Published

Genomic Sequence / Variant

vr.wm-liv-012 · wm-liv-012-genomic-sequence-variant

Represent governed biological sequence identity and computable molecular variation relative to explicit reference and coordinate context.

World Models Physical world and living systems PHY.LIV.MOL

Bundle → Layer → Finding → Questions Classifiers What it is Why it exists Distinguishing features What robots and AI may and may not do Moral aspects Owners Links to other meta-models Identity and identifiers Direct properties Recognition Capabilities and actions Hazards and failure modes Standards and interfaces Context of use Sources

Bundle → Layer → Finding → Questions Filled

6 bundles · 12 layers · 24 findings · 72 questions

Subject boundary, identity and biological class Groups the governed Resource Consumption concern for subject boundary, identity and biological class.

Root kind, authoritative identity and mastership

Groups Resource Consumption context for root kind, authoritative identity and mastership without importing neighboring master lifecycles.

Sequence, variant or combined-package discriminator and root identity

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish sequence, variant or combined-package discriminator and root identity? identity
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify sequence, variant or combined-package discriminator and root identity? authority
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect sequence, variant or combined-package discriminator and root identity? security

Accession, version, computed identifier, alias, registry and master system

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish accession, version, computed identifier, alias, registry and master system? identity
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify accession, version, computed identifier, alias, registry and master system? requirement
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect accession, version, computed identifier, alias, registry and master system? privacy

Molecule, alphabet, organism and reference class

Groups Resource Consumption context for molecule, alphabet, organism and reference class without importing neighboring master lifecycles.

DNA, RNA, protein, alphabet, residue, length, topology and strandedness

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish dna, rna, protein, alphabet, residue, length, topology and strandedness? classification
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify dna, rna, protein, alphabet, residue, length, topology and strandedness? constraint
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect dna, rna, protein, alphabet, residue, length, topology and strandedness? retention

Taxon, reference status, assembly, collection and biological scope

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish taxon, reference status, assembly, collection and biological scope? classification
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify taxon, reference status, assembly, collection and biological scope? process
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect taxon, reference status, assembly, collection and biological scope? access

Sequence content, collection, coordinate and location Groups the governed Resource Consumption concern for sequence content, collection, coordinate and location.

Sequence content, canonicalization, digest and collection membership

Groups Resource Consumption context for sequence content, canonicalization, digest and collection membership without importing neighboring master lifecycles.

Residue content, normalization, length, digest algorithm and retrieval

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish residue content, normalization, length, digest algorithm and retrieval? measurement
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify residue content, normalization, length, digest algorithm and retrieval? event
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect residue content, normalization, length, digest algorithm and retrieval? exception

Sequence collection names, lengths, topologies, digest level and compatibility

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish sequence collection names, lengths, topologies, digest level and compatibility? composition
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify sequence collection names, lengths, topologies, digest level and compatibility? measurement
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect sequence collection names, lengths, topologies, digest level and compatibility? interoperability

Coordinate system, interval, orientation and imprecision

Groups Resource Consumption context for coordinate system, interval, orientation and imprecision without importing neighboring master lifecycles.

Reference context, coordinate base, boundary convention, start, end and strand

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish reference context, coordinate base, boundary convention, start, end and strand? spatial
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify reference context, coordinate base, boundary convention, start, end and strand? evidence
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect reference context, coordinate base, boundary convention, start, end and strand? decision

Sequence location, circular wrap, imprecise range, breakend and adjacency

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish sequence location, circular wrap, imprecise range, breakend and adjacency? spatial
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify sequence location, circular wrap, imprecise range, breakend and adjacency? quality
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect sequence location, circular wrap, imprecise range, breakend and adjacency? identity

Molecular variation state, normalization and composition Groups the governed Resource Consumption concern for molecular variation state, normalization and composition.

Reference, alternate state, class and computed identity

Groups Resource Consumption context for reference, alternate state, class and computed identity without importing neighboring master lifecycles.

