# Vercy AI instruction - YAML 1.2 (JSON-compatible) { "vercy": "1.0-draft", "publication": { "status": "published", "adjudicationStatus": "reviewable-draft", "publishableCanonical": false, "generatedAt": "2026-09-07T09:40:18Z", "synthesisSha256": "c6b0bc55f4905dea131d039c47b476eecb73b3c08e7c3b148069b508f0289449", "providerMode": "single-provider-waiver", "providers": [ "Codex" ], "waivedProviders": [ "Claude", "Grok" ] }, "metaModel": { "id": "WM-LIV-012", "registryId": "vr.wm-liv-012", "name": "Genomic Sequence / Variant", "version": "0.3.0-research.1", "previousVersions": [], "entryKind": "aggregate", "family": "World Models", "category": "Physical world and living systems", "industry": [ "Cross-industry" ], "domain": [ "PHY.LIV.MOL" ], "tags": [ "genomic", "sequence", "variant", "phy.liv.mol" ], "status": "published" }, "canonicalUrl": "https://ver.cy/models/wm-liv-012-genomic-sequence-variant/", "sourceUrl": "https://github.com/ver-cy/world-models/tree/feat/mega-model-registry/research/runs/wm-liv-012", "model": { "registry_id": "vr.wm-liv-012", "model_id": "WM-LIV-012", "name": "Genomic Sequence / Variant", "entry_kind": "aggregate", "purpose": "Represent governed biological sequence identity and computable molecular variation relative to explicit reference and coordinate context.", "scope_statement": "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" ], "boundary_notes": [ { "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.", "source_refs": [ "SRC-003", "SRC-006", "SRC-007" ] }, { "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.", "source_refs": [ "SRC-009", "SRC-015", "SRC-016", "SRC-017" ] }, { "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.", "source_refs": [ "SRC-005", "SRC-009", "SRC-011" ] }, { "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.", "source_refs": [ "SRC-004", "SRC-010", "SRC-012", "SRC-013" ] }, { "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.", "source_refs": [ "SRC-009", "SRC-010", "SRC-013", "SRC-014" ] }, { "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.", "source_refs": [ "SRC-004", "SRC-005", "SRC-008", "SRC-009", "SRC-011" ] } ] }, "sources": [ { "id": "SRC-001", "title": "Variation Representation Specification", "organization": "Global Alliance for Genomics and Health", "url": "https://vrs.ga4gh.org/en/2.0/", "version_or_date": "VRS 2.0 official release, 14 March 2025; 2.1 ballot pending", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines language-neutral molecular variation, sequence locations, normalization and computed identifiers." }, { "id": "SRC-002", "title": "Refget Sequences protocol", "organization": "Global Alliance for Genomics and Health", "url": "https://ga4gh.github.io/refget/sequences/", "version_or_date": "Refget Sequences 2.0.0, approved 2024", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines digest-derived sequence identity, normalization, metadata and whole or ranged retrieval." }, { "id": "SRC-003", "title": "Refget Sequence Collections", "organization": "Global Alliance for Genomics and Health", "url": "https://ga4gh.github.io/refget/seqcols/", "version_or_date": "Sequence Collections 1.0.0, approved 2025", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines digest-derived sequence-collection identity, levels, coordinate systems and compatibility comparison." }, { "id": "SRC-004", "title": "HGVS Sequence Variant Nomenclature", "organization": "Human Genome Variation Society", "url": "https://hgvs-nomenclature.org/stable/", "version_or_date": "HGVS 21.1.4, 11 May 2026", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines reference-sequence-qualified DNA, RNA and protein variant expressions and versioned rules." }, { "id": "SRC-005", "title": "Variant Call Format Specification", "organization": "Global Alliance for Genomics and Health", "url": "https://samtools.github.io/hts-specs/VCFv4.5.pdf", "version_or_date": "VCF 4.5", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines file-level variant records, coordinates, alleles, symbolic forms, genotypes and metadata." }, { "id": "SRC-006", "title": "INSDC Technical Specifications", "organization": "International Nucleotide Sequence Database Collaboration", "url": "https://www.insdc.org/technical-specifications/", "version_or_date": "Live specifications, accessed 7 September 2026", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines shared nucleotide archive submission, validation, feature-table, assembly and representation rules." }, { "id": "SRC-007", "title": "NCBI Reference Sequence Database", "organization": "National Center for Biotechnology Information", "url": "https://www.ncbi.nlm.nih.gov/refseq/", "version_or_date": "Live database documentation, accessed 7 September 2026", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines curated reference sequence accessions and versioned sequence records." }, { "id": "SRC-008", "title": "NCBI Variation Services", "organization": "National Center for Biotechnology Information", "url": "https://api.ncbi.nlm.nih.gov/variation/v0/", "version_or_date": "Variation API v0, accessed 7 September 2026", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Provides SPDI normalization, contextual and canonical allele translation and variation retrieval." }, { "id": "SRC-009", "title": "ClinVar Data Model", "organization": "National Center for Biotechnology Information", "url": "https://www.ncbi.nlm.nih.gov/clinvar/docs/data_model/", "version_or_date": "Live data model, accessed 7 September 2026", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Separates submitted records, variant aggregates and variant-condition aggregates with supporting observations." }, { "id": "SRC-010", "title": "Representation of classifications in ClinVar", "organization": "National Center for Biotechnology Information", "url": "https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/", "version_or_date": "Updated 15 August 2025", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Distinguishes germline, somatic clinical-impact and oncogenicity classifications and their aggregation." }, { "id": "SRC-011", "title": "European Variation Archive", "organization": "European Molecular Biology Laboratory - European Bioinformatics Institute", "url": "https://www.ebi.ac.uk/eva/", "version_or_date": "Live service and model, accessed 7 September 2026", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines study submissions, VCF validation, normalization, SS and RS accessions, merge history and species scope." }, { "id": "SRC-012", "title": "Sequence Ontology", "organization": "Sequence Ontology Project", "url": "https://github.com/The-Sequence-Ontology/SO-Ontologies", "version_or_date": "Living ontology, accessed 7 September 2026", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines sequence features, alterations and predicted molecular consequence classes." }, { "id": "SRC-013", "title": "Sequence Variant Interpretation resources", "organization": "Clinical Genome Resource", "url": "https://www.clinicalgenome.org/working-groups/sequence-variant-interpretation/", "version_or_date": "Living guidance; SVI work reorganized in 2025", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Provides evidence-criterion specifications and gene or disease-specific variant curation guidance." }, { "id": "SRC-014", "title": "Standards and guidelines for interpretation of sequence variants", "organization": "American College of Medical Genetics and Genomics and Association for Molecular Pathology", "url": "https://www.acmg.net/docs/standards_guidelines_for_the_interpretation_of_sequence_variants.pdf", "version_or_date": "ACMG/AMP 2015; replacement in development", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines five-tier Mendelian classification, evidence categories, condition context and reporting expectations." }, { "id": "SRC-015", "title": "FHIR MolecularSequence", "organization": "Health Level Seven International", "url": "https://hl7.org/fhir/R5/molecularsequence.html", "version_or_date": "FHIR R5 5.0.0, Trial Use maturity 1", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines a clinical exchange resource for one molecular sequence with subject, focus and reference context." }, { "id": "SRC-016", "title": "Data Use Ontology", "organization": "Global Alliance for Genomics and Health", "url": "https://www.ga4gh.org/product/data-use-ontology-duo/", "version_or_date": "DUO 1.0, approved 23 February 2021", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines machine-readable permitted-use categories and modifiers for genomic and biomedical datasets." }, { "id": "SRC-017", "title": "Framework for Responsible Sharing of Genomic and Health-Related Data", "organization": "Global Alliance for Genomics and Health", "url": "https://www.ga4gh.org/framework/", "version_or_date": "Current framework, accessed 7 September 2026", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines human-rights, consent, privacy, security, governance and proportionality principles." }, { "id": "SRC-018", "title": "PROV-O: The PROV Ontology", "organization": "World Wide Web Consortium", "url": "https://www.w3.org/TR/prov-o/", "version_or_date": "W3C Recommendation, 30 April 2013", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines entity, activity, agent, derivation, attribution, revision and invalidation provenance." }, { "id": "SRC-019", "title": "Data Quality Vocabulary", "organization": "World Wide Web Consortium", "url": "https://www.w3.org/TR/vocab-dqv/", "version_or_date": "W3C Working Group Note, 15 December 2016", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines quality measurements, annotations, policies, standards and provenance." }, { "id": "SRC-020", "title": "ODRL Information Model 2.2", "organization": "World Wide Web Consortium", "url": "https://www.w3.org/TR/odrl-model/", "version_or_date": "W3C Recommendation, 15 February 2018", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines permissions, prohibitions, duties, constraints and policy parties." }, { "id": "SRC-021", "title": "Date and Time on the Internet", "organization": "Internet Engineering Task Force", "url": "https://www.rfc-editor.org/rfc/rfc3339.html", "version_or_date": "RFC 3339, July 2002", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines timestamps with seconds and an explicit numeric offset or Z." }, { "id": "SRC-022", "title": "JSON Canonicalization Scheme", "organization": "Internet Engineering Task Force", "url": "https://www.rfc-editor.org/rfc/rfc8785.html", "version_or_date": "RFC 8785, June 2020", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines deterministic JSON canonicalization for hashing and signing." }, { "id": "SRC-023", "title": "JSON-LD 1.1", "organization": "World Wide Web Consortium", "url": "https://www.w3.org/TR/json-ld11/", "version_or_date": "W3C Recommendation, 16 July 2020", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines graph identity, contexts, IRIs, typed values and linked-data serialization in JSON." }, { "id": "SRC-024", "title": "Beacon v2 API", "organization": "Global Alliance for Genomics and Health", "url": "https://github.com/ga4gh-beacon/beacon-v2", "version_or_date": "Beacon v2 repository, accessed 7 September 2026", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T09:38:00Z", "relevance": "Defines federated discovery requests and responses for genomic variants and related records." } ], "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.", "rationale": "Separate sequence content, molecular variation and the external biological or clinical context.