# Vercy AI instruction - YAML 1.2 (JSON-compatible) { "vercy": "1.0-draft", "publication": { "status": "published", "adjudicationStatus": "reviewable-draft", "publishableCanonical": false, "generatedAt": "2026-10-06T21:05:33Z", "synthesisSha256": "6a7e148618505c6107164d58810385c1a9382253eb2face5938d908e0e0a656b", "providerMode": "single-provider-waiver", "providers": [ "Codex" ], "waivedProviders": [ "Claude", "Grok" ] }, "metaModel": { "id": "WM-LIV-013", "registryId": "vr.wm-liv-013", "name": "Gene / Genomic Feature", "version": "0.1.0", "previousVersions": [], "entryKind": "entity", "family": "World Models", "category": "Physical world and living systems", "industry": [ "Cross-industry" ], "domain": [ "PHY.LIV.MOL" ], "tags": [ "gene", "genomic", "feature", "phy.liv.mol" ], "status": "published" }, "canonicalUrl": "https://ver.cy/models/wm-liv-013-gene-genomic-feature/", "sourceUrl": "https://github.com/ver-cy/world-models/tree/feat/mega-model-registry/research/runs/wm-liv-013", "model": { "registry_id": "vr.wm-liv-013", "model_id": "WM-LIV-013", "name": "Gene / Genomic Feature", "entry_kind": "entity", "purpose": "Maintain a reusable, evidence-qualified reference to one gene or genomic feature across annotation revisions and sequence contexts.", "scope_statement": "One identified feature reference, including its type, names, versioned placements, structural links and attributed annotations. A gene is a feature profile, not a compulsory template for every feature. The root denotes a biological feature as described by curators, not a physical molecule, whole assembly, variant observation or patient record. Proposed local governance and record operations are design choices, not requirements imposed by the cited standards.", "in_scope": [ "Master and provisional feature identity with taxon and namespace context", "Zero or more versioned placements, explicit unknown mapping status and feature relations", "Attributed structural and functional assertions, exception evidence and local record revisions", "Candidate format mappings, controlled access and local curation operations" ], "out_of_scope": [ "Assembly creation and sequence archive lifecycle", "Variant identity, genotypes, personal genomes and clinical interpretation", "Protein master records, specimen assays and expression measurement lifecycle", "Experimental manipulation, sequence engineering, biological protocols and operational hazard procedures", "Universal gene naming, universal gene structure and automatic cross-species equivalence" ], "boundary_notes": [ { "neighbor": "WM-LIV-011 Genome / Genomic Assembly", "distinction": "Registry parent is navigational context. Placements reference versioned assemblies when available; the feature does not inherit assembly ownership or require a whole-assembly record for every standalone sequence.", "source_refs": [ "SRC-003", "SRC-004" ] }, { "neighbor": "WM-LIV-012 Genomic Sequence / Variant", "distinction": "Sequence and variant masters remain separate. Feature coordinates and variant overlap do not identify an allele, genotype or sample observation.", "source_refs": [ "SRC-003", "SRC-004" ] }, { "neighbor": "WM-LIV-014 Protein / Biomolecule", "distinction": "A gene, transcript feature, CDS and product are separate identities. Functional evidence retains its actual product subject; product lifecycle is external.", "source_refs": [ "SRC-002", "SRC-005" ] }, { "neighbor": "WM-LIV-015 Phenotype / Trait and observation records", "distinction": "Only attributed association references belong here. Trait measurement, expression experiments, diagnosis and causal evaluation remain external.", "source_refs": [ "SRC-005", "SRC-006" ] }, { "neighbor": "Other WM-LIV-013 feature instances", "distinction": "Part, derivation and comparison edges link distinct feature records. Shared parts do not require a tree or imply cross-reference equivalence.", "source_refs": [ "SRC-001", "SRC-003" ] } ] }, "sources": [ { "id": "SRC-001", "title": "Generic Feature Format Version 3 (GFF3)", "organization": "Sequence Ontology project", "url": "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md", "version_or_date": "Specification 1.26, 18 August 2020; mutable branch, commit pin pending", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:03:24Z", "relevance": "Feature typing, multipart locations and relationship encoding; selected format sections reviewed." }, { "id": "SRC-002", "title": "HGNC Guidelines", "organization": "HUGO Gene Nomenclature Committee", "url": "https://www.genenames.org/about/guidelines/", "version_or_date": "Undated live guidelines; reviewed 2026-10-06 UTC; immutable snapshot pending", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:03:24Z", "relevance": "Human nomenclature scope and taxon-qualified names; not a universal naming authority." }, { "id": "SRC-003", "title": "The DDBJ/ENA/GenBank Feature Table Definition", "organization": "International Nucleotide Sequence Database Collaboration", "url": "https://www.insdc.org/submitting-standards/feature-table/", "version_or_date": "Version 11.4, April 2026 as displayed; snapshot pending", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:03:24Z", "relevance": "Feature keys, qualifiers and location operators; selected sections 3.2-3.4 reviewed." }, { "id": "SRC-004", "title": "GFF3 format", "organization": "National Center for Biotechnology Information", "url": "https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/file-formats/annotation-files/about-ncbi-gff3/", "version_or_date": "Datasets v2 documentation; undated page; reviewed 2026-10-06 UTC", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:03:24Z", "relevance": "Annotation dialect, accession versions, export-local IDs and exceptional feature representations." }, { "id": "SRC-005", "title": "Introduction to GO annotations", "organization": "Gene Ontology Consortium", "url": "https://geneontology.org/docs/go-annotations/", "version_or_date": "Undated live documentation; reviewed 2026-10-06 UTC; release pin pending", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:03:24Z", "relevance": "Evidence-qualified gene product assertions and explicit negative annotations." }, { "id": "SRC-006", "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": "2026-10-06T21:03:24Z", "relevance": "Conceptual alignment for attribution, derivation and revisions; no conformance claim." } ], "structure": { "bundles": [ { "id": "bundle-identity", "name": "Identity and classification", "description": "Establish what feature is being referenced without conflating symbols with identity.", "rationale": "Separate this concern so unknowns and competing assertions can be reviewed without silently changing other feature context.", "source_refs": [ "SRC-002", "SRC-004", "SRC-001", "SRC-003" ], "layers": [ { "id": "layer-identification", "name": "Master identity", "description": "Record an authority-scoped identifier or a clearly provisional local identity.", "source_refs": [ "SRC-002", "SRC-004" ], "findings": [ { "id": "identity-record", "name": "Namespace and taxon identity", "description": "Record an authority-scoped identifier or a clearly provisional local identity. Candidate answer groups require an adoption schema; source citations motivate this proposed design.", "source_refs": [ "SRC-002", "SRC-004" ], "questions": [ { "id": "identity-record-q1", "text": "Which namespace and master identifier identify this feature independently of a display symbol?", "kind": "identity", "answer_data": [ "identity-record-master-key" ] }, { "id": "identity-record-q2", "text": "Which taxon and organism context disambiguate this feature from similarly named features?", "kind": "classification", "answer_data": [ "identity-record-taxon-context" ] }, { "id": "identity-record-q3", "text": "Who may assert or reconcile this identity, and what happens when no authority identifier exists?", "kind": "authority", "answer_data": [ "identity-record-identity-authority" ] } ], "data_elements": [ { "id": "identity-record-master-key", "name": "Master key", "description": "Namespace, master accession and identifier status; export-local IDs remain scoped to their artifact.", "value_kind": "identifier", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-002", "SRC-004" ] }, { "id": "identity-record-taxon-context", "name": "Taxon context", "description": "Taxon reference, taxonomy release, supplied organism label and unresolved classification status.