Reference state, alternate state, substitution, insertion, deletion, indel and repeat

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish reference state, alternate state, substitution, insertion, deletion, indel and repeat? state
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify reference state, alternate state, substitution, insertion, deletion, indel and repeat? validation
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect reference state, alternate state, substitution, insertion, deletion, indel and repeat? classification

Normalization, canonical form, defining fields, digest prefix and algorithm version

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish normalization, canonical form, defining fields, digest prefix and algorithm version? identity
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify normalization, canonical form, defining fields, digest prefix and algorithm version? security
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect normalization, canonical form, defining fields, digest prefix and algorithm version? composition

Allele, haplotype, copy number and structural composition

Groups Resource Consumption context for allele, haplotype, copy number and structural composition without importing neighboring master lifecycles.

Allele, cis-phased block, haplotype, variation-set membership and order

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish allele, cis-phased block, haplotype, variation-set membership and order? composition
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify allele, cis-phased block, haplotype, variation-set membership and order? privacy
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect allele, cis-phased block, haplotype, variation-set membership and order? relationship

Copy-number count, copy-number change, adjacency, derivative and structural profile

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.

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? classification
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify copy-number count, copy-number change, adjacency, derivative and structural profile? retention
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect copy-number count, copy-number change, adjacency, derivative and structural profile? state

Expressions, mappings, projections and equivalence Groups the governed Resource Consumption concern for expressions, mappings, projections and equivalence.

HGVS, SPDI, VCF and other expressions

Groups Resource Consumption context for hgvs, spdi, vcf and other expressions without importing neighboring master lifecycles.

HGVS reference, coordinate type, expression, rule version and prediction marker

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish hgvs reference, coordinate type, expression, rule version and prediction marker? interoperability
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify hgvs reference, coordinate type, expression, rule version and prediction marker? access
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect hgvs reference, coordinate type, expression, rule version and prediction marker? lifecycle

SPDI, VCF record, allele decomposition, multiallelic, symbolic and file context

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish spdi, vcf record, allele decomposition, multiallelic, symbolic and file context? interoperability
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify spdi, vcf record, allele decomposition, multiallelic, symbolic and file context? exception
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect spdi, vcf record, allele decomposition, multiallelic, symbolic and file context? temporal

Cross-reference, equivalence, remapping and lift-over

Groups Resource Consumption context for cross-reference, equivalence, remapping and lift-over without importing neighboring master lifecycles.

External accession mapping, relation, source release, method and confidence

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish external accession mapping, relation, source release, method and confidence? relationship
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify external accession mapping, relation, source release, method and confidence? interoperability
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect external accession mapping, relation, source release, method and confidence? spatial

Assembly projection, alignment chain, orientation, normalization and semantic loss

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish assembly projection, alignment chain, orientation, normalization and semantic loss? process
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify assembly projection, alignment chain, orientation, normalization and semantic loss? decision
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect assembly projection, alignment chain, orientation, normalization and semantic loss? provenance

Provenance, evidence, quality, validation and lifecycle Groups the governed Resource Consumption concern for provenance, evidence, quality, validation and lifecycle.

Source, observation, method, pipeline and evidence lineage

Groups Resource Consumption context for source, observation, method, pipeline and evidence lineage without importing neighboring master lifecycles.

Archive, submission, study, specimen, assay, call and observation references

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish archive, submission, study, specimen, assay, call and observation references? evidence
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify archive, submission, study, specimen, assay, call and observation references? identity
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect archive, submission, study, specimen, assay, call and observation references? ownership

Producer, method, software, parameter, reference release, time and derivation

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish producer, method, software, parameter, reference release, time and derivation? provenance
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify producer, method, software, parameter, reference release, time and derivation? classification
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect producer, method, software, parameter, reference release, time and derivation? authority

Validation, concordance, state change and retirement

Groups Resource Consumption context for validation, concordance, state change and retirement without importing neighboring master lifecycles.