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-023", "SRC-004", "SRC-012", "SRC-015" ], "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-023" ], "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-023" ], "questions": [ { "id": "sequence-variant-combined-package-discriminator-and-root-identity-q01", "text": "Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish sequence, variant or combined-package discriminator and root identity?", "kind": "identity", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "sequence-variant-combined-package-discriminator-and-root-identity-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify sequence, variant or combined-package discriminator and root identity?", "kind": "authority", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "sequence-variant-combined-package-discriminator-and-root-identity-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect sequence, variant or combined-package discriminator and root identity?", "kind": "security", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "sequence-variant-combined-package-discriminator-and-root-identity-data", "name": "Sequence, variant or combined-package discriminator and root identity data", "description": "Typed sequence or variation values and references required to answer the governed questions for sequence, variant or combined-package discriminator and root identity.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-023" ] } ], "artifacts": [ { "id": "sequence-variant-combined-package-discriminator-and-root-identity-artifact", "name": "Sequence, variant or combined-package discriminator and root identity evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting sequence, variant or combined-package discriminator and root identity.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-023" ] } ], "inline_only_rationale": null }, { "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-023" ], "questions": [ { "id": "accession-version-computed-identifier-alias-registry-and-master-system-q01", "text": "Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish accession, version, computed identifier, alias, registry and master system?", "kind": "identity", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "accession-version-computed-identifier-alias-registry-and-master-system-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify accession, version, computed identifier, alias, registry and master system?", "kind": "requirement", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "accession-version-computed-identifier-alias-registry-and-master-system-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect accession, version, computed identifier, alias, registry and master system?", "kind": "privacy", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "accession-version-computed-identifier-alias-registry-and-master-system-data", "name": "Accession, version, computed identifier, alias, registry and master system data", "description": "Typed sequence or variation values and references required to answer the governed questions for accession, version, computed identifier, alias, registry and master system.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-023" ] } ], "artifacts": [ { "id": "accession-version-computed-identifier-alias-registry-and-master-system-artifact", "name": "Accession, version, computed identifier, alias, registry and master system evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting accession, version, computed identifier, alias, registry and master system.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-023" ] } ], "inline_only_rationale": null } ] }, { "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-006", "SRC-007", "SRC-012", "SRC-015" ], "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-006", "SRC-007", "SRC-012", "SRC-015" ], "questions": [ { "id": "dna-rna-protein-alphabet-residue-length-topology-and-strandedness-q01", "text": "Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish dna, rna, protein, alphabet, residue, length, topology and strandedness?", "kind": "classification", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "dna-rna-protein-alphabet-residue-length-topology-and-strandedness-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify dna, rna, protein, alphabet, residue, length, topology and strandedness?", "kind": "constraint", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "dna-rna-protein-alphabet-residue-length-topology-and-strandedness-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect dna, rna, protein, alphabet, residue, length, topology and strandedness?", "kind": "retention", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "dna-rna-protein-alphabet-residue-length-topology-and-strandedness-data", "name": "DNA, RNA, protein, alphabet, residue, length, topology and strandedness data", "description": "Typed sequence or variation values and references required to answer the governed questions for dna, rna, protein, alphabet, residue, length, topology and strandedness.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-006", "SRC-007", "SRC-012", "SRC-015" ] } ], "artifacts": [ { "id": "dna-rna-protein-alphabet-residue-length-topology-and-strandedness-artifact", "name": "DNA, RNA, protein, alphabet, residue, length, topology and strandedness evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting dna, rna, protein, alphabet, residue, length, topology and strandedness.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-006", "SRC-007", "SRC-012", "SRC-015" ] } ], "inline_only_rationale": null }, { "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-006", "SRC-007", "SRC-012", "SRC-015" ], "questions": [ { "id": "taxon-reference-status-assembly-collection-and-biological-scope-q01", "text": "Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish taxon, reference status, assembly, collection and biological scope?", "kind": "classification", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "taxon-reference-status-assembly-collection-and-biological-scope-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify taxon, reference status, assembly, collection and biological scope?", "kind": "process", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "taxon-reference-status-assembly-collection-and-biological-scope-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect taxon, reference status, assembly, collection and biological scope?", "kind": "access", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "taxon-reference-status-assembly-collection-and-biological-scope-data", "name": "Taxon, reference status, assembly, collection and biological scope data", "description": "Typed sequence or variation values and references required to answer the governed questions for taxon, reference status, assembly, collection and biological scope.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-006", "SRC-007", "SRC-012", "SRC-015" ] } ], "artifacts": [ { "id": "taxon-reference-status-assembly-collection-and-biological-scope-artifact", "name": "Taxon, reference status, assembly, collection and biological scope evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting taxon, reference status, assembly, collection and biological scope.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-006", "SRC-007", "SRC-012", "SRC-015" ] } ], "inline_only_rationale": null } ] } ] }, { "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.", "rationale": "Make content-addressed sequence and coordinate semantics reproducible.", "source_refs": [ "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-018", "SRC-022", "SRC-023", "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ], "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.", "source_refs": [ "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-018", "SRC-022", "SRC-023" ], "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.", "source_refs": [ "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-018", "SRC-022", "SRC-023" ], "questions": [ { "id": "residue-content-normalization-length-digest-algorithm-and-retrieval-q01", "text": "Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish residue content, normalization, length, digest algorithm and retrieval?", "kind": "measurement", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "residue-content-normalization-length-digest-algorithm-and-retrieval-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify residue content, normalization, length, digest algorithm and retrieval?", "kind": "event", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "residue-content-normalization-length-digest-algorithm-and-retrieval-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect residue content, normalization, length, digest algorithm and retrieval?", "kind": "exception", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "residue-content-normalization-length-digest-algorithm-and-retrieval-data", "name": "Residue content, normalization, length, digest algorithm and retrieval data", "description": "Typed sequence or variation values and references required to answer the governed questions for residue content, normalization, length, digest algorithm and retrieval.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-018", "SRC-022", "SRC-023" ] } ], "artifacts": [ { "id": "residue-content-normalization-length-digest-algorithm-and-retrieval-artifact", "name": "Residue content, normalization, length, digest algorithm and retrieval evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting residue content, normalization, length, digest algorithm and retrieval.