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-002", "SRC-004" ] }, { "id": "identity-record-identity-authority", "name": "Identity authority", "description": "Curator role, master binding, provisional UUID, reconciliation evidence and unresolved candidates.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-002", "SRC-004" ] } ], "artifacts": [ { "id": "identity-record-artifact", "name": "Namespace and taxon identity evidence record", "description": "Versioned local assertion and evidence envelope for namespace and taxon identity; external source payloads remain separately governed.", "media_or_form": [ "application/json", "reference to source artifact" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then local UUID. Serial revisions use monotonic revision keys, never dates as identity.", "source_refs": [ "SRC-002", "SRC-004" ] } ], "inline_only_rationale": null } ] }, { "id": "layer-typing", "name": "Type and naming", "description": "Separate type assertions and naming authority from biological function.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "findings": [ { "id": "classification-record", "name": "Feature class and labels", "description": "Separate type assertions and naming authority from biological function. Candidate answer groups require an adoption schema; source citations motivate this proposed design.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "questions": [ { "id": "classification-record-q1", "text": "Which controlled feature class and vocabulary release apply, and which local label was imported?", "kind": "classification", "answer_data": [ "classification-record-feature-type" ] }, { "id": "classification-record-q2", "text": "Which preferred name, symbol and aliases apply in this naming authority and taxon?", "kind": "identity", "answer_data": [ "classification-record-labels" ] }, { "id": "classification-record-q3", "text": "How are unnamed, predicted, pseudogenic or regulatory features represented without forcing a protein-coding profile?", "kind": "exception", "answer_data": [ "classification-record-profile-status" ] } ], "data_elements": [ { "id": "classification-record-feature-type", "name": "Feature type", "description": "Term identifier, vocabulary release, source key and mapping status; coding status is a separate qualified assertion.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] }, { "id": "classification-record-labels", "name": "Labels", "description": "Authority, preferred label, aliases, language, status and release; official symbols are optional for generic features.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] }, { "id": "classification-record-profile-status", "name": "Profile status", "description": "Applicable profile, evidence, disputed type and fields marked unknown or not applicable.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "artifacts": [ { "id": "classification-record-artifact", "name": "Feature class and labels evidence record", "description": "Versioned local assertion and evidence envelope for feature class and labels; external source payloads remain separately governed.", "media_or_form": [ "application/json", "reference to source artifact" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then local UUID. Serial revisions use monotonic revision keys, never dates as identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "bundle-placement", "name": "Sequence placement", "description": "Keep coordinates interpretable within their exact reference context.", "rationale": "Separate this concern so unknowns and competing assertions can be reviewed without silently changing other feature context.", "source_refs": [ "SRC-003", "SRC-004", "SRC-001" ], "layers": [ { "id": "layer-reference-context", "name": "Reference binding", "description": "A placement is a contextual assertion; it is not the stable feature identity.", "source_refs": [ "SRC-003", "SRC-004" ], "findings": [ { "id": "placement-record", "name": "Versioned placement", "description": "A placement is a contextual assertion; it is not the stable feature identity. Candidate answer groups require an adoption schema; source citations motivate this proposed design.", "source_refs": [ "SRC-003", "SRC-004" ], "questions": [ { "id": "placement-record-q1", "text": "Which sequence accession and version anchor each placement, and is an assembly accession available?", "kind": "spatial", "answer_data": [ "placement-record-reference-binding" ] }, { "id": "placement-record-q2", "text": "Which coordinate convention, strand and interval semantics govern this placement?", "kind": "constraint", "answer_data": [ "placement-record-coordinate-binding" ] }, { "id": "placement-record-q3", "text": "How is an unmapped or multiply placed feature represented without selecting an unsupported location?", "kind": "exception", "answer_data": [ "placement-record-placement-alternatives" ] } ], "data_elements": [ { "id": "placement-record-reference-binding", "name": "Reference binding", "description": "Sequence accession.version, assembly accession.version when applicable, annotation release and placement status.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-003", "SRC-004" ] }, { "id": "placement-record-coordinate-binding", "name": "Coordinate binding", "description": "Origin, closure, units, start, end, strand, sequence topology and representation profile.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-003", "SRC-004" ] }, { "id": "placement-record-placement-alternatives", "name": "Placement alternatives", "description": "Explicit unmapped status or candidate placements with method, evidence, confidence and curator selection status.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-003", "SRC-004" ] } ], "artifacts": [ { "id": "placement-record-artifact", "name": "Versioned placement evidence record", "description": "Versioned local assertion and evidence envelope for versioned placement; external source payloads remain separately governed.", "media_or_form": [ "application/json", "reference to source artifact" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then local UUID. Serial revisions use monotonic revision keys, never dates as identity.", "source_refs": [ "SRC-003", "SRC-004" ] } ], "inline_only_rationale": null } ] }, { "id": "layer-location-detail", "name": "Location exceptions", "description": "Preserve source location semantics rather than flattening every feature into one exact interval.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ], "findings": [ { "id": "location-record", "name": "Multipart and uncertain location", "description": "Preserve source location semantics rather than flattening every feature into one exact interval. Candidate answer groups require an adoption schema; source citations motivate this proposed design.