# Vercy AI instruction - YAML 1.2 (JSON-compatible) { "vercy": "1.0-draft", "publication": { "status": "published", "adjudicationStatus": "reviewable-draft", "publishableCanonical": false, "generatedAt": "2026-10-07T08:35:27Z", "synthesisSha256": "bf6fff67f008db0f890289f6da52db24749c07ca95414c265a4ec40ac8869af4", "providerMode": "single-provider-waiver", "providers": [ "Codex" ], "waivedProviders": [ "Claude", "Grok" ] }, "metaModel": { "id": "WM-LIV-002", "registryId": "vr.wm-liv-002", "name": "Organism Individual", "version": "0.1.0", "previousVersions": [], "entryKind": "entity", "family": "World Models", "category": "Physical world and living systems", "industry": [ "Cross-industry" ], "domain": [ "PHY.LIV.ORG" ], "tags": [ "organism", "individual", "phy.liv.org" ], "status": "published" }, "canonicalUrl": "https://ver.cy/models/wm-liv-002-organism-individual/", "sourceUrl": "https://github.com/ver-cy/world-models/tree/feat/mega-model-registry/research/runs/wm-liv-002", "model": { "registry_id": "vr.wm-liv-002", "model_id": "WM-LIV-002", "name": "Organism Individual", "entry_kind": "entity", "purpose": "Represent one identified living or once-living organism and its evidence-qualified continuity.", "scope_statement": "One biological individual under an explicitly declared individuality criterion. This proposed model holds individual-specific assertions and external record bindings across observations and life stages. It does not equate an organism with a taxon, record, encounter, sample, culture accession or legal person.", "in_scope": [ "Persistent identity, recognition evidence and revisable taxonomic determinations", "Uncertain origin, life status, observed properties, behavior and contextual capability assertions", "Occurrence, custody, lineage, population and sample references with provenance and disclosure controls" ], "out_of_scope": [ "Taxon definitions, population dynamics, pedigrees, sample processing, genome assemblies and clinical diagnosis lifecycles", "Collectives without a defensible individual boundary, including mixed cultures and pooled samples; ambiguous colony, clone, fusion and fission cases await a specialist profile", "Person identity, social roles and health records are separately mastered; any human biological projection requires an approved privacy profile", "Capture, breeding, treatment, cultivation, pathogen manipulation, physical transfer, permit issuance and enforcement operations" ], "boundary_notes": [ { "neighbor": "WM-LIV-001 Taxon", "distinction": "Taxon concepts and nomenclature stay external; carry determination references with vocabulary revisions.", "source_refs": [ "SRC-001", "SRC-002" ] }, { "neighbor": "WM-LIV-003 Population", "distinction": "Membership is time-qualified; population statistics and dynamics stay external.", "source_refs": [ "SRC-001", "SRC-004" ] }, { "neighbor": "WM-LIV-017 Pedigree / Biological Lineage", "distinction": "Reference the lineage assertion and revision; do not own graph reconciliation.", "source_refs": [ "SRC-001", "SRC-002" ] }, { "neighbor": "WM-LIV-023 Clinical / Biological Specimen", "distinction": "Keep material identity, processing and storage external, including whole-body material records.", "source_refs": [ "SRC-003", "SRC-006" ] }, { "neighbor": "WM-MAT-008 Observation / Measurement Record", "distinction": "Link observation evidence and summarize qualified properties; instruments and observation lifecycle stay external.", "source_refs": [ "SRC-003" ] }, { "neighbor": "WM-LIV-015 Phenotype / Trait", "distinction": "Reference trait definitions; individual trait assertions do not define the trait ontology.", "source_refs": [ "SRC-002", "SRC-003" ] }, { "neighbor": "WM-PER-001 Person", "distinction": "Optional privacy-controlled biological projection; social and legal identity are not owned here.", "source_refs": [ "SRC-002", "SRC-005" ] }, { "neighbor": "WM-LIV-021 Disease / Biological Condition", "distinction": "Reference expert condition assertions only; do not infer diagnosis or prescribe treatment.", "source_refs": [ "SRC-002", "SRC-003" ] }, { "neighbor": "Darwin Core Organism and BioSample", "distinction": "Darwin Core includes groups; this model admits only a declared individual. A culture accession, pooled specimen or environmental isolate is not proof of one individual. No legacy alias or relation-ledger entry exists in the frozen registry context.", "source_refs": [ "SRC-001", "SRC-006" ] } ] }, "sources": [ { "id": "SRC-001", "title": "Darwin Core Quick Reference Guide", "organization": "Biodiversity Information Standards (TDWG)", "url": "https://dwc.tdwg.org/terms/", "version_or_date": "Living guide accessed 2026-10-07; release pin unresolved", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-07T08:34:21Z", "relevance": "Organism, Identification, Occurrence, MaterialEntity, behavior and measurement terms support conceptual distinctions. The guide combines normative definitions with informative examples; this model is narrower than dwc:Organism." }, { "id": "SRC-002", "title": "Phenopacket schema - Individual", "organization": "Global Alliance for Genomics and Health", "url": "https://phenopacket-schema.readthedocs.io/en/2.0.0/individual.html", "version_or_date": "2.0.0", "source_type": "schema", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-07T08:34:21Z", "relevance": "Individual identifiers, taxonomy and time-qualified vital status; message-local aliases and references. Human clinical examples are not universal organism rules." }, { "id": "SRC-003", "title": "Semantic Sensor Network Ontology", "organization": "World Wide Web Consortium", "url": "https://www.w3.org/TR/2017/REC-vocab-ssn-20171019/", "version_or_date": "Recommendation 2017-10-19", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-07T08:34:21Z", "relevance": "Feature of interest, observation, sample, procedure, result and distinct phenomenon/result times. Does not prescribe biological capabilities." }, { "id": "SRC-004", "title": "PROV-O: The PROV Ontology", "organization": "World Wide Web Consortium", "url": "https://www.w3.org/TR/2013/REC-prov-o-20130430/", "version_or_date": "Recommendation 2013-04-30", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-07T08:34:21Z", "relevance": "Attribution, derivation and revision of assertions and evidence records. Provenance does not certify truth or permission." }, { "id": "SRC-005", "title": "Current Best Practices for Generalizing Sensitive Species Occurrence Data", "organization": "Global Biodiversity Information Facility", "url": "https://docs.gbif.org/sensitive-species-best-practices/master/en/", "version_or_date": "Version 1.0 November 2020; page build 2023-05-01", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-07T08:34:21Z", "relevance": "Disclosure