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-018", "SRC-022", "SRC-023" ] } ], "inline_only_rationale": null }, { "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.", "source_refs": [ "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-018", "SRC-022", "SRC-023" ], "questions": [ { "id": "sequence-collection-names-lengths-topologies-digest-level-and-compatibility-q01", "text": "Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish sequence collection names, lengths, topologies, digest level and compatibility?", "kind": "composition", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "sequence-collection-names-lengths-topologies-digest-level-and-compatibility-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify sequence collection names, lengths, topologies, digest level and compatibility?", "kind": "measurement", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "sequence-collection-names-lengths-topologies-digest-level-and-compatibility-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect sequence collection names, lengths, topologies, digest level and compatibility?", "kind": "interoperability", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "sequence-collection-names-lengths-topologies-digest-level-and-compatibility-data", "name": "Sequence collection names, lengths, topologies, digest level and compatibility data", "description": "Typed sequence or variation values and references required to answer the governed questions for sequence collection names, lengths, topologies, digest level and compatibility.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-018", "SRC-022", "SRC-023" ] } ], "artifacts": [ { "id": "sequence-collection-names-lengths-topologies-digest-level-and-compatibility-artifact", "name": "Sequence collection names, lengths, topologies, digest level and compatibility evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting sequence collection names, lengths, topologies, digest level and compatibility.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-018", "SRC-022", "SRC-023" ] } ], "inline_only_rationale": null } ] }, { "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.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ], "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.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ], "questions": [ { "id": "reference-context-coordinate-base-boundary-convention-start-end-and-strand-q01", "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?", "kind": "spatial", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "reference-context-coordinate-base-boundary-convention-start-end-and-strand-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify reference context, coordinate base, boundary convention, start, end and strand?", "kind": "evidence", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "reference-context-coordinate-base-boundary-convention-start-end-and-strand-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect reference context, coordinate base, boundary convention, start, end and strand?", "kind": "decision", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "reference-context-coordinate-base-boundary-convention-start-end-and-strand-data", "name": "Reference context, coordinate base, boundary convention, start, end and strand data", "description": "Typed sequence or variation values and references required to answer the governed questions for reference context, coordinate base, boundary convention, start, end and strand.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ] } ], "artifacts": [ { "id": "reference-context-coordinate-base-boundary-convention-start-end-and-strand-artifact", "name": "Reference context, coordinate base, boundary convention, start, end and strand evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting reference context, coordinate base, boundary convention, start, end and strand.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ] } ], "inline_only_rationale": null }, { "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.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ], "questions": [ { "id": "sequence-location-circular-wrap-imprecise-range-breakend-and-adjacency-q01", "text": "Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish sequence location, circular wrap, imprecise range, breakend and adjacency?", "kind": "spatial", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "sequence-location-circular-wrap-imprecise-range-breakend-and-adjacency-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify sequence location, circular wrap, imprecise range, breakend and adjacency?", "kind": "quality", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "sequence-location-circular-wrap-imprecise-range-breakend-and-adjacency-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect sequence location, circular wrap, imprecise range, breakend and adjacency?", "kind": "identity", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "sequence-location-circular-wrap-imprecise-range-breakend-and-adjacency-data", "name": "Sequence location, circular wrap, imprecise range, breakend and adjacency data", "description": "Typed sequence or variation values and references required to answer the governed questions for sequence location, circular wrap, imprecise range, breakend and adjacency.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ] } ], "artifacts": [ { "id": "sequence-location-circular-wrap-imprecise-range-breakend-and-adjacency-artifact", "name": "Sequence location, circular wrap, imprecise range, breakend and adjacency evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting sequence location, circular wrap, imprecise range, breakend and adjacency.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ] } ], "inline_only_rationale": null } ] } ] }, { "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.", "rationale": "Represent variation independently from any observation or interpretation.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ], "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.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ], "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.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ], "questions": [ { "id": "reference-state-alternate-state-substitution-insertion-deletion-indel-and-repeat-q01", "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?", "kind": "state", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "reference-state-alternate-state-substitution-insertion-deletion-indel-and-repeat-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify reference state, alternate state, substitution, insertion, deletion, indel and repeat?", "kind": "validation", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "reference-state-alternate-state-substitution-insertion-deletion-indel-and-repeat-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect reference state, alternate state, substitution, insertion, deletion, indel and repeat?", "kind": "classification", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "reference-state-alternate-state-substitution-insertion-deletion-indel-and-repeat-data", "name": "Reference state, alternate state, substitution, insertion, deletion, indel and repeat data", "description": "Typed sequence or variation values and references required to answer the governed questions for reference state, alternate state, substitution, insertion, deletion, indel and repeat.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ] } ], "artifacts": [ { "id": "reference-state-alternate-state-substitution-insertion-deletion-indel-and-repeat-artifact", "name": "Reference state, alternate state, substitution, insertion, deletion, indel and repeat evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting reference state, alternate state, substitution, insertion, deletion, indel and repeat.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ] } ], "inline_only_rationale": null }, { "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.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ], "questions": [ { "id": "normalization-canonical-form-defining-fields-digest-prefix-and-algorithm-version-q01", "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?", "kind": "identity", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "normalization-canonical-form-defining-fields-digest-prefix-and-algorithm-version-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify normalization, canonical form, defining fields, digest prefix and algorithm version?", "kind": "security", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "normalization-canonical-form-defining-fields-digest-prefix-and-algorithm-version-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect normalization, canonical form, defining fields, digest prefix and algorithm version?", "kind": "composition", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "normalization-canonical-form-defining-fields-digest-prefix-and-algorithm-version-data", "name": "Normalization, canonical form, defining fields, digest prefix and algorithm version data", "description": "Typed sequence or variation values and references required to answer the governed questions for normalization, canonical form, defining fields, digest prefix and algorithm version.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ] } ], "artifacts": [ { "id": "normalization-canonical-form-defining-fields-digest-prefix-and-algorithm-version-artifact", "name": "Normalization, canonical form, defining fields, digest prefix and algorithm version evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting normalization, canonical form, defining fields, digest prefix and algorithm version.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ] } ], "inline_only_rationale": null } ] }, { "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.", "source_refs": [ "SRC-001", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ], "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.", "source_refs": [ "SRC-001", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ], "questions": [ { "id": "allele-cis-phased-block-haplotype-variation-set-membership-and-order-q01", "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?", "kind": "composition", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "allele-cis-phased-block-haplotype-variation-set-membership-and-order-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify allele, cis-phased block, haplotype, variation-set membership and order?", "kind": "privacy", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "allele-cis-phased-block-haplotype-variation-set-membership-and-order-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect allele, cis-phased block, haplotype, variation-set membership and order?", "kind": "relationship", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "allele-cis-phased-block-haplotype-variation-set-membership-and-order-data", "name": "Allele, cis-phased block, haplotype, variation-set membership and order data", "description": "Typed sequence or variation values and references required to answer the governed questions for allele, cis-phased block, haplotype, variation-set membership and order.