Syntax, reference allele, coordinate, normalization, digest, round trip and concordance

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish syntax, reference allele, coordinate, normalization, digest, round trip and concordance? validation
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify syntax, reference allele, coordinate, normalization, digest, round trip and concordance? composition
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect syntax, reference allele, coordinate, normalization, digest, round trip and concordance? requirement

Proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state? lifecycle
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state? relationship
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state? constraint

Context, interpretation, access, retention and interoperability Groups the governed Resource Consumption concern for context, interpretation, access, retention and interoperability.

Biological, clinical and population context references

Groups Resource Consumption context for biological, clinical and population context references without importing neighboring master lifecycles.

Gene, transcript, protein, feature, consequence and functional-effect reference

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish gene, transcript, protein, feature, consequence and functional-effect reference? relationship
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify gene, transcript, protein, feature, consequence and functional-effect reference? state
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect gene, transcript, protein, feature, consequence and functional-effect reference? process

Person, specimen, call, genotype, frequency, condition, interpretation and decision reference

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish person, specimen, call, genotype, frequency, condition, interpretation and decision reference? relationship
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify person, specimen, call, genotype, frequency, condition, interpretation and decision reference? lifecycle
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect person, specimen, call, genotype, frequency, condition, interpretation and decision reference? event

Sensitivity, consent, access, retention and loss-aware exchange

Groups Resource Consumption context for sensitivity, consent, access, retention and loss-aware exchange without importing neighboring master lifecycles.

Sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit

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.

Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit? privacy
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit? temporal
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit? measurement

VRS, refget, HGVS, VCF, SPDI, FHIR, Beacon, JSON-LD projection and conformance

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.

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? interoperability
Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify vrs, refget, hgvs, vcf, spdi, fhir, beacon, json-ld projection and conformance? spatial
Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect vrs, refget, hgvs, vcf, spdi, fhir, beacon, json-ld projection and conformance? evidence

Classifiers Filled

Family: World Models
Category: Physical world and living systems
Entry kind: aggregate
Navigation path: NAV.PHY.LIV.MOL
Domain: PHY.LIV.MOL
Industry: Cross-industry
Tags: genomicsequencevariantphy.liv.mol

What it is Filled

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.

In scope

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 of scope

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

Why it exists Filled

Represent governed biological sequence identity and computable molecular variation relative to explicit reference and coordinate context.

Distinguishing features Filled

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.

What robots and AI may and may not do Filled

Must not

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.

Only with a human decision

Clinical interpretation and reporting of variants.
Granting access to identifiable genomic data.
Merging or retiring curated variant identities.

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.

Moral aspects Filled

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.

Who is affected

Individuals whose genomes are sequenced
Biological relatives
Patients receiving genetic results
Source communities and populations

Owners Filled

Steward

Declare Dimension owner, sequence and variation masters, archive authority, curators, validators, clinical reviewers, data-use approvers and auditors.

Roles

Dimension owner: Own namespace, mastership, delegation, access, retention and federation rules.
Sequence archive or reference authority: Own accessions, versions, releases, corrections and withdrawal commitments.
Sequence curator: Own molecule, alphabet, content, reference status, collection and annotation boundaries.
Variation curator or bioinformatician: Own normalized state, location, composition, computed identifiers and mappings.
Laboratory or assay steward: Own specimen, assay, run, call and evidence records outside this model.
Clinical genomic reviewer: Own condition-specific evidence interpretation and clinical-significance assertions outside this model.
Data steward or access committee: Own consent, permitted use, purpose, minimum disclosure, retention and access decisions.
Validator or auditor: Review identity, reference, coordinates, normalization, provenance, lifecycle and disclosure without rewriting originals.