risk, documented location generalization, authorization and leakage across duplicate records." }, { "id": "SRC-006", "title": "BioSample Submission FAQ", "organization": "National Center for Biotechnology Information", "url": "https://www.ncbi.nlm.nih.gov/biosample/docs/submission/faq/", "version_or_date": "Living documentation accessed 2026-10-07; release pin unresolved", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-07T08:34:21Z", "relevance": "BioSample describes physical source material; accession validation is not proof of organism identity. Missingness and specimen distinctions inform proposed bindings." }, { "id": "SRC-007", "title": "RFC 3339 - Date and Time on the Internet: Timestamps", "organization": "Internet Engineering Task Force", "url": "https://www.rfc-editor.org/rfc/rfc3339", "version_or_date": "July 2002; later updates not assessed", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-07T08:34:21Z", "relevance": "Syntax for known instants; proposed model separately preserves imprecise dates and intervals without fabricated seconds." } ], "structure": { "bundles": [ { "id": "b-identity", "name": "Identity and determination", "description": "Continuity of one individual and assertions about its classification.", "rationale": "Proposed model grouping of evidence-backed concerns; source vocabularies do not prescribe this hierarchy.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ], "layers": [ { "id": "l-identity-scope", "name": "Individual identity", "description": "Proposed identity dossier: declare the individual boundary before resolving aliases. Appearance, shared genotype, labels and sample accessions alone do not establish sameness.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ], "findings": [ { "id": "f-identity-scope", "name": "Qualified recognition", "description": "Proposed identity dossier: declare the individual boundary before resolving aliases. Appearance, shared genotype, labels and sample accessions alone do not establish sameness.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ], "questions": [ { "id": "f-identity-scope-q1", "text": "Which master identifier and issuer distinguish this individual from its records and marks?", "kind": "identity", "answer_data": [ "f-identity-scope-data1: Master identifier, namespace, issuer, record identifiers and alias validity periods" ] }, { "id": "f-identity-scope-q2", "text": "What individuality criterion admits this subject and excludes a group or mixed culture?", "kind": "definition", "answer_data": [ "f-identity-scope-data2: Boundary criterion, profile version, scope evidence and unresolved boundary status" ] }, { "id": "f-identity-scope-q3", "text": "Which recognition evidence supports continuity when marks are lost or appearance changes?", "kind": "evidence", "answer_data": [ "f-identity-scope-data3: Recognition method, evidence references, observer, encounter time and uncertainty" ] }, { "id": "f-identity-scope-q4", "text": "How are competing identity matches or reused tags held for review without automatic merging?", "kind": "exception", "answer_data": [ "f-identity-scope-data4: Candidate matches, disputed identifiers, reviewer and reversible resolution record" ] } ], "data_elements": [ { "id": "f-identity-scope-data1", "name": "Master identifier", "description": "Master identifier, namespace, issuer, record identifiers and alias validity periods. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] }, { "id": "f-identity-scope-data2", "name": "Boundary criterion", "description": "Boundary criterion, profile version, scope evidence and unresolved boundary status. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] }, { "id": "f-identity-scope-data3", "name": "Recognition method", "description": "Recognition method, evidence references, observer, encounter time and uncertainty. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] }, { "id": "f-identity-scope-data4", "name": "Candidate matches", "description": "Candidate matches, disputed identifiers, reviewer and reversible resolution record. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] } ], "artifacts": [ { "id": "f-identity-scope-artifact", "name": "Qualified recognition evidence dossier", "description": "Versioned local index of assertions and authorized references; underlying evidence stays in its authoritative master.", "media_or_form": [ "Structured assertion record", "Evidence reference index" ], "serial": true, "identity_strategy": "Master-system artifact identifier, else governed IRI, else Dimension UUID; stable identity plus revision and digest. Dates are metadata.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] } ], "inline_only_rationale": null } ] }, { "id": "l-determination", "name": "Taxonomic determination", "description": "Proposed determination register references taxon concepts with evidence and revision history. Unresolved identification is allowed and never creates a new organism by itself.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ], "findings": [ { "id": "f-determination", "name": "Revisable classification", "description": "Proposed determination register references taxon concepts with evidence and revision history. Unresolved identification is allowed and never creates a new organism by itself.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ], "questions": [ { "id": "f-determination-q1", "text": "Which taxon concept and vocabulary release does each determination reference?", "kind": "classification", "answer_data": [ "f-determination-data1: Taxon reference, rank, verbatim label, concept authority and vocabulary version" ] }, { "id": "f-determination-q2", "text": "Who made the determination using which evidence and method?", "kind": "provenance", "answer_data": [ "f-determination-data2: Determiner, method reference, determination date, source material and confidence" ] }, { "id": "f-determination-q3", "text": "Which determinations are accepted, disputed or superseded for this profile?", "kind": "state", "answer_data": [ "f-determination-data3: Assertion status, selection rationale and competing determination references" ] }, { "id": "f-determination-q4", "text": "What uncertainty or hybrid qualification would an export lose?", "kind": "interoperability", "answer_data": [ "f-determination-data4: Qualifier, unresolved rank, hybrid assertion and mapping loss report" ] } ], "data_elements": [ { "id": "f-determination-data1", "name": "Taxon reference", "description": "Taxon reference, rank, verbatim label, concept authority and vocabulary version. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] }, { "id": "f-determination-data2", "name": "Determiner", "description": "Determiner, method reference, determination date, source material and confidence. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] }, { "id": "f-determination-data3", "name": "Assertion status", "description": "Assertion status, selection rationale and competing determination references. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] }, { "id": "f-determination-data4", "name": "Qualifier", "description": "Qualifier, unresolved rank, hybrid assertion and mapping loss report. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] } ], "artifacts": [ { "id": "f-determination-artifact", "name": "Revisable classification evidence dossier", "description": "Versioned local index of assertions and authorized references; underlying evidence stays in its authoritative master.", "media_or_form": [ "Structured assertion record", "Evidence reference index" ], "serial": true, "identity_strategy": "Master-system artifact identifier, else governed IRI, else Dimension UUID; stable identity plus revision and digest. Dates are metadata.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "b-history", "name": "Life history and condition", "description": "Individual-specific chronology with explicit uncertainty.", "rationale": "Proposed model grouping of evidence-backed concerns; source vocabularies do not prescribe this hierarchy.", "source_refs": [ "SRC-002", "SRC-003", "SRC-007", "SRC-001" ], "layers": [ { "id": "l-origin", "name": "Origin and chronology", "description": "Proposed origin assertions separate biological beginnings from first encounter and record creation. Unknown origin remains unknown.", "source_refs": [ "SRC-002", "SRC-003", "SRC-007" ], "findings": [ { "id": "f-origin", "name": "Qualified origin", "description": "Proposed origin assertions separate biological beginnings from first encounter and record creation. Unknown origin remains unknown.", "source_refs": [ "SRC-002", "SRC-003", "SRC-007" ], "questions": [ { "id": "f-origin-q1", "text": "What event is asserted as this individual's origin?", "kind": "event", "answer_data": [ "f-origin-data1: Event type, evidence reference, asserted place and origin interpretation" ] }, { "id": "f-origin-q2", "text": "How precise is the origin time and what interval or age estimate is supported?", "kind": "temporal", "answer_data": [ "f-origin-data2: Original date or interval, precision, estimation method, age reference time and uncertainty" ] }, { "id": "f-origin-q3", "text": "Which evidence separates origin from first encounter or registration?", "kind": "provenance", "answer_data": [ "f-origin-data3: Source assertion, encounter reference, recorded time and basis for distinction" ] }, { "id": "f-origin-q4", "text": "How are incompatible dates or impossible chronology flagged without inventing a birth date?", "kind": "constraint", "answer_data": [ "f-origin-data4: Conflicting intervals, profile constraint, review status and unresolved values" ] } ], "data_elements": [ { "id": "f-origin-data1", "name": "Event type", "description": "Event type, evidence reference, asserted place and origin interpretation. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-003", "SRC-007" ] }, { "id": "f-origin-data2", "name": "Original date or interval", "description": "Original date or interval, precision, estimation method, age reference time and uncertainty. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-003", "SRC-007" ] }, { "id": "f-origin-data3", "name": "Source assertion", "description": "Source assertion, encounter reference, recorded time and basis for distinction. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-003", "SRC-007" ] }, { "id": "f-origin-data4", "name": "Conflicting intervals", "description": "Conflicting intervals, profile constraint, review status and unresolved values. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-003", "SRC-007" ] } ], "artifacts": [ { "id": "f-origin-artifact", "name": "Qualified origin evidence dossier", "description": "Versioned local index of assertions and authorized references; underlying evidence stays in its authoritative master.", "media_or_form": [ "Structured assertion record", "Evidence reference index" ], "serial": true, "identity_strategy": "Master-system artifact identifier, else governed IRI, else Dimension UUID; stable identity plus revision and digest. Dates are metadata.", "source_refs": [ "SRC-002", "SRC-003", "SRC-007" ] } ], "inline_only_rationale": null } ] }, { "id": "l-vitality", "name": "Vitality and development", "description": "Proposed state assertions include unknown, alive, dead and profile-specific development or dormancy descriptions. Absence from an observation is not evidence of death.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "findings": [ { "id": "f-vitality", "name": "Time-qualified life status", "description": "Proposed state assertions include unknown, alive, dead and profile-specific development or dormancy descriptions. Absence from an observation is not evidence of death.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "questions": [ { "id": "f-vitality-q1", "text": "What life status is supported at the stated observation time?", "kind": "state", "answer_data": [ "f-vitality-data1: Vital status, effective time, evidence and uncertainty" ] }, { "id": "f-vitality-q2", "text": "Which life stage or developmental transition is documented?", "kind": "lifecycle", "answer_data": [ "f-vitality-data2: Stage concept, transition reference, method and profile applicability" ] }, { "id": "f-vitality-q3", "text": "When does the latest status become stale or conflict with another report?", "kind": "quality", "answer_data": [ "f-vitality-data3: As-of time, freshness policy, contrary evidence and reconciliation status" ] }, { "id": "f-vitality-q4", "text": "What supports a reported death and any proposed cause?", "kind": "evidence", "answer_data": [ "f-vitality-data4: Death evidence, time interval, cause assertion, qualification and responsible expert reference" ] } ], "data_elements": [ { "id": "f-vitality-data1", "name": "Vital status", "description": "Vital status, effective time, evidence and uncertainty. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] }, { "id": "f-vitality-data2", "name": "Stage concept", "description": "Stage concept, transition reference, method and profile applicability. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] }, { "id": "f-vitality-data3", "name": "As-of time", "description": "As-of time, freshness policy, contrary evidence and reconciliation status. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] }, { "id": "f-vitality-data4", "name": "Death evidence", "description": "Death evidence, time interval, cause assertion, qualification and responsible expert reference. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "artifacts": [ { "id": "f-vitality-artifact", "name": "Time-qualified life status evidence dossier", "description": "Versioned local index of assertions and authorized references; underlying evidence stays in its authoritative master.", "media_or_form": [ "Structured assertion record", "Evidence reference index" ], "serial": true, "identity_strategy": "Master-system artifact identifier, else governed IRI, else Dimension UUID; stable identity plus revision and digest. Dates are metadata.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "b-properties", "name": "Observed properties and behavior", "description": "Evidence-bound physical and behavioral descriptions.", "rationale": "Proposed model grouping of evidence-backed concerns; source vocabularies do not prescribe this hierarchy.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004" ], "layers": [ { "id": "l-measurement", "name": "Physical and phenotypic properties", "description": "Proposed summaries point to observation masters. A measured value requires a defined property and context; sample measurements are not silently promoted to whole-organism properties.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "findings": [ { "id": "f-measurement", "name": "Qualified measurement summary", "description": "Proposed summaries point to observation masters. A measured value requires a defined property and context; sample measurements are not silently promoted to whole-organism properties.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "questions": [ { "id": "f-measurement-q1", "text": "Which property was measured and in what units and anatomical scope?", "kind": "measurement", "answer_data": [ "f-measurement-data1: Property concept, value, unit, body part or whole-organism scope and observation reference" ] }, { "id": "f-measurement-q2", "text": "What method, conditions and uncertainty qualify this value?", "kind": "quality", "answer_data": [ "f-measurement-data2: Instrument or observer, method revision, conditions, calibration reference and uncertainty" ] }, { "id": "f-measurement-q3", "text": "What evidence supports a sex or reproductive-state assertion for the applicable biological profile?", "kind": "classification", "answer_data": [ "f-measurement-data3: Trait type, observation time, method, profile vocabulary and unknown or not-applicable reason" ] }, { "id": "f-measurement-q4", "text": "Which disagreements or transformations prevent comparing measurements directly?", "kind": "validation", "answer_data": [ "f-measurement-data4: Original value, conversion rule, incompatible methods, observation times and review outcome" ] } ], "data_elements": [ { "id": "f-measurement-data1", "name": "Property concept", "description": "Property concept, value, unit, body part or whole-organism scope and observation reference. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] }, { "id": "f-measurement-data2", "name": "Instrument or observer", "description": "Instrument or observer, method revision, conditions, calibration reference and uncertainty. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] }, { "id": "f-measurement-data3", "name": "Trait type", "description": "Trait type, observation time, method, profile vocabulary and unknown or not-applicable reason. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] }, { "id": "f-measurement-data4", "name": "Original value", "description": "Original value, conversion rule, incompatible methods, observation times and review outcome. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "artifacts": [ { "id": "f-measurement-artifact", "name": "Qualified measurement summary evidence dossier", "description": "Versioned local index of assertions and authorized references; underlying evidence stays in its authoritative master.", "media_or_form": [ "Structured assertion record", "Evidence reference index" ], "serial": true, "identity_strategy": "Master-system artifact identifier, else governed IRI, else Dimension UUID; stable identity plus revision and digest. Dates are metadata.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "inline_only_rationale": null } ] }, { "id": "l-behavior", "name": "Behavior and capabilities", "description": "Proposed local distinction between recorded behavior, inferred capacity and permitted action. Taxon expectations cannot certify an individual's present capability; no handling instructions are provided.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ], "findings": [ { "id": "f-behavior", "name": "Observed action and inferred capacity", "description": "Proposed local distinction between recorded behavior, inferred capacity and permitted action. Taxon expectations cannot certify an individual's present capability; no handling instructions are provided.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ], "questions": [ { "id": "f-behavior-q1", "text": "What behavior was observed in this individual under what conditions?", "kind": "event", "answer_data": [ "f-behavior-data1: Behavior concept, observation reference, duration, setting and observer" ] }, { "id": "f-behavior-q2", "text": "What evidence supports an asserted capability and what are its limits?", "kind": "evidence", "answer_data": [ "f-behavior-data2: Capability assertion, supporting observations, conditions, inference method and confidence" ] }, { "id": "f-behavior-q3", "text": "Which observed impairment or environmental condition limits the asserted capability?", "kind": "constraint", "answer_data": [ "f-behavior-data3: Limitation, effective interval, evidence and uncertainty" ] }, { "id": "f-behavior-q4", "text": "Which policy and qualified authority govern a proposed interaction with this individual?", "kind": "authority", "answer_data": [ "f-behavior-data4: Interaction category, permission reference, welfare or biosafety restriction and refusal condition" ] } ], "data_elements": [ { "id": "f-behavior-data1", "name": "Behavior concept", "description": "Behavior concept, observation reference, duration, setting and observer. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] }, { "id": "f-behavior-data2", "name": "Capability assertion", "description": "Capability assertion, supporting observations, conditions, inference method and confidence. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] }, { "id": "f-behavior-data3", "name": "Limitation", "description": "Limitation, effective interval, evidence and uncertainty. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] }, { "id": "f-behavior-data4", "name": "Interaction category", "description": "Interaction category, permission reference, welfare or biosafety restriction and refusal condition. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] } ], "artifacts": [ { "id": "f-behavior-artifact", "name": "Observed action and inferred capacity evidence dossier", "description": "Versioned local index of assertions and authorized references; underlying evidence stays in its authoritative master.", "media_or_form": [ "Structured assertion record", "Evidence reference index" ], "serial": true, "identity_strategy": "Master-system artifact identifier, else governed IRI, else Dimension UUID; stable identity plus revision and digest. Dates are metadata.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "b-context", "name": "Occurrence and stewardship", "description": "Where an individual was evidenced and which roles apply.", "rationale": "Proposed model grouping of evidence-backed concerns; source vocabularies do not prescribe this hierarchy.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005", "SRC-004" ], "layers": [ { "id": "l-occurrence", "name": "Location and encounter", "description": "Proposed links preserve the context of presence or non-detection. Latest encounter location is not automatically current location, and generalized coordinates are not precise measurements.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ], "findings": [ { "id": "f-occurrence", "name": "Spatiotemporal occurrence binding", "description": "Proposed links preserve the context of presence or non-detection. Latest encounter location is not automatically current location, and generalized coordinates are not precise measurements.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ], "questions": [ { "id": "f-occurrence-q1", "text": "Where and when was this individual encountered?", "kind": "spatial", "answer_data": [ "f-occurrence-data1: Occurrence reference, coordinates or place, coordinate system, uncertainty and time interval" ] }, { "id": "f-occurrence-q2", "text": "What evidence associates the encounter with this individual?", "kind": "evidence", "answer_data": [ "f-occurrence-data2: Observer, detection method, recognition confidence and supporting artifact" ] }, { "id": "f-occurrence-q3", "text": "What sampling context limits interpretation of non-detection?", "kind": "quality", "answer_data": [ "f-occurrence-data3: Survey reference, effort or method reference, non-detection claim and inference limits" ] }, { "id": "f-occurrence-q4", "text": "Which location details must be withheld or generalized for this recipient?", "kind": "privacy", "answer_data": [ "f-occurrence-data4: Sensitivity policy, approved resolution, generalization method and redacted metadata" ] } ], "data_elements": [ { "id": "f-occurrence-data1", "name": "Occurrence reference", "description": "Occurrence reference, coordinates or place, coordinate system, uncertainty and time interval. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ] }, { "id": "f-occurrence-data2", "name": "Observer", "description": "Observer, detection method, recognition confidence and supporting artifact. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ] }, { "id": "f-occurrence-data3", "name": "Survey reference", "description": "Survey reference, effort or method reference, non-detection claim and inference limits. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ] }, { "id": "f-occurrence-data4", "name": "Sensitivity policy", "description": "Sensitivity policy, approved resolution, generalization method and redacted metadata. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ] } ], "artifacts": [ { "id": "f-occurrence-artifact", "name": "Spatiotemporal occurrence binding evidence dossier", "description": "Versioned local index of assertions and authorized references; underlying evidence stays in its authoritative master.", "media_or_form": [ "Structured assertion record", "Evidence reference index" ], "serial": true, "identity_strategy": "Master-system artifact identifier, else governed IRI, else Dimension UUID; stable identity plus revision and digest. Dates are metadata.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005" ] } ], "inline_only_rationale": null } ] }, { "id": "l-stewardship", "name": "Custody and responsibility", "description": "Proposed role bindings distinguish record steward, keeper, custodian and any lawful owner. A role entry is not proof of legal title or permission; no ownership role applies to a human subject.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005" ], "findings": [ { "id": "f-stewardship", "name": "Qualified stewardship roles", "description": "Proposed role bindings distinguish record steward, keeper, custodian and any lawful owner. A role entry is not proof of legal title or permission; no ownership role applies to a human subject.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005" ], "questions": [ { "id": "f-stewardship-q1", "text": "Which parties hold record stewardship, physical custody or an applicable ownership role?", "kind": "ownership", "answer_data": [ "f-stewardship-data1: Party references, role scope, basis, effective interval and not-applicable reason" ] }, { "id": "f-stewardship-q2", "text": "Which evidence dates each custody change and any gap?", "kind": "temporal", "answer_data": [ "f-stewardship-data2: Transfer record reference, effective interval, acknowledgment and unresolved gap" ] }, { "id": "f-stewardship-q3", "text": "Which external authorization or restriction is relevant to the asserted custody?", "kind": "authority", "answer_data": [ "f-stewardship-data3: Permit or policy reference, issuing authority, scope, expiry and verification status" ] }, { "id": "f-stewardship-q4", "text": "How is disputed responsibility represented without deciding title or executing a transfer?", "kind": "exception", "answer_data": [ "f-stewardship-data4: Conflicting role assertions, evidence, reviewer and unresolved status" ] } ], "data_elements": [ { "id": "f-stewardship-data1", "name": "Party references", "description": "Party references, role scope, basis, effective interval and not-applicable reason. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-004", "SRC-005" ] }, { "id": "f-stewardship-data2", "name": "Transfer record reference", "description": "Transfer record reference, effective interval, acknowledgment and unresolved gap. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-004", "SRC-005" ] }, { "id": "f-stewardship-data3", "name": "Permit or policy reference", "description": "Permit or policy reference, issuing authority, scope, expiry and verification status. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-004", "SRC-005" ] }, { "id": "f-stewardship-data4", "name": "Conflicting role assertions", "description": "Conflicting role assertions, evidence, reviewer and unresolved status. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-004", "SRC-005" ] } ], "artifacts": [ { "id": "f-stewardship-artifact", "name": "Qualified stewardship roles evidence dossier", "description": "Versioned local index of assertions and authorized references; underlying evidence stays in its authoritative master.", "media_or_form": [ "Structured assertion record", "Evidence reference index" ], "serial": true, "identity_strategy": "Master-system artifact identifier, else governed IRI, else Dimension UUID; stable identity plus revision and digest. Dates are metadata.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "b-relations", "name": "Biological relationships and material evidence", "description": "Links to separately governed biological contexts.", "rationale": "Proposed model grouping of evidence-backed concerns; source vocabularies do not prescribe this hierarchy.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-003", "SRC-006" ], "layers": [ { "id": "l-kinship", "name": "Lineage and membership", "description": "Proposed references preserve pedigree assertions and population memberships without maintaining those models' graphs or dynamics. Clonal relation does not imply identical individual identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ], "findings": [ { "id": "f-kinship", "name": "Qualified relationship bindings", "description": "Proposed references preserve pedigree assertions and population memberships without maintaining those models' graphs or dynamics. Clonal relation does not imply identical individual identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ], "questions": [ { "id": "f-kinship-q1", "text": "What parentage or clonal relationship is asserted with another individual?", "kind": "relationship", "answer_data": [ "f-kinship-data1: Related individual reference, relationship type, direction, evidence and confidence" ] }, { "id": "f-kinship-q2", "text": "Which pedigree or lineage authority maintains the relationship?", "kind": "provenance", "answer_data": [ "f-kinship-data2: Pedigree reference, revision, maintainer role and assertion provenance" ] }, { "id": "f-kinship-q3", "text": "To which population is membership asserted for a given period?", "kind": "temporal", "answer_data": [ "f-kinship-data3: Population reference, membership basis, interval and uncertainty" ] }, { "id": "f-kinship-q4", "text": "What boundary review is required after fusion, fission or ambiguous clonal growth?", "kind": "exception", "answer_data": [ "f-kinship-data4: Affected identifiers, biological event reference, proposed continuity decision and specialist review" ] } ], "data_elements": [ { "id": "f-kinship-data1", "name": "Related individual reference", "description": "Related individual reference, relationship type, direction, evidence and confidence. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] }, { "id": "f-kinship-data2", "name": "Pedigree reference", "description": "Pedigree reference, revision, maintainer role and assertion provenance. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] }, { "id": "f-kinship-data3", "name": "Population reference", "description": "Population reference, membership basis, interval and uncertainty. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] }, { "id": "f-kinship-data4", "name": "Affected identifiers", "description": "Affected identifiers, biological event reference, proposed continuity decision and specialist review. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] } ], "artifacts": [ { "id": "f-kinship-artifact", "name": "Qualified relationship bindings evidence dossier", "description": "Versioned local index of assertions and authorized references; underlying evidence stays in its authoritative master.", "media_or_form": [ "Structured assertion record", "Evidence reference index" ], "serial": true, "identity_strategy": "Master-system artifact identifier, else governed IRI, else Dimension UUID; stable identity plus revision and digest. Dates are metadata.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] } ], "inline_only_rationale": null } ] }, { "id": "l-material", "name": "Samples and derivatives", "description": "Proposed links keep organism, sample and analytical accession identities distinct. A pooled or environmental sample can have unresolved contributors and is not a single individual.", "source_refs": [ "SRC-003", "SRC-006", "SRC-002" ], "findings": [ { "id": "f-material", "name": "Source-material bindings", "description": "Proposed links keep organism, sample and analytical accession identities distinct. A pooled or environmental sample can have unresolved contributors and is not a single individual.", "source_refs": [ "SRC-003", "SRC-006", "SRC-002" ], "questions": [ { "id": "f-material-q1", "text": "Which separately identified sample or preserved material is linked to this individual?", "kind": "composition", "answer_data": [ "f-material-data1: Material identifier, sample master, source relationship and evidence reference" ] }, { "id": "f-material-q2", "text": "Which sampling record supports the claimed source relationship?", "kind": "provenance", "answer_data": [ "f-material-data2: Sampling reference, collector role, time, source site on organism and provenance" ] }, { "id": "f-material-q3", "text": "How are pooling, contamination or uncertain donor attribution recorded?", "kind": "validation", "answer_data": [ "f-material-data3: Contributor references, attribution uncertainty, material quality flags and review state" ] }, { "id": "f-material-q4", "text": "How are organism and sample identifiers mapped across analytical records?", "kind": "interoperability", "answer_data": [ "f-material-data4: Identifier mapping, namespace, export scope, consent or access reference and loss report" ] } ], "data_elements": [ { "id": "f-material-data1", "name": "Material identifier", "description": "Material identifier, sample master, source relationship and evidence reference. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-003", "SRC-006", "SRC-002" ] }, { "id": "f-material-data2", "name": "Sampling reference", "description": "Sampling reference, collector role, time, source site on organism and provenance. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-003", "SRC-006", "SRC-002" ] }, { "id": "f-material-data3", "name": "Contributor references", "description": "Contributor references, attribution uncertainty, material quality flags and review state. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-003", "SRC-006", "SRC-002" ] }, { "id": "f-material-data4", "name": "Identifier mapping", "description": "Identifier mapping, namespace, export scope, consent or access reference and loss report. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-003", "SRC-006", "SRC-002" ] } ], "artifacts": [ { "id": "f-material-artifact", "name": "Source-material bindings evidence dossier", "description": "Versioned local index of assertions and authorized references; underlying evidence stays in its authoritative master.", "media_or_form": [ "Structured assertion record", "Evidence reference index" ], "serial": true, "identity_strategy": "Master-system artifact identifier, else governed IRI, else Dimension UUID; stable identity plus revision and digest. Dates are metadata.", "source_refs": [ "SRC-003", "SRC-006", "SRC-002" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "b-assurance", "name": "Evidence governance and exchange", "description": "Accountable assertions and controlled projections.", "rationale": "Proposed model grouping of evidence-backed concerns; source vocabularies do not prescribe this hierarchy.", "source_refs": [ "SRC-005", "SRC-004", "SRC-006", "SRC-003", "SRC-007" ], "layers": [ { "id": "l-disclosure", "name": "Disclosure and retention", "description": "Proposed local policy gate protects sensitive locations and linked personal or genomic information. An open metadata license does not authorize disclosure of every linked record.", "source_refs": [ "SRC-005", "SRC-004", "SRC-006" ], "findings": [ { "id": "f-disclosure", "name": "Recipient-specific evidence access", "description": "Proposed local policy gate protects sensitive locations and linked personal or genomic information. An open metadata license does not authorize disclosure of every linked record.", "source_refs": [ "SRC-005", "SRC-004", "SRC-006" ], "questions": [ { "id": "f-disclosure-q1", "text": "Which evidence is available to this requester for the declared purpose?", "kind": "access", "answer_data": [ "f-disclosure-data1: Requester role, purpose, policy revision, permitted scope and decision reference" ] }, { "id": "f-disclosure-q2", "text": "Can linked media, identifiers or duplicate records reveal withheld information?", "kind": "security", "answer_data": [ "f-disclosure-data2: Linkage risk review, media metadata treatment and approved export view" ] }, { "id": "f-disclosure-q3", "text": "What retention and disposal policy governs the individual record and its evidence?", "kind": "retention", "answer_data": [ "f-disclosure-data3: Retention trigger, duration, hold, disposition authority and linked-master dependencies" ] }, { "id": "f-disclosure-q4", "text": "Who may approve a documented access exception and when does it expire?", "kind": "exception", "answer_data": [ "f-disclosure-data4: Exception authority, rationale, scope, expiry and audit reference" ] } ], "data_elements": [ { "id": "f-disclosure-data1", "name": "Requester role", "description": "Requester role, purpose, policy revision, permitted scope and decision reference. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-005", "SRC-004", "SRC-006" ] }, { "id": "f-disclosure-data2", "name": "Linkage risk review", "description": "Linkage risk review, media metadata treatment and approved export view. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-005", "SRC-004", "SRC-006" ] }, { "id": "f-disclosure-data3", "name": "Retention trigger", "description": "Retention trigger, duration, hold, disposition authority and linked-master dependencies. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-005", "SRC-004", "SRC-006" ] }, { "id": "f-disclosure-data4", "name": "Exception authority", "description": "Exception authority, rationale, scope, expiry and audit reference. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-005", "SRC-004", "SRC-006" ] } ], "artifacts": [ { "id": "f-disclosure-artifact", "name": "Recipient-specific evidence access evidence dossier", "description": "Versioned local index of assertions and authorized references; underlying evidence stays in its authoritative master.", "media_or_form": [ "Structured assertion record", "Evidence reference index" ], "serial": true, "identity_strategy": "Master-system artifact identifier, else governed IRI, else Dimension UUID; stable identity plus revision and digest. Dates are metadata.", "source_refs": [ "SRC-005", "SRC-004", "SRC-006" ] } ], "inline_only_rationale": null } ] }, { "id": "l-quality", "name": "Revision and interoperability", "description": "Proposed evidence and mapping register distinguishes observation from inference and correction from biological change. Standards alignments remain conceptual until fixtures validate the selected profile.", "source_refs": [ "SRC-004", "SRC-003", "SRC-007", "SRC-006" ], "findings": [ { "id": "f-quality", "name": "Assertion quality and mapping", "description": "Proposed evidence and mapping register distinguishes observation from inference and correction from biological change. Standards alignments remain conceptual until fixtures validate the selected profile.", "source_refs": [ "SRC-004", "SRC-003", "SRC-007", "SRC-006" ], "questions": [ { "id": "f-quality-q1", "text": "Which source and transformation produced each assertion revision?", "kind": "provenance", "answer_data": [ "f-quality-data1: Source identifier, agent, method, revision relation and recorded timestamp" ] }, { "id": "f-quality-q2", "text": "How are contradictory assertions retained and resolved?", "kind": "decision", "answer_data": [ "f-quality-data2: Conflict set, evidence comparison, reviewer decision and unresolved status" ] }, { "id": "f-quality-q3", "text": "Which versioned mappings preserve identity, missingness and qualified times?", "kind": "interoperability", "answer_data": [ "f-quality-data3: Target schema version, field mapping, not-collected or unknown semantics and loss declarations" ] }, { "id": "f-quality-q4", "text": "Which acceptance fixtures demonstrate the proposed boundary and export behavior?", "kind": "validation", "answer_data": [ "f-quality-data4: Fixture identifiers, expected results, validation version, failures and unresolved gaps" ] } ], "data_elements": [ { "id": "f-quality-data1", "name": "Source identifier", "description": "Source identifier, agent, method, revision relation and recorded timestamp. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-004", "SRC-003", "SRC-007", "SRC-006" ] }, { "id": "f-quality-data2", "name": "Conflict set", "description": "Conflict set, evidence comparison, reviewer decision and unresolved status. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-004", "SRC-003", "SRC-007", "SRC-006" ] }, { "id": "f-quality-data3", "name": "Target schema version", "description": "Target schema version, field mapping, not-collected or unknown semantics and loss declarations. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-004", "SRC-003", "SRC-007", "SRC-006" ] }, { "id": "f-quality-data4", "name": "Fixture identifiers", "description": "Fixture identifiers, expected results, validation version, failures and unresolved gaps. Candidate field group; nested instance schema and binding remain a conformance hold.