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ] } ], "artifacts": [ { "id": "allele-cis-phased-block-haplotype-variation-set-membership-and-order-artifact", "name": "Allele, cis-phased block, haplotype, variation-set membership and order evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting allele, cis-phased block, haplotype, variation-set membership and order.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ] } ], "inline_only_rationale": null }, { "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.", "source_refs": [ "SRC-001", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ], "questions": [ { "id": "copy-number-count-copy-number-change-adjacency-derivative-and-structural-profile-q01", "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?", "kind": "classification", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "copy-number-count-copy-number-change-adjacency-derivative-and-structural-profile-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify copy-number count, copy-number change, adjacency, derivative and structural profile?", "kind": "retention", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "copy-number-count-copy-number-change-adjacency-derivative-and-structural-profile-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect copy-number count, copy-number change, adjacency, derivative and structural profile?", "kind": "state", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "copy-number-count-copy-number-change-adjacency-derivative-and-structural-profile-data", "name": "Copy-number count, copy-number change, adjacency, derivative and structural profile data", "description": "Typed sequence or variation values and references required to answer the governed questions for copy-number count, copy-number change, adjacency, derivative and structural profile.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ] } ], "artifacts": [ { "id": "copy-number-count-copy-number-change-adjacency-derivative-and-structural-profile-artifact", "name": "Copy-number count, copy-number change, adjacency, derivative and structural profile evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting copy-number count, copy-number change, adjacency, derivative and structural profile.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-005", "SRC-008", "SRC-011", "SRC-012" ] } ], "inline_only_rationale": null } ] } ] }, { "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.", "rationale": "Preserve source meaning across nomenclatures, assemblies and formats.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015", "SRC-002", "SRC-003", "SRC-009", "SRC-018" ], "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.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ], "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.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ], "questions": [ { "id": "hgvs-reference-coordinate-type-expression-rule-version-and-prediction-marker-q01", "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?", "kind": "interoperability", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "hgvs-reference-coordinate-type-expression-rule-version-and-prediction-marker-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify hgvs reference, coordinate type, expression, rule version and prediction marker?", "kind": "access", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "hgvs-reference-coordinate-type-expression-rule-version-and-prediction-marker-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect hgvs reference, coordinate type, expression, rule version and prediction marker?", "kind": "lifecycle", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "hgvs-reference-coordinate-type-expression-rule-version-and-prediction-marker-data", "name": "HGVS reference, coordinate type, expression, rule version and prediction marker data", "description": "Typed sequence or variation values and references required to answer the governed questions for hgvs reference, coordinate type, expression, rule version and prediction marker.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ] } ], "artifacts": [ { "id": "hgvs-reference-coordinate-type-expression-rule-version-and-prediction-marker-artifact", "name": "HGVS reference, coordinate type, expression, rule version and prediction marker evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting hgvs reference, coordinate type, expression, rule version and prediction marker.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ] } ], "inline_only_rationale": null }, { "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.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ], "questions": [ { "id": "spdi-vcf-record-allele-decomposition-multiallelic-symbolic-and-file-context-q01", "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?", "kind": "interoperability", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "spdi-vcf-record-allele-decomposition-multiallelic-symbolic-and-file-context-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify spdi, vcf record, allele decomposition, multiallelic, symbolic and file context?", "kind": "exception", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "spdi-vcf-record-allele-decomposition-multiallelic-symbolic-and-file-context-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect spdi, vcf record, allele decomposition, multiallelic, symbolic and file context?", "kind": "temporal", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "spdi-vcf-record-allele-decomposition-multiallelic-symbolic-and-file-context-data", "name": "SPDI, VCF record, allele decomposition, multiallelic, symbolic and file context data", "description": "Typed sequence or variation values and references required to answer the governed questions for spdi, vcf record, allele decomposition, multiallelic, symbolic and file context.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ] } ], "artifacts": [ { "id": "spdi-vcf-record-allele-decomposition-multiallelic-symbolic-and-file-context-artifact", "name": "SPDI, VCF record, allele decomposition, multiallelic, symbolic and file context evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting spdi, vcf record, allele decomposition, multiallelic, symbolic and file context.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008", "SRC-011", "SRC-015" ] } ], "inline_only_rationale": null } ] }, { "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-008", "SRC-009", "SRC-011", "SRC-018" ], "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-008", "SRC-009", "SRC-011", "SRC-018" ], "questions": [ { "id": "external-accession-mapping-relation-source-release-method-and-confidence-q01", "text": "Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish external accession mapping, relation, source release, method and confidence?", "kind": "relationship", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "external-accession-mapping-relation-source-release-method-and-confidence-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify external accession mapping, relation, source release, method and confidence?", "kind": "interoperability", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "external-accession-mapping-relation-source-release-method-and-confidence-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect external accession mapping, relation, source release, method and confidence?", "kind": "spatial", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "external-accession-mapping-relation-source-release-method-and-confidence-data", "name": "External accession mapping, relation, source release, method and confidence data", "description": "Typed sequence or variation values and references required to answer the governed questions for external accession mapping, relation, source release, method and confidence.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-008", "SRC-009", "SRC-011", "SRC-018" ] } ], "artifacts": [ { "id": "external-accession-mapping-relation-source-release-method-and-confidence-artifact", "name": "External accession mapping, relation, source release, method and confidence evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting external accession mapping, relation, source release, method and confidence.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-008", "SRC-009", "SRC-011", "SRC-018" ] } ], "inline_only_rationale": null }, { "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-008", "SRC-009", "SRC-011", "SRC-018" ], "questions": [ { "id": "assembly-projection-alignment-chain-orientation-normalization-and-semantic-loss-q01", "text": "Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish assembly projection, alignment chain, orientation, normalization and semantic loss?", "kind": "process", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "assembly-projection-alignment-chain-orientation-normalization-and-semantic-loss-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify assembly projection, alignment chain, orientation, normalization and semantic loss?", "kind": "decision", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "assembly-projection-alignment-chain-orientation-normalization-and-semantic-loss-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect assembly projection, alignment chain, orientation, normalization and semantic loss?", "kind": "provenance", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "assembly-projection-alignment-chain-orientation-normalization-and-semantic-loss-data", "name": "Assembly projection, alignment chain, orientation, normalization and semantic loss data", "description": "Typed sequence or variation values and references required to answer the governed questions for assembly projection, alignment chain, orientation, normalization and semantic loss.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-008", "SRC-009", "SRC-011", "SRC-018" ] } ], "artifacts": [ { "id": "assembly-projection-alignment-chain-orientation-normalization-and-semantic-loss-artifact", "name": "Assembly projection, alignment chain, orientation, normalization and semantic loss evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting assembly projection, alignment chain, orientation, normalization and semantic loss.