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ], "questions": [ { "id": "location-record-q1", "text": "Which ordered segments and location operators define this feature placement?", "kind": "composition", "answer_data": [ "location-record-location-expression" ] }, { "id": "location-record-q2", "text": "Which endpoints or segments are partial, uncertain or exceptional?", "kind": "quality", "answer_data": [ "location-record-location-quality" ] }, { "id": "location-record-q3", "text": "Which length is reported, and how were its units and calculation basis determined?", "kind": "measurement", "answer_data": [ "location-record-derived-length" ] } ], "data_elements": [ { "id": "location-record-location-expression", "name": "Location expression", "description": "Original expression, ordered segments, join or order semantics, remote references and source format.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] }, { "id": "location-record-location-quality", "name": "Location quality", "description": "Endpoint bounds, partial status, circular origin crossing, exception reason and supporting evidence.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] }, { "id": "location-record-derived-length", "name": "Derived length", "description": "Value, bp or nt unit, genomic span versus joined length, included segments, method and uncertainty; no inferred expression level.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] } ], "artifacts": [ { "id": "location-record-artifact", "name": "Multipart and uncertain location evidence record", "description": "Versioned local assertion and evidence envelope for multipart and uncertain location; external source payloads remain separately governed.", "media_or_form": [ "application/json", "reference to source artifact" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then local UUID. Serial revisions use monotonic revision keys, never dates as identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "bundle-structure", "name": "Feature relationships", "description": "Express a feature graph without assuming one transcript or one parent.", "rationale": "Separate this concern so unknowns and competing assertions can be reviewed without silently changing other feature context.", "source_refs": [ "SRC-001", "SRC-003", "SRC-002", "SRC-004", "SRC-005" ], "layers": [ { "id": "layer-part-relations", "name": "Structural membership", "description": "Store typed edges and independently resolvable endpoints.", "source_refs": [ "SRC-001", "SRC-003" ], "findings": [ { "id": "part-record", "name": "Parts and derivation", "description": "Store typed edges and independently resolvable endpoints. Candidate answer groups require an adoption schema; source citations motivate this proposed design.", "source_refs": [ "SRC-001", "SRC-003" ], "questions": [ { "id": "part-record-q1", "text": "Which features are parts of this feature under the selected annotation profile?", "kind": "composition", "answer_data": [ "part-record-part-edges" ] }, { "id": "part-record-q2", "text": "Which links express derivation rather than part membership?", "kind": "relationship", "answer_data": [ "part-record-derivation-edges" ] }, { "id": "part-record-q3", "text": "How are shared parts, disconnected references and cycles checked before an edge is accepted?", "kind": "validation", "answer_data": [ "part-record-graph-check" ] } ], "data_elements": [ { "id": "part-record-part-edges", "name": "Part edges", "description": "Child and parent references, relation type, annotation release and evidence.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003" ] }, { "id": "part-record-derivation-edges", "name": "Derivation edges", "description": "Source and target feature identifiers, typed relation, assertion provenance and applicable profile.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003" ] }, { "id": "part-record-graph-check", "name": "Graph check", "description": "Endpoint resolution, allowed relation profile, shared-parent support, cycle result and unresolved errors.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-003" ] } ], "artifacts": [ { "id": "part-record-artifact", "name": "Parts and derivation evidence record", "description": "Versioned local assertion and evidence envelope for parts and derivation; external source payloads remain separately governed.", "media_or_form": [ "application/json", "reference to source artifact" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then local UUID. Serial revisions use monotonic revision keys, never dates as identity.", "source_refs": [ "SRC-001", "SRC-003" ] } ], "inline_only_rationale": null } ] }, { "id": "layer-products", "name": "Transcripts and products", "description": "Distinguish a genomic feature from its transcript or protein product and from profile selections.", "source_refs": [ "SRC-002", "SRC-004", "SRC-005" ], "findings": [ { "id": "product-record", "name": "Product correspondence", "description": "Distinguish a genomic feature from its transcript or protein product and from profile selections. Candidate answer groups require an adoption schema; source citations motivate this proposed design.", "source_refs": [ "SRC-002", "SRC-004", "SRC-005" ], "questions": [ { "id": "product-record-q1", "text": "Which transcript or protein accessions are linked to the feature and by which assertion?", "kind": "relationship", "answer_data": [ "product-record-product-links" ] }, { "id": "product-record-q2", "text": "Which coding constraints or translation exceptions apply to the selected CDS profile?", "kind": "constraint", "answer_data": [ "product-record-coding-context" ] }, { "id": "product-record-q3", "text": "Which transcript selection policy applies for this use, and what alternatives remain?", "kind": "decision", "answer_data": [ "product-record-selection-policy" ] } ], "data_elements": [ { "id": "product-record-product-links", "name": "Product links", "description": "Product accession.version, subject feature, relation, source release and correspondence evidence.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-004", "SRC-005" ] }, { "id": "product-record-coding-context", "name": "Coding context", "description": "CDS phase, genetic-code reference, completeness, source exception and validation status; absent for inapplicable feature types.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-002", "SRC-004", "SRC-005" ] }, { "id": "product-record-selection-policy", "name": "Selection policy", "description": "Use context, policy version, selected accession, alternatives and selection rationale; no universal canonical transcript.