Links to other meta-models Filled

references

WM-LIV-011 - Resolve the registered biological parent without importing organism, genome or other container lifecycle.
Organism, specimen, person, assay, call, genotype, phenotype, disease, evidence and clinical-decision masters - Resolve observation and interpretation context without conflating it with molecular definition.

aligned

GA4GH VRS 2.0 - Project computable sequence location, molecular variation, composition, normalization and identifier semantics.
GA4GH refget Sequences 2.0 and Sequence Collections 1.0 - Project digest-derived sequence and collection identity, retrieval and compatibility.
HGVS 21.1.4 and VCF 4.5 - Project human-readable nomenclature and file-level variant exchange without treating either as universal identity.
INSDC, NCBI RefSeq and NCBI Variation Services - Project sequence accession, archive, SPDI normalization and translation context.
ClinVar and European Variation Archive - Project archive accessions, submissions, aggregate records, merge history and evidence links while keeping interpretation external.
Sequence Ontology, ClinGen and ACMG/AMP - Project variation and consequence terms plus condition-specific evidence guidance as external contextual assertions.
HL7 FHIR R5 MolecularSequence and GA4GH Beacon v2 - Project clinical sequence exchange and federated discovery views with maturity and privacy limits.
GA4GH DUO and Responsible Sharing Framework - Project permitted-use, consent, privacy, security and governance context.
W3C PROV-O, DQV and ODRL 2.2 - Project derivation, quality and rights constraints.
RFC 3339, RFC 8785 and JSON-LD 1.1 - Project unambiguous clocks, deterministic JSON and linked-data graph identity.

neighbor

WM-LIV-011 - 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.
Specimen, person and consent - 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.
Assay, read, alignment, call and genotype - Observed evidence and computational calls support a variation assertion but do not define the molecular variant or become its identity.
Gene, transcript, protein and consequence - Feature and consequence annotations are versioned projections on external reference annotations and remain distinct from sequence state and measured functional effects.
Disease and clinical interpretation - Condition-specific classification, evidence assessment, patient interpretation and treatment decision are independent assertions with their own actors, dates, criteria and provenance.
Archive accession and textual expression - 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.

parent

WM-LIV-011

What else AI and robots need to interact with it Filled

Sources Filled

Variation Representation Specification - Global Alliance for Genomics and Health
Refget Sequences protocol - Global Alliance for Genomics and Health
Refget Sequence Collections - Global Alliance for Genomics and Health
HGVS Sequence Variant Nomenclature - Human Genome Variation Society
Variant Call Format Specification - Global Alliance for Genomics and Health
INSDC Technical Specifications - International Nucleotide Sequence Database Collaboration
NCBI Reference Sequence Database - National Center for Biotechnology Information
NCBI Variation Services - National Center for Biotechnology Information
ClinVar Data Model - National Center for Biotechnology Information
Representation of classifications in ClinVar - National Center for Biotechnology Information
European Variation Archive - European Molecular Biology Laboratory - European Bioinformatics Institute
Sequence Ontology - Sequence Ontology Project
Sequence Variant Interpretation resources - Clinical Genome Resource
Standards and guidelines for interpretation of sequence variants - American College of Medical Genetics and Genomics and Association for Molecular Pathology
FHIR MolecularSequence - Health Level Seven International
Data Use Ontology - Global Alliance for Genomics and Health
Framework for Responsible Sharing of Genomic and Health-Related Data - Global Alliance for Genomics and Health
PROV-O: The PROV Ontology - World Wide Web Consortium
Data Quality Vocabulary - World Wide Web Consortium
ODRL Information Model 2.2 - World Wide Web Consortium
Date and Time on the Internet - Internet Engineering Task Force
JSON Canonicalization Scheme - Internet Engineering Task Force
JSON-LD 1.1 - World Wide Web Consortium
Beacon v2 API - Global Alliance for Genomics and Health

Open questions

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.

Machine files

Card as JSON Specification AGENTS.md Source Card backlog vercy.card/1

Provenance

world-models research · reviewable-draft

Built from: models/wm-liv-012-genomic-sequence-variant/spec.yaml, ver-cy/world-models/card-supplements/wm-liv-012-genomic-sequence-variant.json