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-008", "SRC-009", "SRC-011", "SRC-018" ] } ], "inline_only_rationale": null } ] } ] }, { "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.", "rationale": "Make every molecular assertion reproducible and correctable without erasing history.", "source_refs": [ "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-013", "SRC-014", "SRC-018", "SRC-019", "SRC-001", "SRC-002", "SRC-003", "SRC-004" ], "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.", "source_refs": [ "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-013", "SRC-014", "SRC-018", "SRC-019" ], "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.", "source_refs": [ "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-013", "SRC-014", "SRC-018", "SRC-019" ], "questions": [ { "id": "archive-submission-study-specimen-assay-call-and-observation-references-q01", "text": "Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish archive, submission, study, specimen, assay, call and observation references?", "kind": "evidence", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "archive-submission-study-specimen-assay-call-and-observation-references-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify archive, submission, study, specimen, assay, call and observation references?", "kind": "identity", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "archive-submission-study-specimen-assay-call-and-observation-references-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect archive, submission, study, specimen, assay, call and observation references?", "kind": "ownership", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "archive-submission-study-specimen-assay-call-and-observation-references-data", "name": "Archive, submission, study, specimen, assay, call and observation references data", "description": "Typed sequence or variation values and references required to answer the governed questions for archive, submission, study, specimen, assay, call and observation references.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-013", "SRC-014", "SRC-018", "SRC-019" ] } ], "artifacts": [ { "id": "archive-submission-study-specimen-assay-call-and-observation-references-artifact", "name": "Archive, submission, study, specimen, assay, call and observation references evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting archive, submission, study, specimen, assay, call and observation references.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-013", "SRC-014", "SRC-018", "SRC-019" ] } ], "inline_only_rationale": null }, { "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.", "source_refs": [ "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-013", "SRC-014", "SRC-018", "SRC-019" ], "questions": [ { "id": "producer-method-software-parameter-reference-release-time-and-derivation-q01", "text": "Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish producer, method, software, parameter, reference release, time and derivation?", "kind": "provenance", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "producer-method-software-parameter-reference-release-time-and-derivation-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify producer, method, software, parameter, reference release, time and derivation?", "kind": "classification", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "producer-method-software-parameter-reference-release-time-and-derivation-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect producer, method, software, parameter, reference release, time and derivation?", "kind": "authority", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "producer-method-software-parameter-reference-release-time-and-derivation-data", "name": "Producer, method, software, parameter, reference release, time and derivation data", "description": "Typed sequence or variation values and references required to answer the governed questions for producer, method, software, parameter, reference release, time and derivation.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-013", "SRC-014", "SRC-018", "SRC-019" ] } ], "artifacts": [ { "id": "producer-method-software-parameter-reference-release-time-and-derivation-artifact", "name": "Producer, method, software, parameter, reference release, time and derivation evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting producer, method, software, parameter, reference release, time and derivation.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-013", "SRC-014", "SRC-018", "SRC-019" ] } ], "inline_only_rationale": null } ] }, { "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-019" ], "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-019" ], "questions": [ { "id": "syntax-reference-allele-coordinate-normalization-digest-round-trip-and-concordance-q01", "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?", "kind": "validation", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "syntax-reference-allele-coordinate-normalization-digest-round-trip-and-concordance-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify syntax, reference allele, coordinate, normalization, digest, round trip and concordance?", "kind": "composition", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "syntax-reference-allele-coordinate-normalization-digest-round-trip-and-concordance-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect syntax, reference allele, coordinate, normalization, digest, round trip and concordance?", "kind": "requirement", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "syntax-reference-allele-coordinate-normalization-digest-round-trip-and-concordance-data", "name": "Syntax, reference allele, coordinate, normalization, digest, round trip and concordance data", "description": "Typed sequence or variation values and references required to answer the governed questions for syntax, reference allele, coordinate, normalization, digest, round trip and concordance.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-019" ] } ], "artifacts": [ { "id": "syntax-reference-allele-coordinate-normalization-digest-round-trip-and-concordance-artifact", "name": "Syntax, reference allele, coordinate, normalization, digest, round trip and concordance evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting syntax, reference allele, coordinate, normalization, digest, round trip and concordance.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-019" ] } ], "inline_only_rationale": null }, { "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-019" ], "questions": [ { "id": "proposed-active-merged-split-deprecated-withdrawn-superseded-and-replaced-state-q01", "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?", "kind": "lifecycle", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "proposed-active-merged-split-deprecated-withdrawn-superseded-and-replaced-state-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state?", "kind": "relationship", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "proposed-active-merged-split-deprecated-withdrawn-superseded-and-replaced-state-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state?", "kind": "constraint", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "proposed-active-merged-split-deprecated-withdrawn-superseded-and-replaced-state-data", "name": "Proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state data", "description": "Typed sequence or variation values and references required to answer the governed questions for proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-019" ] } ], "artifacts": [ { "id": "proposed-active-merged-split-deprecated-withdrawn-superseded-and-replaced-state-artifact", "name": "Proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting proposed, active, merged, split, deprecated, withdrawn, superseded and replaced state.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-009", "SRC-011", "SRC-018", "SRC-019" ] } ], "inline_only_rationale": null } ] } ] }, { "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.", "rationale": "Reference biological and clinical meaning while enforcing genomic-data governance.", "source_refs": [ "SRC-009", "SRC-010", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-024", "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-011", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023" ], "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.", "source_refs": [ "SRC-009", "SRC-010", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-024" ], "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.", "source_refs": [ "SRC-009", "SRC-010", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-024" ], "questions": [ { "id": "gene-transcript-protein-feature-consequence-and-functional-effect-reference-q01", "text": "Which sequence or molecular-variation identity, class, reference context, coordinate convention and release establish gene, transcript, protein, feature, consequence and functional-effect reference?", "kind": "relationship", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "gene-transcript-protein-feature-consequence-and-functional-effect-reference-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify gene, transcript, protein, feature, consequence and functional-effect reference?", "kind": "state", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "gene-transcript-protein-feature-consequence-and-functional-effect-reference-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect gene, transcript, protein, feature, consequence and functional-effect reference?", "kind": "process", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "gene-transcript-protein-feature-consequence-and-functional-effect-reference-data", "name": "Gene, transcript, protein, feature, consequence and functional-effect reference data", "description": "Typed sequence or variation values and references required to answer the governed questions for gene, transcript, protein, feature, consequence and functional-effect reference.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-009", "SRC-010", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-024" ] } ], "artifacts": [ { "id": "gene-transcript-protein-feature-consequence-and-functional-effect-reference-artifact", "name": "Gene, transcript, protein, feature, consequence and functional-effect reference evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting gene, transcript, protein, feature, consequence and functional-effect reference.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-009", "SRC-010", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-024" ] } ], "inline_only_rationale": null }, { "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.", "source_refs": [ "SRC-009", "SRC-010", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-024" ], "questions": [ { "id": "person-specimen-call-genotype-frequency-condition-interpretation-and-decision-reference-q01", "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?", "kind": "relationship", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "person-specimen-call-genotype-frequency-condition-interpretation-and-decision-reference-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify person, specimen, call, genotype, frequency, condition, interpretation and decision reference?", "kind": "lifecycle", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "person-specimen-call-genotype-frequency-condition-interpretation-and-decision-reference-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect person, specimen, call, genotype, frequency, condition, interpretation and decision reference?", "kind": "event", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "person-specimen-call-genotype-frequency-condition-interpretation-and-decision-reference-data", "name": "Person, specimen, call, genotype, frequency, condition, interpretation and decision reference data", "description": "Typed sequence or variation values and references required to answer the governed questions for person, specimen, call, genotype, frequency, condition, interpretation and decision reference.