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-002", "SRC-004", "SRC-005" ] } ], "artifacts": [ { "id": "product-record-artifact", "name": "Product correspondence evidence record", "description": "Versioned local assertion and evidence envelope for product correspondence; external source payloads remain separately governed.", "media_or_form": [ "application/json", "reference to source artifact" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then local UUID. Serial revisions use monotonic revision keys, never dates as identity.", "source_refs": [ "SRC-002", "SRC-004", "SRC-005" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "bundle-annotation", "name": "Annotation and recognition", "description": "Qualify biological assertions with their evidence and actual subject.", "rationale": "Separate this concern so unknowns and competing assertions can be reviewed without silently changing other feature context.", "source_refs": [ "SRC-005", "SRC-006", "SRC-002", "SRC-004" ], "layers": [ { "id": "layer-functional-assertions", "name": "Function assertions", "description": "Link assertions to the relevant gene product or explicitly declared subject without inferring clinical effect.", "source_refs": [ "SRC-005", "SRC-006" ], "findings": [ { "id": "function-record", "name": "Evidence-qualified function", "description": "Link assertions to the relevant gene product or explicitly declared subject without inferring clinical effect. Candidate answer groups require an adoption schema; source citations motivate this proposed design.", "source_refs": [ "SRC-005", "SRC-006" ], "questions": [ { "id": "function-record-q1", "text": "Which subject, relation, ontology term and evidence reference form each functional assertion?", "kind": "evidence", "answer_data": [ "function-record-functional-assertions" ] }, { "id": "function-record-q2", "text": "Which assertions are explicitly negated, disputed or absent from the available annotation?", "kind": "exception", "answer_data": [ "function-record-assertion-status" ] }, { "id": "function-record-q3", "text": "Which method, curator and biological context support the assertion?", "kind": "provenance", "answer_data": [ "function-record-assertion-context" ] } ], "data_elements": [ { "id": "function-record-functional-assertions", "name": "Functional assertions", "description": "Subject accession, relation, term, evidence code, reference and annotation release.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-005", "SRC-006" ] }, { "id": "function-record-assertion-status", "name": "Assertion status", "description": "Qualifier, competing assertion references and unknown status; missing annotation is not a negative result.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-005", "SRC-006" ] }, { "id": "function-record-assertion-context", "name": "Assertion context", "description": "Experimental or computational evidence class, attribution, context extension and creation or revision time.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-005", "SRC-006" ] } ], "artifacts": [ { "id": "function-record-artifact", "name": "Evidence-qualified function evidence record", "description": "Versioned local assertion and evidence envelope for evidence-qualified function; external source payloads remain separately governed.", "media_or_form": [ "application/json", "reference to source artifact" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then local UUID. Serial revisions use monotonic revision keys, never dates as identity.", "source_refs": [ "SRC-005", "SRC-006" ] } ], "inline_only_rationale": null } ] }, { "id": "layer-recognition", "name": "Recognition and comparison", "description": "Record recognition evidence and external relationship claims without turning similarity into identity.", "source_refs": [ "SRC-002", "SRC-004", "SRC-006" ], "findings": [ { "id": "recognition-record", "name": "Candidate correspondence", "description": "Record recognition evidence and external relationship claims without turning similarity into identity. Candidate answer groups require an adoption schema; source citations motivate this proposed design.", "source_refs": [ "SRC-002", "SRC-004", "SRC-006" ], "questions": [ { "id": "recognition-record-q1", "text": "What sequence alignment or annotation evidence supports recognition of this feature?", "kind": "evidence", "answer_data": [ "recognition-record-recognition-evidence" ] }, { "id": "recognition-record-q2", "text": "Which external comparative relationships are asserted, with what type and provenance?", "kind": "relationship", "answer_data": [ "recognition-record-comparative-links" ] }, { "id": "recognition-record-q3", "text": "Which competing loci, paralog candidates or contradictory evidence prevent confident correspondence?", "kind": "quality", "answer_data": [ "recognition-record-recognition-limits" ] } ], "data_elements": [ { "id": "recognition-record-recognition-evidence", "name": "Recognition evidence", "description": "Evidence artifact references, source feature, target reference, method version and acceptance decision.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-004", "SRC-006" ] }, { "id": "recognition-record-comparative-links", "name": "Comparative links", "description": "Target feature and taxon, relationship label, method, source release and uncertainty; no inferred one-to-one equivalence.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-004", "SRC-006" ] }, { "id": "recognition-record-recognition-limits", "name": "Recognition limits", "description": "Candidate references, ambiguity reason, evidence limits and reviewer disposition; automated resolution may remain refused.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-002", "SRC-004", "SRC-006" ] } ], "artifacts": [ { "id": "recognition-record-artifact", "name": "Candidate correspondence evidence record", "description": "Versioned local assertion and evidence envelope for candidate correspondence; external source payloads remain separately governed.", "media_or_form": [ "application/json", "reference to source artifact" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then local UUID. Serial revisions use monotonic revision keys, never dates as identity.", "source_refs": [ "SRC-002", "SRC-004", "SRC-006" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "bundle-continuity", "name": "Curation continuity", "description": "Keep revision history distinct from biological change and mapping claims.", "rationale": "Separate this concern so unknowns and competing assertions can be reviewed without silently changing other feature context.", "source_refs": [ "SRC-004", "SRC-006", "SRC-001", "SRC-003" ], "layers": [ { "id": "layer-revision", "name": "Revision lineage", "description": "Use local revision and supersession assertions with accountable attribution.", "source_refs": [ "SRC-004", "SRC-006" ], "findings": [ { "id": "revision-record", "name": "Feature record lifecycle", "description": "Use local revision and supersession assertions with accountable attribution. Candidate answer groups require an adoption schema; source citations motivate this proposed design.", "source_refs": [ "SRC-004", "SRC-006" ], "questions": [ { "id": "revision-record-q1", "text": "What is the local record state, and which evidence supports a revision, split, merge or withdrawal?", "kind": "lifecycle", "answer_data": [ "revision-record-revision-state" ] }, { "id": "revision-record-q2", "text": "Which source release time, curation event time and ingestion time apply to this revision?", "kind": "temporal", "answer_data": [ "revision-record-revision-times" ] }, { "id": "revision-record-q3", "text": "Which curator may approve this revision and how are concurrent or conflicting edits resolved?", "kind": "authority", "answer_data": [ "revision-record-revision-authority" ] } ], "data_elements": [ { "id": "revision-record-revision-state", "name": "Revision state", "description": "Draft, reviewed, superseded or withdrawn state; predecessor and successor references, change type and rationale.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-004", "SRC-006" ] }, { "id": "revision-record-revision-times", "name": "Revision times", "description": "Separate timestamps or source dates with precision, time zone and provenance; do not fabricate seconds for source date-only values.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-004", "SRC-006" ] }, { "id": "revision-record-revision-authority", "name": "Revision authority", "description": "Role, expected prior revision, review decision, conflict record and source authority; local edits cannot rename external masters.