivity, consent, access, retention and loss-aware exchange without importing neighboring master lifecycles.","findings":[{"id":"sensitivity-consent-data-use-purpose-role-jurisdiction-retention-and-audit","name":"Sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit","description":"Records sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit?","id":"sensitivity-consent-data-use-purpose-role-jurisdiction-retention-and-audit-q01","kind":"privacy"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit?","id":"sensitivity-consent-data-use-purpose-role-jurisdiction-retention-and-audit-q02","kind":"temporal"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit?","id":"sensitivity-consent-data-use-purpose-role-jurisdiction-retention-and-audit-q03","kind":"measurement"}]},{"id":"vrs-refget-hgvs-vcf-spdi-fhir-beacon-jsonld-projection-and-conformance","name":"VRS, refget, HGVS, VCF, SPDI, FHIR, Beacon, JSON-LD projection and conformance","description":"Records vrs, refget, hgvs, vcf, spdi, fhir, beacon, json-ld projection and conformance as a source-qualified Genomic Sequence / Variant assertion while organisms, specimens, persons, observations, interpretations and decisions retain external mastership.","questions":[{"text":"Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish vrs, refget, hgvs, vcf, spdi, fhir, beacon, json-ld projection and conformance?","id":"vrs-refget-hgvs-vcf-spdi-fhir-beacon-jsonld-projection-and-conformance-q01","kind":"interoperability"},{"text":"Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify vrs, refget, hgvs, vcf, spdi, fhir, beacon, json-ld projection and conformance?","id":"vrs-refget-hgvs-vcf-spdi-fhir-beacon-jsonld-projection-and-conformance-q02","kind":"spatial"},{"text":"Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect vrs, refget, hgvs, vcf, spdi, fhir, beacon, json-ld projection and conformance?","id":"vrs-refget-hgvs-vcf-spdi-fhir-beacon-jsonld-projection-and-conformance-q03","kind":"evidence"}]}]}]}]},"agentConduct":{"may":["Validate variant expressions and reference accessions.","Compute content digests for sequences and variants.","Normalise variants and propose equivalence mappings across expressions.","Remap coordinates between assemblies with the method recorded."],"mustNot":["Assign a clinical significance or recommend clinical action.","Link a variant to an identified person outside an authorised context.","Disclose genomic data beyond consent and access terms.","Merge variant identities on the basis of a shared label.","Change an archived accession record."],"requiresHuman":["Clinical interpretation and reporting of variants.","Granting access to identifiable genomic data.","Merging or retiring curated variant identities."]},"ethics":{"considerations":["Genomic data can identify a person and reveal information about relatives who did not consent.","Misinterpreting a variant can lead to wrong diagnosis or treatment.","Genetic information can lead to discrimination in employment or insurance.","Communities that provide samples should share in the benefits and control use of their data."],"affectedParties":["Individuals whose genomes are sequenced","Biological relatives","Patients receiving genetic results","Source communities and populations"]},"owners":{"steward":"Declare Dimension owner, sequence and variation masters, archive authority, curators, validators, clinical reviewers, data-use approvers and auditors.","roles":[{"name":"Dimension owner","responsibilities":["Own namespace, mastership, delegation, access, retention and federation rules."]},{"name":"Sequence archive or reference authority","responsibilities":["Own accessions, versions, releases, corrections and withdrawal commitments."]},{"name":"Sequence curator","responsibilities":["Own molecule, alphabet, content, reference status, collection and annotation boundaries."]},{"name":"Variation curator or bioinformatician","responsibilities":["Own normalized state, location, composition, computed identifiers and mappings."]},{"name":"Laboratory or assay steward","responsibilities":["Own specimen, assay, run, call and evidence records outside this model."]