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-009", "SRC-010", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-024" ] } ], "artifacts": [ { "id": "person-specimen-call-genotype-frequency-condition-interpretation-and-decision-reference-artifact", "name": "Person, specimen, call, genotype, frequency, condition, interpretation and decision reference evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting person, specimen, call, genotype, frequency, condition, interpretation and decision reference.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-009", "SRC-010", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-024" ] } ], "inline_only_rationale": null } ] }, { "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ], "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ], "questions": [ { "id": "sensitivity-consent-data-use-purpose-role-jurisdiction-retention-and-audit-q01", "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?", "kind": "privacy", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "sensitivity-consent-data-use-purpose-role-jurisdiction-retention-and-audit-q02", "text": "Which organism, specimen, observation, method, actor, authority, provenance and access rules qualify sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit?", "kind": "temporal", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "sensitivity-consent-data-use-purpose-role-jurisdiction-retention-and-audit-q03", "text": "Which mappings, lifecycle changes, quality checks, competing assertions and interoperability losses affect sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit?", "kind": "measurement", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "sensitivity-consent-data-use-purpose-role-jurisdiction-retention-and-audit-data", "name": "Sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit data", "description": "Typed sequence or variation values and references required to answer the governed questions for sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ] } ], "artifacts": [ { "id": "sensitivity-consent-data-use-purpose-role-jurisdiction-retention-and-audit-artifact", "name": "Sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting sensitivity, consent, data use, purpose, role, jurisdiction, retention and audit.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ] } ], "inline_only_rationale": null }, { "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.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ], "questions": [ { "id": "vrs-refget-hgvs-vcf-spdi-fhir-beacon-jsonld-projection-and-conformance-q01", "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?", "kind": "interoperability", "answer_data": [ "root discriminator, authoritative identifier, accession and version, computed identifier and status", "molecule, alphabet, sequence digest, collection or assembly, coordinate base, interval and orientation", "variation class, reference and alternate state, normalization algorithm and expression profile" ] }, { "id": "vrs-refget-hgvs-vcf-spdi-fhir-beacon-jsonld-projection-and-conformance-q02", "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?", "kind": "spatial", "answer_data": [ "taxon, organism, specimen, assay, call, study and source-archive references", "producer, curator, method, software, parameters, evidence, confidence, validation and clocks", "consent, permitted use, purpose, role, jurisdiction, sensitivity, retention and audit basis" ] }, { "id": "vrs-refget-hgvs-vcf-spdi-fhir-beacon-jsonld-projection-and-conformance-q03", "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?", "kind": "evidence", "answer_data": [ "external accessions, mapping relation, source and target releases, lift-over method and confidence", "active, merged, split, deprecated, withdrawn, superseded or replaced state with immutable predecessors", "syntax, reference, coordinate, normalization, digest, concordance, round-trip and semantic-loss results" ] } ], "data_elements": [ { "id": "vrs-refget-hgvs-vcf-spdi-fhir-beacon-jsonld-projection-and-conformance-data", "name": "VRS, refget, HGVS, VCF, SPDI, FHIR, Beacon, JSON-LD projection and conformance data", "description": "Typed sequence or variation values and references required to answer the governed questions for vrs, refget, hgvs, vcf, spdi, fhir, beacon, json-ld projection and conformance.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ] } ], "artifacts": [ { "id": "vrs-refget-hgvs-vcf-spdi-fhir-beacon-jsonld-projection-and-conformance-artifact", "name": "VRS, refget, HGVS, VCF, SPDI, FHIR, Beacon, JSON-LD projection and conformance evidence manifest", "description": "Digest-addressed manifest of reference context, defining values, expressions, mappings, validation, lifecycle and provenance supporting vrs, refget, hgvs, vcf, spdi, fhir, beacon, json-ld projection and conformance.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/plain", "text/vcf", "text/markdown", "external reference" ], "serial": true, "identity_strategy": "Authoritative sequence or variation identifier first, then release-pinned computed identifier, then Dimension UUID or ULID; include root kind, accession version, reference context and digest.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ] } ], "inline_only_rationale": null } ] } ] } ] }, "functions": [ { "id": "register-sequence-or-variant", "name": "Register sequence or variant", "description": "Create stable root identity with a sequence, variant or combined-package discriminator and explicit mastership.", "inputs": [ "subject proposal", "root kind", "master authority" ], "outputs": [ "subject identifier", "initial revision" ], "preconditions": [ "active Dimension", "identifier authority" ], "effects": [ "identity and unknowns are appended without importing neighboring masters" ], "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-007", "SRC-011" ] }, { "id": "normalize-identify-sequence", "name": "Normalize and identify sequence", "description": "Normalize residue content and calculate release-pinned sequence and collection digests.", "inputs": [ "sequence content", "alphabet", "normalization profile" ], "outputs": [ "sequence digest", "collection membership" ], "preconditions": [ "content authorized", "algorithm pinned" ], "effects": [ "input content is unchanged and digest derivation is retained" ], "source_refs": [ "SRC-002", "SRC-003", "SRC-022" ] }, { "id": "define-molecular-variation", "name": "Define molecular variation", "description": "Create a normalized variation from explicit reference context, location and alternate state.", "inputs": [ "reference sequence", "location", "alternate state", "variation class" ], "outputs": [ "variation definition", "computed identifier" ], "preconditions": [ "reference resolvable", "coordinate convention explicit" ], "effects": [ "definition remains distinct from calls and interpretations" ], "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008" ] }, { "id": "compose-variation", "name": "Compose variation", "description": "Compose alleles into cis-phased blocks, haplotypes, variation sets or structural representations.", "inputs": [ "member variations", "composition kind", "phase or order" ], "outputs": [ "composed variation" ], "preconditions": [ "member identities valid", "composition semantics pinned" ], "effects": [ "members remain independently resolvable" ], "source_refs": [ "SRC-001", "SRC-005", "SRC-012" ] }, { "id": "translate-expression", "name": "Translate expression", "description": "Translate among HGVS, SPDI, VCF and VRS under pinned rules without asserting untested equivalence.", "inputs": [ "source expression", "source profile", "target profile" ], "outputs": [ "target expression", "translation report" ], "preconditions": [ "reference and rule versions pinned" ], "effects": [ "source expression, normalization steps and losses are retained" ], "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008" ] }, { "id": "remap-reference-context", "name": "Remap reference context", "description": "Project a location or variation across an alignment or assembly with method and uncertainty.", "inputs": [ "source variant", "target reference", "alignment resource" ], "outputs": [ "projected candidate", "mapping evidence" ], "preconditions": [ "alignment and assembly releases pinned" ], "effects": [ "projection is never silent identity equivalence" ], "source_refs": [ "SRC-003", "SRC-004", "SRC-008", "SRC-011" ] }, { "id": "validate-concordance", "name": "Validate and compare concordance", "description": "Run syntax, reference, coordinate, normalization, digest and round-trip checks.", "inputs": [ "subject revision", "validation profile", "comparison targets" ], "outputs": [ "validation report", "concordance assertions" ], "preconditions": [ "validators and releases pinned" ], "effects": [ "validation remains distinct from clinical interpretation" ], "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005", "SRC-008", "SRC-019" ] }, { "id": "attach-provenance-context", "name": "Attach provenance and context", "description": "Link source archives, submissions, studies, observations and methods without importing their lifecycle.", "inputs": [ "subject revision", "external references", "provenance assertions" ], "outputs": [ "qualified provenance links" ], "preconditions": [ "external identities resolvable", "purpose authorized" ], "effects": [ "molecular definition remains stable and assertions remain attributable" ], "source_refs": [ "SRC-006", "SRC-009", "SRC-011", "SRC-018" ] }, { "id": "govern-lifecycle", "name": "Merge, split, deprecate or replace", "description": "Append lifecycle transitions and successor mappings while preserving old identifiers and audit history.", "inputs": [ "subject revision", "reason", "successors" ], "outputs": [ "lifecycle assertion", "migration map" ], "preconditions": [ "curation authority", "impact assessed" ], "effects": [ "old identifiers resolve and external records are not silently rewritten" ], "source_refs": [ "SRC-007", "SRC-009", "SRC-011", "SRC-018" ] }, { "id": "project-authorized-view", "name": "Project authorized view", "description": "Produce a minimum-necessary standards projection with consent, use and semantic-loss controls.", "inputs": [ "subject revision", "recipient purpose", "target profile" ], "outputs": [ "authorized projection", "conformance and loss report" ], "preconditions": [ "access decision granted", "target release pinned" ], "effects": [ "disclosure is audited and