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-004", "SRC-006" ] } ], "artifacts": [ { "id": "revision-record-artifact", "name": "Feature record lifecycle evidence record", "description": "Versioned local assertion and evidence envelope for feature record lifecycle; external source payloads remain separately governed.", "media_or_form": [ "application/json", "reference to source artifact" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then local UUID. Serial revisions use monotonic revision keys, never dates as identity.", "source_refs": [ "SRC-004", "SRC-006" ] } ], "inline_only_rationale": null } ] }, { "id": "layer-projection", "name": "Projection and exchange", "description": "Preserve a source representation and expose loss or ambiguity in mappings.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-006" ], "findings": [ { "id": "projection-record", "name": "Transformation accountability", "description": "Preserve a source representation and expose loss or ambiguity in mappings. Candidate answer groups require an adoption schema; source citations motivate this proposed design.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-006" ], "questions": [ { "id": "projection-record-q1", "text": "Which source dialect and target profile define an import or export mapping?", "kind": "interoperability", "answer_data": [ "projection-record-format-binding" ] }, { "id": "projection-record-q2", "text": "What transformation evidence supports a proposed coordinate remapping?", "kind": "process", "answer_data": [ "projection-record-transform-evidence" ] }, { "id": "projection-record-q3", "text": "Which round-trip losses or semantic changes require refusal or curator review?", "kind": "validation", "answer_data": [ "projection-record-projection-check" ] } ], "data_elements": [ { "id": "projection-record-format-binding", "name": "Format binding", "description": "Format version, dialect, vocabulary release, field mapping and unsupported constructs.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-006" ] }, { "id": "projection-record-transform-evidence", "name": "Transform evidence", "description": "Input and output reference versions, external method version, parameters, mapping evidence and unmapped or multiple results.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-006" ] }, { "id": "projection-record-projection-check", "name": "Projection check", "description": "Identity scope, uncertainty preservation, relation preservation, loss report and disposition; no coordinate overwrite by default.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-006" ] } ], "artifacts": [ { "id": "projection-record-artifact", "name": "Transformation accountability evidence record", "description": "Versioned local assertion and evidence envelope for transformation accountability; external source payloads remain separately governed.", "media_or_form": [ "application/json", "reference to source artifact" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then local UUID. Serial revisions use monotonic revision keys, never dates as identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-006" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "bundle-stewardship", "name": "Stewardship and assurance", "description": "Govern local evidence and access without claiming ownership of biological subjects.", "rationale": "Separate this concern so unknowns and competing assertions can be reviewed without silently changing other feature context.", "source_refs": [ "SRC-006", "SRC-005" ], "layers": [ { "id": "layer-evidence-custody", "name": "Evidence custody", "description": "Keep supporting artifacts attributable and retrievable under adopting policy.", "source_refs": [ "SRC-006" ], "findings": [ { "id": "custody-record", "name": "Artifacts and rights", "description": "Keep supporting artifacts attributable and retrievable under adopting policy. Candidate answer groups require an adoption schema; source citations motivate this proposed design.", "source_refs": [ "SRC-006" ], "questions": [ { "id": "custody-record-q1", "text": "Which stewardship role maintains this feature record and which source reuse conditions apply?", "kind": "ownership", "answer_data": [ "custody-record-stewardship" ] }, { "id": "custody-record-q2", "text": "Which artifact identifiers, versions and digests allow an assertion to be traced?", "kind": "provenance", "answer_data": [ "custody-record-evidence-index" ] }, { "id": "custody-record-q3", "text": "Which local retention policy governs withdrawn evidence and what minimal tombstone may remain?", "kind": "retention", "answer_data": [ "custody-record-retention-policy" ] } ], "data_elements": [ { "id": "custody-record-stewardship", "name": "Stewardship", "description": "Record steward, master-system binding, license reference and reuse decision; stewardship is not ownership of a gene.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-006" ] }, { "id": "custody-record-evidence-index", "name": "Evidence index", "description": "Master artifact ID, version, location, digest, creator and assertion linkage; a digest does not establish scientific truth.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-006" ] }, { "id": "custody-record-retention-policy", "name": "Retention policy", "description": "Policy reference, disposition authority, hold, deletion scope and safe tombstone; referenced archive deletion is external.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-006" ] } ], "artifacts": [ { "id": "custody-record-artifact", "name": "Artifacts and rights evidence record", "description": "Versioned local assertion and evidence envelope for artifacts and rights; external source payloads remain separately governed.", "media_or_form": [ "application/json", "reference to source artifact" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then local UUID. Serial revisions use monotonic revision keys, never dates as identity.", "source_refs": [ "SRC-006" ] } ], "inline_only_rationale": null } ] }, { "id": "layer-assurance", "name": "Access and acceptance", "description": "Proposed adoption controls protect sensitive linked context and make unresolved assurance visible.", "source_refs": [ "SRC-005", "SRC-006" ], "findings": [ { "id": "assurance-record", "name": "Use limits and readiness", "description": "Proposed adoption controls protect sensitive linked context and make unresolved assurance visible. Candidate answer groups require an adoption schema; source citations motivate this proposed design.", "source_refs": [ "SRC-005", "SRC-006" ], "questions": [ { "id": "assurance-record-q1", "text": "Which audiences may read or export each feature assertion and its linked evidence?", "kind": "access", "answer_data": [ "assurance-record-access-policy" ] }, { "id": "assurance-record-q2", "text": "Which privacy or biological-risk review is required before accepting sensitive context?", "kind": "security", "answer_data": [ "assurance-record-risk-review" ] }, { "id": "assurance-record-q3", "text": "What evidence must be present before this record can be accepted for its stated research use?", "kind": "validation", "answer_data": [ "assurance-record-acceptance-report" ] } ], "data_elements": [ { "id": "assurance-record-access-policy", "name": "Access policy", "description": "Purpose, audience, bundle/layer/finding/artifact scope, restricted linkage and review decision; public feature metadata does not release private evidence.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-005", "SRC-006" ] }, { "id": "assurance-record-risk-review", "name": "Risk review", "description": "Policy reference, reviewer role, sensitivity, permitted metadata and refusal reason; operational biological procedures remain excluded.