},{"name":"Clinical genomic reviewer","responsibilities":["Own condition-specific evidence interpretation and clinical-significance assertions outside this model."]},{"name":"Data steward or access committee","responsibilities":["Own consent, permitted use, purpose, minimum disclosure, retention and access decisions."]},{"name":"Validator or auditor","responsibilities":["Review identity, reference, coordinates, normalization, provenance, lifecycle and disclosure without rewriting originals."]}],"masterSystems":[]},"relations":[{"target":"WM-LIV-011","type":"references","note":"Resolve the registered biological parent without importing organism, genome or other container lifecycle."},{"target":"Organism, specimen, person, assay, call, genotype, phenotype, disease, evidence and clinical-decision masters","type":"references","note":"Resolve observation and interpretation context without conflating it with molecular definition."},{"target":"GA4GH VRS 2.0","type":"aligned","note":"Project computable sequence location, molecular variation, composition, normalization and identifier semantics."},{"target":"GA4GH refget Sequences 2.0 and Sequence Collections 1.0","type":"aligned","note":"Project digest-derived sequence and collection identity, retrieval and compatibility."},{"target":"HGVS 21.1.4 and VCF 4.5","type":"aligned","note":"Project human-readable nomenclature and file-level variant exchange without treating either as universal identity."},{"target":"INSDC, NCBI RefSeq and NCBI Variation Services","type":"aligned","note":"Project sequence accession, archive, SPDI normalization and translation context."},{"target":"ClinVar and European Variation Archive","type":"aligned","note":"Project archive accessions, submissions, aggregate records, merge history and evidence links while keeping interpretation external."},{"target":"Sequence Ontology, ClinGen and ACMG/AMP","type":"aligned","note":"Project variation and consequence terms plus condition-specific evidence guidance as external contextual assertions."},{"target":"HL7 FHIR R5 MolecularSequence and GA4GH Beacon v2","type":"aligned","note":"Project clinical sequence exchange and federated discovery views with maturity and privacy limits."},{"target":"GA4GH DUO and Responsible Sharing Framework","type":"aligned","note":"Project permitted-use, consent, privacy, security and governance context."},{"target":"W3C PROV-O, DQV and ODRL 2.2","type":"aligned","note":"Project derivation, quality and rights constraints."},{"target":"RFC 3339, RFC 8785 and JSON-LD 1.1","type":"aligned","note":"Project unambiguous clocks, deterministic JSON and linked-data graph identity."},{"target":"WM-LIV-011","type":"neighbor","note":"The registered parent is retained as a reference pending boundary review; this model does not own its organism, genome, chromosome, gene or other biological-container master."},{"target":"Specimen, person and consent","type":"neighbor","note":"A sequence or variant may be observed from a specimen linked to a person under consent. Those identities, authorization and lifecycle remain external and protected."},{"target":"Assay, read, alignment, call and genotype","type":"neighbor","note":"Observed evidence and computational calls support a variation assertion but do not define the molecular variant or become its identity."},{"target":"Gene, transcript, protein and consequence","type":"neighbor","note":"Feature and consequence annotations are versioned projections on external reference annotations and remain distinct from sequence state and measured functional effects."},{"target":"Disease and clinical interpretation","type":"neighbor","note":"Condition-specific classification, evidence assessment, patient interpretation and treatment decision are independent assertions with their own actors, dates, criteria and provenance."},{"target":"Archive accession and textual expression","type":"neighbor","note":"RefSNP, ClinVar, EVA, HGVS, SPDI and VCF records identify or express source-specific objects; mappings require pinned releases and do not silently replace computed molecular identity."