canonical identity is preserved" ], "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ] } ], "composition": [ { "target": "WM-LIV-011", "relation": "REFERENCE", "purpose": "Resolve the registered biological parent without importing organism, genome or other container lifecycle.", "required": false, "source_refs": [ "SRC-003", "SRC-006", "SRC-007" ] }, { "target": "Organism, specimen, person, assay, call, genotype, phenotype, disease, evidence and clinical-decision masters", "relation": "REFERENCE", "purpose": "Resolve observation and interpretation context without conflating it with molecular definition.", "required": false, "source_refs": [ "SRC-009", "SRC-010", "SRC-013", "SRC-014", "SRC-015", "SRC-017" ] }, { "target": "GA4GH VRS 2.0", "relation": "ALIGN", "purpose": "Project computable sequence location, molecular variation, composition, normalization and identifier semantics.", "required": false, "source_refs": [ "SRC-001" ] }, { "target": "GA4GH refget Sequences 2.0 and Sequence Collections 1.0", "relation": "ALIGN", "purpose": "Project digest-derived sequence and collection identity, retrieval and compatibility.", "required": false, "source_refs": [ "SRC-002", "SRC-003" ] }, { "target": "HGVS 21.1.4 and VCF 4.5", "relation": "ALIGN", "purpose": "Project human-readable nomenclature and file-level variant exchange without treating either as universal identity.", "required": false, "source_refs": [ "SRC-004", "SRC-005" ] }, { "target": "INSDC, NCBI RefSeq and NCBI Variation Services", "relation": "ALIGN", "purpose": "Project sequence accession, archive, SPDI normalization and translation context.", "required": false, "source_refs": [ "SRC-006", "SRC-007", "SRC-008" ] }, { "target": "ClinVar and European Variation Archive", "relation": "ALIGN", "purpose": "Project archive accessions, submissions, aggregate records, merge history and evidence links while keeping interpretation external.", "required": false, "source_refs": [ "SRC-009", "SRC-010", "SRC-011" ] }, { "target": "Sequence Ontology, ClinGen and ACMG/AMP", "relation": "ALIGN", "purpose": "Project variation and consequence terms plus condition-specific evidence guidance as external contextual assertions.", "required": false, "source_refs": [ "SRC-012", "SRC-013", "SRC-014" ] }, { "target": "HL7 FHIR R5 MolecularSequence and GA4GH Beacon v2", "relation": "ALIGN", "purpose": "Project clinical sequence exchange and federated discovery views with maturity and privacy limits.", "required": false, "source_refs": [ "SRC-015", "SRC-024" ] }, { "target": "GA4GH DUO and Responsible Sharing Framework", "relation": "ALIGN", "purpose": "Project permitted-use, consent, privacy, security and governance context.", "required": false, "source_refs": [ "SRC-016", "SRC-017" ] }, { "target": "W3C PROV-O, DQV and ODRL 2.2", "relation": "ALIGN", "purpose": "Project derivation, quality and rights constraints.", "required": false, "source_refs": [ "SRC-018", "SRC-019", "SRC-020" ] }, { "target": "RFC 3339, RFC 8785 and JSON-LD 1.1", "relation": "ALIGN", "purpose": "Project unambiguous clocks, deterministic JSON and linked-data graph identity.", "required": false, "source_refs": [ "SRC-021", "SRC-022", "SRC-023" ] } ], "serviceLayers": { "dimension": { "owner_package_requirements": [ "Declare Dimension owner, sequence and variation masters, archive authority, curators, validators, clinical reviewers, data-use approvers and auditors.", "Register sequence, collection, assembly, coordinate, variation, nomenclature, status, quality, consent, access, retention and projection profiles.", "Register organism, specimen, person, assay, call, genotype, phenotype, disease, evidence and clinical-decision masters separately.", "Pin species, reference, clinical, jurisdictional, privacy and exchange profiles." ], "namespace_guidance": "Mint only Dimension-owned sequence package, variation assertion, mapping, validation and lifecycle identifiers locally; preserve INSDC, RefSeq, refget, VRS, RefSNP, ClinVar, EVA, specimen and person identifiers as typed external references.", "registry_links": [ "https://ver.cy/models/", "https://ver.cy/model-agent-protocol.md", "Dimension-local biological identity, reference, coordinate, nomenclature, consent, access, retention and provenance registries" ] }, "canon_and_patch": { "canonicalization_rules": [ "Canonicalize by registry ID, model version, root discriminator, authoritative accession and version or release-pinned computed identifier, reference context, defining state and normalization algorithm; never by display name, coordinate string, filename or hash alone.", "Keep sequence content, collection, assembly, location, molecular variation, expression, archive accession, observed call, genotype, consequence and clinical interpretation distinct." ], "patch_rules": [ "Additive extensions declare target node, species or clinical profile, authority, source, method, reference release, access, effective time and interoperability impact.", "Breaking identity, coordinate, normalization or composition changes require a new immutable revision, successor mapping, migration report, compatibility declaration and continued resolution of prior identifiers." ], "compatibility_rules": [ "Consumers may ignore unknown additive fields only when root kind, sequence or variation identity, reference context, coordinate and normalization meaning remain intact.", "VRS, refget, HGVS, VCF, SPDI, FHIR, Beacon and JSON-LD mappings pin source and target releases and declare transformed, inferred, omitted or non-round-trippable values." ] }, "artifact_rules": { "identity_priority": [ "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." ], "timestamp_rule": "Record event timestamps in RFC 3339 with seconds and explicit numeric offset or Z; keep collection, observation, analysis, submission, accession, normalization, interpretation, review, publication, correction and ingestion times distinct.", "serial_naming_rule": "Name serial artifacts as {subject-id}--{artifact-kind}--{revision-or-assertion-id}; never use sample name, person name, coordinate, date, filename or digest alone as identity.", "integrity_rule": "Store digest, media type, byte length, issuer, subject kind, reference and rules versions, method, clocks, provenance, validation, sensitivity, consent, permitted use, access marking and semantic-loss declaration." }, "policies": [ "The adopting Dimension declares who may register sequences, normalize variation, curate mappings, validate, interpret, approve, disclose, retain, correct and tombstone records.", "Every usable molecular variant requires stable identity, explicit reference accession and version or digest, coordinate convention, reference and alternate state, class, normalization profile, provenance and validation status.", "Agents never infer pathogenicity from molecular existence, an observed call from a variation definition, equivalence from a shared label, or coordinate compatibility from an assembly nickname.", "Organisms, specimens, persons, assays, calls, genotypes, frequencies, phenotypes, diseases, interpretations and decisions remain external masters.", "Agents may validate syntax, calculate deterministic digests and create low-risk candidate mappings under delegation; clinical interpretation, access grants, identity merges, protected disclosure and irreversible removal require accountable authority." ], "crud": { "read": [ "Resolve active Dimension, purpose, role, root kind, identity, reference and coordinate profile, consent, permitted use, sensitivity, release, assurance and access; return the minimum necessary projection." ], "create": [ "Create a stable root discriminator and identity, reference context, owner, provenance and explicit unknowns before sequence content, variant state, expressions or mappings are added." ], "update": [ "Append an immutable content, normalization, mapping, validation, lifecycle or correction assertion with actor, authority, reason, source, method, reference release, RFC 3339 effective time and predecessor." ], "delete": [ "Apply consent, archive, clinical, legal, audit, retention and hold rules; tombstone eligible Dimension-owned assertions while preserving material provenance, accession resolution and non-cascading external records." ] }, "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." ] } ], "access": { "default_rule": "Deny protected genomic content, linked person or specimen identifiers and mutation unless active Dimension, role, purpose, consent, permitted use, jurisdiction and field policy grant the action; expose the minimum necessary projection.", "scopes": [ "bundle", "layer", "finding", "artifact" ], "exceptions": [ "Emergency, public-health or legally compelled access must be grounded, time-limited, purpose-bound, attributable, independently reviewed and unable to erase immutable provenance or legal-hold evidence." ], "audit_requirements": [ "Log actor, role, purpose, subject and reference identity, action, decision, policy and standard versions, RFC 3339 timestamp with offset, affected fields, recipient, source evidence and outcome for privileged mutation or disclosure." ] }, "agents_bootstrap": { "filename": "AGENTS.md", "required_fields": [ "Name", "Type", "Specification URL", "Storage type URL", "Interface URL", "Processes URL" ], "read_order": [ "Read the nearest Dimension-owner AGENTS.md, active biological and clinical profiles, master systems, consent, data-use, access, retention and jurisdiction rules.", "Read this model AGENTS.md, pinned spec.yaml and required organism, specimen, assay, call, interpretation, policy and evidence instructions before mutation." ] } }, "coverage": { "claim": "WM-LIV-012 covers governed biological sequence and molecular-variation identity, sequence content, reference and coordinate context, normalized defining state, composition, expressions, mappings, provenance, validation, lifecycle, protected access, retention and loss-aware interoperability. Species, pangenome, complex-variation, clinical, jurisdictional and independent-review questions remain deferred.", "confidence": "medium", "checklist": [ { "dimension": "identity", "status": "covered", "notes": "Sequence, collection, location, variation, expression, accession, mapping, validation and lifecycle identities remain distinct." }, { "dimension": "classification and definition", "status": "covered", "notes": "Root kind, molecule, alphabet, reference status and small, repeat, copy-number and structural variation profiles are explicit." }, { "dimension": "direct properties", "status": "covered", "notes": "Residue content, alphabet, length, topology, strandedness, digest, location, reference and alternate state are covered with method and release context." }, { "dimension": "recognition and observation", "status": "covered", "notes": "Agents distinguish subjects through accessions plus versions, content