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-005", "SRC-006" ] }, { "id": "assurance-record-acceptance-report", "name": "Acceptance report", "description": "Identity, profile, coordinate, graph, evidence, access and release checks; unresolved holds; no clinical or universal conformance certification.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-005", "SRC-006" ] } ], "artifacts": [ { "id": "assurance-record-artifact", "name": "Use limits and readiness evidence record", "description": "Versioned local assertion and evidence envelope for use limits and readiness; external source payloads remain separately governed.", "media_or_form": [ "application/json", "reference to source artifact" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then local UUID. Serial revisions use monotonic revision keys, never dates as identity.", "source_refs": [ "SRC-005", "SRC-006" ] } ], "inline_only_rationale": null } ] } ] } ] }, "functions": [ { "id": "fn-resolve-feature", "name": "Resolve a feature reference", "description": "Resolve scoped identifiers against supplied evidence without equating symbols or export IDs. Proposed, unimplemented record operation.", "inputs": [ "Namespace and identifier", "Taxon context", "Candidate master bindings" ], "outputs": [ "Resolved reference with evidence, or unresolved candidate set" ], "preconditions": [ "Adopting policy authorizes the caller and purpose", "Expected local revision is current", "Input authority and taxon context available" ], "effects": [ "Returns a local resolution report; never merges external masters" ], "source_refs": [ "SRC-002", "SRC-004" ] }, { "id": "fn-check-placement", "name": "Check a placement record", "description": "Proposed local profile check; no implemented coordinate engine is claimed. Proposed, unimplemented record operation.", "inputs": [ "Feature revision", "Versioned reference", "Location expression and profile" ], "outputs": [ "Profile check report or refusal with missing context" ], "preconditions": [ "Adopting policy authorizes the caller and purpose", "Expected local revision is current", "Reference version and convention supplied" ], "effects": [ "Flags unsupported or inconsistent placement; does not modify sequence masters" ], "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] }, { "id": "fn-link-assertion", "name": "Link an annotation assertion", "description": "Attach attributed evidence to its declared subject. Proposed, unimplemented record operation.", "inputs": [ "Subject and relation", "Evidence and reference", "Current local revision" ], "outputs": [ "New assertion revision or rejection report" ], "preconditions": [ "Adopting policy authorizes the caller and purpose", "Expected local revision is current", "Evidence retrievable within access policy", "Qualifier and subject type explicit" ], "effects": [ "Adds local evidence linkage; does not infer function or diagnosis" ], "source_refs": [ "SRC-005", "SRC-006" ] }, { "id": "fn-review-edges", "name": "Review feature edges", "description": "Proposed local relation validation against a pinned feature profile. Proposed, unimplemented record operation.", "inputs": [ "Typed edges", "Endpoint revisions", "Allowed relation profile" ], "outputs": [ "Edge acceptance report or unresolved errors" ], "preconditions": [ "Adopting policy authorizes the caller and purpose", "Expected local revision is current", "Endpoints and vocabulary version available" ], "effects": [ "Records shared-part and cycle checks; does not infer biological equivalence" ], "source_refs": [ "SRC-001", "SRC-003" ] }, { "id": "fn-record-projection", "name": "Record a transformation result", "description": "Register evidence from an external mapping operation, including ambiguous and failed outcomes. Proposed, unimplemented record operation.", "inputs": [ "Input and output bindings", "Method and evidence", "Loss report" ], "outputs": [ "Versioned transformation report or rejection" ], "preconditions": [ "Adopting policy authorizes the caller and purpose", "Expected local revision is current", "Both reference versions pinned", "Original source preserved" ], "effects": [ "Adds candidate placement evidence; no automatic lift-over or overwrite" ], "source_refs": [ "SRC-004", "SRC-006" ] }, { "id": "fn-revise-feature", "name": "Revise or retire a local feature record", "description": "Proposed controlled local curation operation with concurrency checks. Proposed, unimplemented record operation.", "inputs": [ "Expected revision", "Patch or retirement rationale", "Curator authorization" ], "outputs": [ "New revision or tombstone proposal, or conflict refusal" ], "preconditions": [ "Adopting policy authorizes the caller and purpose", "Expected local revision is current", "Curator role authorized", "Retention and sensitivity policies evaluated" ], "effects": [ "Preserves resolvable lineage under retention policy; does not mutate external archives" ], "source_refs": [ "SRC-006" ] } ], "composition": [ { "target": "WM-LIV-011", "relation": "REFERENCE", "purpose": "Optional versioned assembly context for a placement; registry parent is not assumed structural inheritance.", "required": false, "source_refs": [ "SRC-004" ] }, { "target": "WM-LIV-012", "relation": "REFERENCE", "purpose": "External sequence reference and optional variant association; sequence and variant lifecycles remain external.", "required": false, "source_refs": [ "SRC-003", "SRC-004" ] }, { "target": "WM-LIV-014", "relation": "REFERENCE", "purpose": "Product master reference with explicit feature-to-product evidence.", "required": false, "source_refs": [ "SRC-004", "SRC-005" ] }, { "target": "WM-LIV-015", "relation": "REFERENCE", "purpose": "Optional attributed phenotype association; observations and causal interpretation are not copied.", "required": false, "source_refs": [ "SRC-005", "SRC-006" ] }, { "target": "WM-LIV-013 feature instance", "relation": "REFERENCE", "purpose": "Typed graph edge between separately identified features; shared parents permitted under a pinned relation profile.", "required": false, "source_refs": [ "SRC-001" ] }, { "target": "GFF3 and INSDC feature table", "relation": "ALIGN", "purpose": "Candidate exchange mappings preserving dialect, local ID scope, location semantics and reported loss.", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] }, { "target": "Gene Ontology annotation model", "relation": "ALIGN", "purpose": "Evidence-qualified product assertion references; not a disease or clinical interpretation engine.", "required": false, "source_refs": [ "SRC-005" ] }, { "target": "PROV-O", "relation": "ALIGN", "purpose": "Conceptual derivation, attribution and revision alignment only.", "required": false, "source_refs": [ "SRC-006" ] } ], "serviceLayers": { "dimension": { "owner_package_requirements": [ "Name the responsible scientific steward and local curator roles without company ownership assignments", "Bind approved master namespaces, taxon scope, reference profiles and adoption schema", "Declare access, reuse, retention and sensitive-context review policies", "Keep reference versions and annotation release selections explicit" ], "namespace_guidance": "Use an adopting-Dimension namespace for local records. Preserve external accession case and version; do not fabricate authority identifiers or use symbols, dates or coordinates as universal identity.", "registry_links": [ "vr.wm-liv-013", "WM-LIV-011", "WM-LIV-012", "WM-LIV-014", "WM-LIV-015" ] }, "canon_and_patch": { "canonicalization_rules": [ "Canonicalize only within a declared namespace and profile; retain the imported representation and mapping report", "Coordinates and symbol changes are assertions, not automatic feature identity