},{"target":"WM-LIV-011","type":"parent"}],"interaction":{"identity":{"applicability":"required","items":["Authoritative master-system identifier, accession plus version or archive identifier for a sequence or variation record.","Release-pinned refget or VRS computed identifier derived from canonical content.","Adopting-Dimension UUID or ULID for an assertion when no authoritative external identity exists."]},"properties":{"applicability":"not-applicable","items":[]},"recognition":{"applicability":"required","items":["A variant has a reference sequence accession and version, a location with a coordinate convention, a reference state and an alternate state.","Often confused with a genotype call, a gene, a transcript and a clinical interpretation."]},"capabilities":{"applicability":"required","items":["Register sequence or variant: Create stable root identity with a sequence, variant or combined-package discriminator and explicit mastership.","Normalize and identify sequence: Normalize residue content and calculate release-pinned sequence and collection digests.","Define molecular variation: Create a normalized variation from explicit reference context, location and alternate state.","Compose variation: Compose alleles into cis-phased blocks, haplotypes, variation sets or structural representations.","Translate expression: Translate among HGVS, SPDI, VCF and VRS under pinned rules without asserting untested equivalence.","Remap reference context: Project a location or variation across an alignment or assembly with method and uncertainty.","Validate and compare concordance: Run syntax, reference, coordinate, normalization, digest and round-trip checks.","Attach provenance and context: Link source archives, submissions, studies, observations and methods without importing their lifecycle.","Merge, split, deprecate or replace: Append lifecycle transitions and successor mappings while preserving old identifiers and audit history.","Project authorized view: Produce a minimum-necessary standards projection with consent, use and semantic-loss controls."]},"hazards":{"applicability":"required","items":["Re-identification of individuals from genomic data.","Wrong coordinates from mixing assemblies or coordinate conventions.","Wrong clinical decisions from misclassified variants.","Discrimination based on genetic information."]},"interfaces":{"applicability":"required","items":["HGVS variant nomenclature.","GA4GH VRS and refget.","HL7 FHIR MolecularSequence.","VCF file format.","INSDC sequence accessions."]},"context":{"applicability":"required","items":["Human clinical guidance does not govern all species, research uses, somatic profiles or jurisdictions.","FHIR MolecularSequence is Trial Use and GA4GH VRS 2.1 is under ballot, so production profiles must pin maturity and exact releases.","Consent, privacy, retention, incidental findings and clinical-reporting rules depend on law, institution, population and intended use."]}},"sources":[{"title":"Variation Representation Specification","url":"https://vrs.ga4gh.org/en/2.0/","note":"Global Alliance for Genomics and Health"},{"title":"Refget Sequences protocol","url":"https://ga4gh.github.io/refget/sequences/","note":"Global Alliance for Genomics and Health"},{"title":"Refget Sequence Collections","url":"https://ga4gh.github.io/refget/seqcols/","note":"Global Alliance for Genomics and Health"},{"title":"HGVS Sequence Variant Nomenclature","url":"https://hgvs-nomenclature.org/stable/","note":"Human Genome Variation Society"},{"title":"Variant Call Format Specification","url":"https://samtools.github.io/hts-specs/VCFv4.5.pdf","note":"Global Alliance for Genomics and Health"},{"title":"INSDC Technical Specifications","url":"https://www.insdc.org/technical-specifications/","note":"International Nucleotide Sequence Database Collaboration"},{"title":"NCBI Reference Sequence Database","url":"https://www.ncbi.nlm.nih.gov/refseq/","note":"National Center for Biotechnology Information"},{"title":"NCBI Variation Services","url":"https://api.ncbi.nlm.nih.gov/variation/v0/","note":"National Center for Biotechnology Information"},{"title":"ClinVar Data Model","url":"https://www.ncbi.nlm.nih.gov/clinvar/docs/data_model/","note":"National Center for Biotechnology Information"},{"title":"Representation of classifications