digests, defining fields and normalized reference context rather than labels alone." }, { "dimension": "capabilities and possible actions", "status": "covered", "notes": "Normalize, identify, compose, translate, remap, validate, link, govern and project operations expose preconditions and effects." }, { "dimension": "lifecycle", "status": "covered", "notes": "Proposed, active, merged, split, deprecated, withdrawn, superseded and replaced states preserve immutable predecessors." }, { "dimension": "relationships", "status": "covered", "notes": "Collection membership, composition, reference, expression, mapping, successor and external contextual links are typed." }, { "dimension": "temporal", "status": "covered", "notes": "Collection, observation, analysis, accession, interpretation, review, correction and ingestion clocks remain distinct." }, { "dimension": "spatial", "status": "covered", "notes": "Sequence locations capture coordinate base, boundary convention, interval, orientation, strand, circularity and imprecision." }, { "dimension": "provenance", "status": "covered", "notes": "Archives, submissions, studies, methods, software, parameters, reference releases, evidence and derivations are linked." }, { "dimension": "ownership", "status": "covered", "notes": "Sequence archive, variation curator, laboratory, clinical reviewer, data steward and access authority are not conflated." }, { "dimension": "validation", "status": "covered", "notes": "Syntax, reference allele, coordinate, normalization, digest, concordance, translation and round-trip checks are explicit." }, { "dimension": "access", "status": "covered", "notes": "Consent, DUO permitted use, purpose, role, jurisdiction, sensitivity, minimum projection and audit are represented." }, { "dimension": "retention and deletion", "status": "covered", "notes": "Archive commitments, withdrawal, correction, legal hold, identifier continuity and tombstones are non-cascading." }, { "dimension": "interoperability", "status": "covered", "notes": "VRS, refget, HGVS, VCF, SPDI, FHIR, Beacon and JSON-LD projections pin releases and disclose loss." } ], "known_omissions": [ "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." ], "conflicts": [ "The registered slash-name combines immutable sequence content and variation relative to a reference; a mandatory root discriminator is required.", "HGVS, SPDI, VCF, VRS, RefSNP, ClinVar and EVA identifiers have different defining contexts and cannot be collapsed without pinned normalization and round-trip evidence.", "A molecular variant, an observed call, a genotype, a predicted consequence and a condition-specific classification are separate assertions with different masters." ], "regional_assumptions": [ "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." ], "adversarial_checks": [ "Reject a variant without a resolvable reference sequence version or digest, coordinate convention, defining state and normalization profile.", "Reject accession without version where content may change and reject assembly nickname as sufficient coordinate identity.", "Reject reverse-complement, boundary-base, interval-end, circular-wrap or multi-allelic transformations without explicit rules and tests.", "Reject a shared HGVS, SPDI, VCF, rs or label string as proof of molecular identity without source-release and normalization evidence.", "Reject predicted molecular consequence represented as experimentally observed function or clinical significance.", "Reject merge, split, deprecation, withdrawal or replacement that destroys prior identifiers, evidence or external references.", "Reject person-level sequence content, calls or linked identifiers disclosed without purpose, consent, permitted use, minimum-necessary scope and audit." ] }, "researchAdjudication": { "providerMode": "single-provider-waiver", "activeProviders": [ "codex" ], "waivedProviders": [ "claude", "grok" ], "providerPolicy": { "contract_version": "1.0.0", "mode": "single-provider-waiver", "effective_at": "2026-09-06T00:00:00Z", "scope": "Canonical single-stream subject-model research after the six-workstream consolidation", "active_providers": [ "codex" ], "waived_providers": [ { "provider": "claude", "authorized_by": "repository owner", "authorized_at": "2026-09-06T00:00:00Z", "reason": "Claude produced no result on prior 1800-second and 900-second attempts and again timed out on bounded 600-second Sonnet and 300-second Haiku passes. The owner prioritized completion over provider availability." }, { "provider": "grok", "authorized_by": "repository owner", "authorized_at": "2026-09-06T00:00:00Z", "reason": "The repository owner authorized completion without Grok when Grok is unavailable, slow or schema-invalid. Grok may still be attempted as a bounded supplemental reviewer, but its failure never blocks a valid Claude plus no-tools result." } ], "review_rule": "Codex may complete source-grounded fallback research after bounded Claude and Grok attempts fail. It requires a separate no-tools adversarial audit and remains reviewable-draft with a visible absence-of-external-review hold.", "supplemental_provider_attempts": [ { "provider": "claude", "required": false, "maximum_attempts": 1, "failure_policy": "record-and-continue", "admission_rule": "Use only a locally schema-valid result whose sources and boundaries survive adjudication." }, { "provider": "grok", "required": false, "maximum_attempts": 1, "failure_policy": "record-and-continue", "admission_rule": "Use only a locally schema-valid result whose sources and boundaries survive adjudication." } ] }, "boundaryDecision": { "entry_kind": "aggregate", "status": "reclassified", "rationale": "The registry-plane value standalone-mm does not identify the subject kind. The slash-name combines content-addressed sequence and reference-relative molecular variation, so a governed aggregate with a mandatory sequence, variant or combined-package discriminator is required." }, "decisions": [ { "concept": "Sequence and variant aggregate boundary", "disposition": "accepted-with-mandatory-discriminator", "rationale": "Sequence content may exist independently while a variation requires a reference context; the discriminator prevents their identities and lifecycle from being collapsed." }, { "concept": "WM-LIV-011 parent signal", "disposition": "held-as-reference", "rationale": "The registered parent remains navigational until reviewed and does not authorize this model to own organism, genome, chromosome, gene or specimen masters." }, { "concept": "Sequence identity chain", "disposition": "accepted", "rationale": "Authoritative accession plus version and canonical content digest are retained together with molecule, alphabet, length, topology, collection and source authority." }, { "concept": "Molecular variation identity", "disposition": "accepted-with-reference-context", "rationale": "Defining identity includes explicit sequence reference, coordinate convention, location, reference and alternate state, class, normalization algorithm and identifier version." }, { "concept": "Variant, call, genotype and interpretation distinction", "disposition": "kept-distinct", "rationale": "A molecular definition, an observation from an assay, a person-level genotype, predicted consequence and condition-specific clinical assertion have separate masters and provenance." }, { "concept": "HGVS, SPDI, VCF and archive accessions", "disposition": "accepted-as-versioned-expressions-and-mappings", "rationale": "Source-specific expressions and identifiers do not prove cross-system molecular equivalence without pinned references, normalization and round-trip evidence." }, { "concept": "Assembly projection and lift-over", "disposition": "accepted-as-qualified-candidate-mapping", "rationale": "Every projection retains source and target assemblies, alignment resource, orientation, method, uncertainty, validation and semantic loss; it never silently rewrites identity." }, { "concept": "Clinical and functional meaning", "disposition": "externalized", "rationale": "Sequence Ontology consequences, ClinGen or ACMG criteria, ClinVar classifications and clinical decisions are linked assertions, not intrinsic properties of the molecular variant." }, { "concept": "Genomic privacy and permitted use", "disposition": "accepted-with-deny-by-default-access", "rationale": "Person or specimen linkage, consent, purpose, DUO permitted use, jurisdiction, minimum necessity and audit govern disclosure independently from public molecular knowledge." }, { "concept": "Provider waiver and local no-tools audit", "disposition": "accepted-with-mandatory-hold", "rationale": "One bounded Claude Sonnet attempt and one bounded Grok attempt timed out. Codex separately audits the frozen validated result and comparison without acquiring new facts, so assurance remains reviewable-draft." } ], "publicationHolds": [ "Absence-of-external-review hold: the bounded Claude Sonnet and Grok attempts timed out before producing admissible results; no external result was admitted.", "Relation hold: WM-LIV-011 remains a reference until its registered parent direction and biological scope are jointly reviewed.", "Boundary hold: organisms, specimens, persons, consent, assays, reads, alignments, calls, genotypes, frequencies, features, phenotypes, diseases, interpretations and decisions remain external masters.", "Reference hold: every usable coordinate or expression requires an immutable sequence version or digest, collection or assembly release, coordinate convention and normalization profile.", "Profile hold: pangenome, mitochondrial, repeat, cytogenetic, copy-number, structural, somatic, non-human and clinical profiles require specialist review.", "Maturity hold: FHIR MolecularSequence is Trial Use, VRS 2.1 is under ballot and the ACMG/AMP replacement is in development; production mappings must pin approved releases.", "Privacy hold: consent, DUO permitted use, purpose, jurisdiction, minimum-necessary disclosure, security, retention and audit must be bound before person-level genomic use.", "Interoperability hold: VRS, refget, HGVS, VCF, SPDI, FHIR, Beacon and archive mappings require exact releases, conformance, normalization, round-trip and semantic-loss tests.", "Clinical hold: no pathogenicity, functional effect, disease association or treatment inference is approved by this molecular definition.", "Completeness hold: the 24-source draft is broad but does not claim universal species, reference, nomenclature, laboratory, clinical, legal or operational coverage.", "Independent external review was explicitly waived by the repository owner; this codex-only result remains a reviewable draft." ], "deferredResearch": [ "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." ] }, "statistics": { "sources": 24, "bundles": 6, "layers": 12, "findings": 24, "questions": 72, "artifacts": 24, "functions": 10 } }