changes", "Unknown, unavailable, disputed, absent and not applicable remain distinct" ], "patch_rules": [ "Require expected revision, curator role, change rationale and evidence", "Splits, merges, retyping and accession reconciliation create reviewed lineage links; preserve alternatives", "Refuse silent coordinate convention changes, access expansion or replacement of original evidence" ], "compatibility_rules": [ "Pin vocabulary, assembly, sequence, annotation and mapping versions independently", "Report lossy export explicitly and refuse a target binding unable to retain critical semantics", "Nested answer groups are candidates; executable instance schemas and fixtures remain an adoption hold" ] }, "artifact_rules": { "identity_priority": [ "Authoritative master-system artifact identifier plus explicit revision", "Governed global identifier or IRI", "UUID or ULID assigned by the adopting Dimension" ], "timestamp_rule": "Recorded events use RFC 3339 with seconds and an explicit offset or Z. Keep source event, observation and ingestion times separate. Preserve source date-only precision without inventing a timestamp.", "serial_naming_rule": "Stable artifact ID plus monotonic revision token; descriptive filenames may include dates but dates are never identity.", "integrity_rule": "Record media type, byte length and cryptographic digest when bytes are available; a digest verifies bytes, not biological validity. Source bodies were not fetched by the local HTTP checker in this run." }, "policies": [ "These are proposed local adoption controls; cited biological formats do not confer access authority, legal compliance or clinical readiness", "Reference metadata may be public while linked samples, personal genomes and unpublished evidence remain restricted under the adopting policy", "Do not infer diagnosis, phenotype causality or participant identity from feature annotation", "Biological-risk and controlled-material matters remain at metadata and policy level; experimental instructions are out of scope", "Independent review, live source verification and executable conformance remain visible holds" ], "crud": { "read": [ "Resolve caller purpose and per-scope access before displaying annotations or evidence", "Display version, qualifier, uncertainty and review holds with results" ], "create": [ "Assign scoped provisional identity if no master exists; capture taxon and evidence before promotion", "Explicitly record missing placements and optional product links instead of inventing values" ], "update": [ "Use expected revision and curator approval for identity reconciliation, graph edits and changing evidence", "Retain source representation, local change rationale and conflicting assertions" ], "delete": [ "Retire local feature revisions with resolvable safe tombstones when permitted by retention policy", "Sensitive payload erasure, retention holds and artifact disposal are executed by the adopting storage authority; this model records its decision reference", "Never interpret local deletion as withdrawal of a biological entity or deletion from an external archive" ] }, "roles": [ { "name": "Scientific steward", "responsibilities": [ "Own the local profile and adoption decisions, not the biological gene" ] }, { "name": "Feature curator", "responsibilities": [ "Review identity, evidence and revision proposals within granted scope" ] }, { "name": "Evidence custodian", "responsibilities": [ "Preserve permitted evidence, integrity metadata and retention decisions" ] }, { "name": "Access reviewer", "responsibilities": [ "Assess sensitive context and purpose-bound disclosure" ] }, { "name": "Consumer agent", "responsibilities": [ "Read authorized records and surface ambiguity; refuse unsupported inference" ] } ], "access": { "default_rule": "Apply adopting-Dimension least-privilege policy; no public release of linked evidence is implied by public feature identifiers.", "scopes": [ "bundle", "layer", "finding", "artifact" ], "exceptions": [ "Public export requires a reviewed public profile with sensitive links excluded", "Emergency or exceptional access needs an applicable recorded authority; no automatic bypass" ], "audit_requirements": [ "Reference the adopting audit service for actor, purpose, policy version, operation and result", "Avoid copying sensitive sequence or participant payloads into audit metadata" ] }, "agents_bootstrap": { "filename": "AGENTS.md", "required_fields": [ "Name", "Type", "Specification URL", "Storage type URL", "Interface URL", "Processes URL" ], "read_order": [ "AGENTS.md", "spec.yaml including researchAdjudication holds", "Adopting Dimension policy and pinned subject profiles", "Authorized feature evidence and external master bindings" ] } }, "coverage": { "claim": "Source-grounded proposed structure for one reusable gene or genomic feature reference. Identity, contextual placements, typed relations and attributed evidence are distinct. A separate local no-tools self-audit supports reviewable-draft release only; independent review, source pins, adoption policies and executable conformance remain open.", "confidence": "medium", "checklist": [ { "dimension": "identity", "status": "covered", "notes": "Scoped master and provisional references; symbols are labels" }, { "dimension": "lifecycle", "status": "covered", "notes": "Local revision, supersession and retirement with explicit authority" }, { "dimension": "relationships", "status": "covered", "notes": "Typed feature edges and separate assembly, sequence, product and trait masters" }, { "dimension": "temporal", "status": "covered", "notes": "Source release, event, observation and ingestion time separated" }, { "dimension": "provenance", "status": "covered", "notes": "Evidence, method, attribution and derivation references" }, { "dimension": "ownership", "status": "covered", "notes": "Scientific stewardship roles; no biological ownership claim" }, { "dimension": "validation", "status": "gap", "notes": "Research structure validated; executable instance profile remains a gap" }, { "dimension": "access", "status": "covered", "notes": "Proposed audience and purpose policy at all four scopes" }, { "dimension": "retention and deletion", "status": "covered", "notes": "Policy-bound local retirement and external storage execution" }, { "dimension": "interoperability", "status": "covered", "notes": "Candidate GFF3, INSDC, GO and PROV mappings with loss reports" }, { "dimension": "direct properties", "status": "covered", "notes": "Type, placements, derived length and uncertainties; measured expression external" }, { "dimension": "recognition", "status": "covered", "notes": "Competing evidence and unresolved correspondence" }, { "dimension": "capabilities and operations", "status": "covered", "notes": "Six proposed local record functions; no experimental execution" }, { "dimension": "source verification", "status": "gap", "notes": "Web content reviewed in selected sections; direct HTTP and immutable pins pending" } ], "known_omissions": [ "Graph genome path coordinate profiles and taxon-specific complex loci require additional research", "Exhaustive exchange round-trip mappings, nested data schemas and executable acceptance fixtures are not implemented", "Independent external review and immutable source snapshots remain absent", "Privacy, licensing and biological-risk adoption policies require qualified review; no legal requirements have been researched here", "Orthology inference, sequence alignment, coordinate remapping and expression quantification are external operations" ], "conflicts": [], "regional_assumptions": [ "HGNC guidance applies to its stated nomenclature scope and is