in ClinVar","url":"https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/","note":"National Center for Biotechnology Information"},{"title":"European Variation Archive","url":"https://www.ebi.ac.uk/eva/","note":"European Molecular Biology Laboratory - European Bioinformatics Institute"},{"title":"Sequence Ontology","url":"https://github.com/The-Sequence-Ontology/SO-Ontologies","note":"Sequence Ontology Project"},{"title":"Sequence Variant Interpretation resources","url":"https://www.clinicalgenome.org/working-groups/sequence-variant-interpretation/","note":"Clinical Genome Resource"},{"title":"Standards and guidelines for interpretation of sequence variants","url":"https://www.acmg.net/docs/standards_guidelines_for_the_interpretation_of_sequence_variants.pdf","note":"American College of Medical Genetics and Genomics and Association for Molecular Pathology"},{"title":"FHIR MolecularSequence","url":"https://hl7.org/fhir/R5/molecularsequence.html","note":"Health Level Seven International"},{"title":"Data Use Ontology","url":"https://www.ga4gh.org/product/data-use-ontology-duo/","note":"Global Alliance for Genomics and Health"},{"title":"Framework for Responsible Sharing of Genomic and Health-Related Data","url":"https://www.ga4gh.org/framework/","note":"Global Alliance for Genomics and Health"},{"title":"PROV-O: The PROV Ontology","url":"https://www.w3.org/TR/prov-o/","note":"World Wide Web Consortium"},{"title":"Data Quality Vocabulary","url":"https://www.w3.org/TR/vocab-dqv/","note":"World Wide Web Consortium"},{"title":"ODRL Information Model 2.2","url":"https://www.w3.org/TR/odrl-model/","note":"World Wide Web Consortium"},{"title":"Date and Time on the Internet","url":"https://www.rfc-editor.org/rfc/rfc3339.html","note":"Internet Engineering Task Force"},{"title":"JSON Canonicalization Scheme","url":"https://www.rfc-editor.org/rfc/rfc8785.html","note":"Internet Engineering Task Force"},{"title":"JSON-LD 1.1","url":"https://www.w3.org/TR/json-ld11/","note":"World Wide Web Consortium"},{"title":"Beacon v2 API","url":"https://github.com/ga4gh-beacon/beacon-v2","note":"Global Alliance for Genomics and Health"}],"openQuestions":["Resolve WM-LIV-011 parent direction and map organism, genome, chromosome, gene, specimen, assay, call, genotype and interpretation sibling boundaries.","Develop species-specific, pangenome, mitochondrial, repeat, copy-number, structural, somatic and cytogenetic profiles with domain experts.","Pin production crosswalks to exact VRS, refget, HGVS, VCF, SPDI, FHIR, Beacon, INSDC, RefSeq, ClinVar, EVA and ontology releases and execute conformance suites.","Obtain independent molecular genetics, bioinformatics, laboratory, clinical genomics, privacy, ethics, legal, security and records review.","Species, pangenome, mitochondrial, repeat, cytogenetic, copy-number, structural, somatic and clinical profiles require expert review.","Organisms, genomes, chromosomes, genes, transcripts, proteins, specimens, people, assays, calls, genotypes, frequencies, phenotypes, diseases, interpretations and decisions remain neighboring masters.","Automated clinical classification, treatment selection, universal assembly lift-over and unrestricted person-level genomic disclosure remain outside scope."],"resources":{"spec":"/models/wm-liv-012-genomic-sequence-variant/spec.yaml","agents":"/models/wm-liv-012-genomic-sequence-variant/AGENTS.md","source":"https://github.com/ver-cy/world-models/tree/feat/mega-model-registry/research/runs/wm-liv-012"},"provenance":{"origin":"world-models research","builtFrom":["models/wm-liv-012-genomic-sequence-variant/spec.yaml","ver-cy/world-models/card-supplements/wm-liv-012-genomic-sequence-variant.json"],"providers":["Codex"],"researchStatus":"reviewable-draft","generatedAt":"2026-09-07T09:40:18Z","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 sequence variant is information about a genome; the specimen carries the physical properties.","_supplement":"Sections authored in card supplement 1.0.0 by Claude (Opus 5.5) (2026-10-05, unreviewed). Written from the published specification and established practice in the field; no new sources were read. Unreviewed."},"score":1.0}}