not generalized to all organisms", "No jurisdiction-specific legal or clinical conformity is claimed" ], "adversarial_checks": [ "Same symbol in different taxa must not merge features", "GFF3 export-local identity must not become a global accession", "Unknown strand, circular and partial locations must survive profile mapping", "Shared exon and CDS exceptions must not force a simple tree or one protein per gene", "Missing GO annotation must not become a negative function assertion", "Source date-only precision must not become a fabricated event timestamp", "Clinical conclusions and operational biological procedures remain out of scope" ] }, "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": "entity", "status": "accepted", "rationale": "One feature reference retains local identity across attributed annotation revisions. Assemblies, sequence and variant masters, products and observations remain external. The registry standalone-mm value describes a catalogue plane; its parent supplies optional assembly context rather than mandatory inheritance." }, "decisions": [ { "concept": "Root boundary and registry contract", "disposition": "accepted", "rationale": "The frozen registry has no legacy alias and the relation ledger has no rows. All nodes concern the feature reference; the recorded assembly parent is qualified as context without copying the assembly lifecycle." }, { "concept": "Identity record", "disposition": "accepted", "rationale": "Its three questions preserve namespace, taxon and assertion authority. Provisional identity is explicit; symbols and export-local IDs cannot silently become global identity." }, { "concept": "Classification record", "disposition": "accepted with scope limits", "rationale": "Type and naming are separately attributed. Generic features are not forced to have a coding profile or official human gene symbol; vocabulary release remains an adoption dependency." }, { "concept": "Placement record", "disposition": "accepted", "rationale": "An unplaced feature is permitted while an asserted placement needs exact sequence context and convention. Optional assembly composition does not grant permission for ambiguous coordinates." }, { "concept": "Location record", "disposition": "accepted with profile dependency", "rationale": "Ordered segments, original operators, partial boundaries and calculation basis preserve uncertainty. Generic answer groups are insufficient to implement all location constraints without a profile." }, { "concept": "Part record", "disposition": "accepted", "rationale": "Typed graph edges allow shared parts and distinguish derivation. Cycle and endpoint checks are proposed local profile checks, not a claim of an already implemented graph validator." }, { "concept": "Product record", "disposition": "accepted", "rationale": "Feature and product accessions remain distinct. Coding constraints apply only to a selected CDS profile, and transcript selection is use-specific rather than universal." }, { "concept": "Function record", "disposition": "accepted", "rationale": "Assertions retain actual subject, relation, qualifier and evidence. Missing annotations cannot establish negative function, and product function cannot silently become a clinical conclusion." }, { "concept": "Recognition record", "disposition": "qualified", "rationale": "Correspondence and comparative relations are imported assertions with method and uncertainty. No orthology inference or similarity-based automatic identity merge is authorized." }, { "concept": "Revision record", "disposition": "accepted", "rationale": "Local state changes have evidence, lineage, curator authority and concurrency controls. Biological identity changes are not inferred from annotation releases, and date-only sources preserve precision." }, { "concept": "Projection record", "disposition": "accepted as evidence handling", "rationale": "The model registers external transformation results and losses. It does not implement coordinate remapping or claim exchange round-trip conformance." }, { "concept": "Custody record", "disposition": "accepted as local policy design", "rationale": "Stewardship, integrity and disposition questions are accountable local controls. PROV alignment does not establish legal rights, perpetual retention or scientific truth." }, { "concept": "Assurance record", "disposition": "accepted with adoption hold", "rationale": "Audience, sensitivity and acceptance decisions remain profile-bound. Clinical readiness, lawful disclosure and biological-risk procedures are not inferred from reference metadata." }, { "concept": "Functions, composition and service rules", "disposition": "accepted as proposed only", "rationale": "All six functions operate on local evidence records with refusal conditions. Eight composition entries delegate separate masters or name alignments; all eight service sections keep authority, retention and source limits visible." }, { "concept": "Source and conformance assurance", "disposition": "limited", "rationale": "Six primary documents support the concerns through selected web sections. No direct HTTP was attempted and no immutable source body was captured. Nested schemas, fixtures and complex profiles remain deferred." }, { "concept": "External provider independence", "disposition": "waived and held", "rationale": "Claude and Grok were skipped with zero attempts under the owner instruction. The frozen no-tools audit is local Codex self-review and cannot establish independent external agreement." } ], "publicationHolds": [ "Independent external review is absent. Claude and Grok were skipped under the owner-authorized single-provider waiver; the separate local Codex no-tools audit is self-review, not an independent second-provider pass.", "Source verification is incomplete. Selected sections of six primary documents were reviewed through the web tool. Direct HTTP was not attempted because it is blocked in this sandbox; all six statuses are unmeasured, with zero attempts and zero measured HTTP 200 responses. Immutable snapshots, content hashes, version pins and independent claim verification remain pending. The coordinator must run check_sources.py outside the sandbox.", "Nested instance schemas, pinned neighbor bindings, exchange mappings, graph-coordinate and taxon-specific profiles, executable operations and acceptance fixtures remain incomplete. The candidate answer groups and conceptual alignments do not establish runtime conformance.", "Qualified adoption review is required for source licensing, privacy, access, retention, clinical-use boundaries and biological-risk policy. No jurisdiction-specific legal or clinical compliance has been established. Operational biological procedures remain outside scope.", "Independent external review was explicitly waived by the repository owner; this codex-only result remains a reviewable draft." ], "deferredResearch": [ "Pin source snapshots and annotation/vocabulary releases, verify each admitted claim and license, and record direct HTTP observations without treating HTTP success as substantive verification.", "Develop adoption schemas and meaningful fixtures for unplaced features, partial and circular locations, shared parts, CDS exceptions, negated evidence, revision splits/merges, projection loss and restricted evidence.", "Research graph-path and taxon-specific feature profiles and bind referenced models without duplicating their master lifecycles.", "Restore independent external review before canonical or publishable-draft promotion." ] }, "statistics": { "sources": 6, "bundles": 6, "layers": 12, "findings": 12, "questions": 36, "artifacts": 12, "functions": 6 } }