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-004", "SRC-003", "SRC-007", "SRC-006" ] } ], "artifacts": [ { "id": "f-quality-artifact", "name": "Assertion quality and mapping evidence dossier", "description": "Versioned local index of assertions and authorized references; underlying evidence stays in its authoritative master.", "media_or_form": [ "Structured assertion record", "Evidence reference index" ], "serial": true, "identity_strategy": "Master-system artifact identifier, else governed IRI, else Dimension UUID; stable identity plus revision and digest. Dates are metadata.", "source_refs": [ "SRC-004", "SRC-003", "SRC-007", "SRC-006" ] } ], "inline_only_rationale": null } ] } ] } ] }, "functions": [ { "id": "fn-register-individual", "name": "Register a bounded individual", "description": "Proposed, unimplemented local record operation. Create only after scope and identity checks; never infer sameness from genotype alone.", "inputs": [ "identity criterion and issuer-qualified identifier" ], "outputs": [ "local individual record or boundary-review refusal" ], "preconditions": [ "Authorized record-editor or disclosure-reviewer role and declared purpose", "Current revision and optimistic concurrency token match", "Applicable profile and evidence references are available; otherwise refuse or flag unresolved" ], "effects": [ "Create only after scope and identity checks; never infer sameness from genotype alone.", "Retain a provenance reference and revision; no physical or external action is authorized." ], "source_refs": [ "SRC-001", "SRC-002" ] }, { "id": "fn-record-determination", "name": "Record a determination", "description": "Proposed, unimplemented local record operation. Append a qualified classification without changing the organism identity.", "inputs": [ "taxon reference, evidence and supersession reason" ], "outputs": [ "new assertion revision or unresolved-reference refusal" ], "preconditions": [ "Authorized record-editor or disclosure-reviewer role and declared purpose", "Current revision and optimistic concurrency token match", "Applicable profile and evidence references are available; otherwise refuse or flag unresolved" ], "effects": [ "Append a qualified classification without changing the organism identity.", "Retain a provenance reference and revision; no physical or external action is authorized." ], "source_refs": [ "SRC-001", "SRC-004" ] }, { "id": "fn-link-observation", "name": "Link a qualified observation", "description": "Proposed, unimplemented local record operation. Record evidence linkage without executing measurement, handling or diagnosis.", "inputs": [ "observation reference, asserted subject match and property summary" ], "outputs": [ "qualified binding or mismatch refusal" ], "preconditions": [ "Authorized record-editor or disclosure-reviewer role and declared purpose", "Current revision and optimistic concurrency token match", "Applicable profile and evidence references are available; otherwise refuse or flag unresolved" ], "effects": [ "Record evidence linkage without executing measurement, handling or diagnosis.", "Retain a provenance reference and revision; no physical or external action is authorized." ], "source_refs": [ "SRC-003", "SRC-004" ] }, { "id": "fn-revise-status", "name": "Revise an as-of status", "description": "Proposed, unimplemented local record operation. Preserve competing evidence; never infer death from non-detection.", "inputs": [ "life-status evidence, effective time and conflict set" ], "outputs": [ "new status assertion or unresolved-conflict report" ], "preconditions": [ "Authorized record-editor or disclosure-reviewer role and declared purpose", "Current revision and optimistic concurrency token match", "Applicable profile and evidence references are available; otherwise refuse or flag unresolved" ], "effects": [ "Preserve competing evidence; never infer death from non-detection.", "Retain a provenance reference and revision; no physical or external action is authorized." ], "source_refs": [ "SRC-002", "SRC-003", "SRC-004" ] }, { "id": "fn-link-material", "name": "Link source material", "description": "Proposed, unimplemented local record operation. Link distinct identities without processing specimens or asserting pooled material is one individual.", "inputs": [ "sample identifier, organism reference and attribution evidence" ], "outputs": [ "source binding or uncertain-attribution refusal" ], "preconditions": [ "Authorized record-editor or disclosure-reviewer role and declared purpose", "Current revision and optimistic concurrency token match", "Applicable profile and evidence references are available; otherwise refuse or flag unresolved" ], "effects": [ "Link distinct identities without processing specimens or asserting pooled material is one individual.", "Retain a provenance reference and revision; no physical or external action is authorized." ], "source_refs": [ "SRC-003", "SRC-006" ] }, { "id": "fn-prepare-view", "name": "Prepare a recipient view", "description": "Proposed, unimplemented local record operation. Apply approved redactions and record mapping loss; no external transmission or policy enforcement engine is implemented.", "inputs": [ "purpose, access decision reference and target schema profile" ], "outputs": [ "local minimized export candidate or denied-view report" ], "preconditions": [ "Authorized record-editor or disclosure-reviewer role and declared purpose", "Current revision and optimistic concurrency token match", "Applicable profile and evidence references are available; otherwise refuse or flag unresolved" ], "effects": [ "Apply approved redactions and record mapping loss; no external transmission or policy enforcement engine is implemented.", "Retain a provenance reference and revision; no physical or external action is authorized." ], "source_refs": [ "SRC-005", "SRC-004" ] } ], "composition": [ { "target": "WM-LIV-001 Taxon", "relation": "REFERENCE", "purpose": "Proposed binding, not a frozen registry edge. Taxon concepts and nomenclature stay external; carry determination references with vocabulary revisions.", "required": false, "source_refs": [ "SRC-001", "SRC-002" ] }, { "target": "WM-LIV-003 Population", "relation": "REFERENCE", "purpose": "Proposed binding, not a frozen registry edge. Membership is time-qualified; population statistics and dynamics stay external.", "required": false, "source_refs": [ "SRC-001", "SRC-004" ] }, { "target": "WM-LIV-017 Pedigree / Biological Lineage", "relation": "REFERENCE", "purpose": "Proposed binding, not a frozen registry edge. Reference the lineage assertion and revision; do not own graph reconciliation.", "required": false, "source_refs": [ "SRC-001", "SRC-002" ] }, { "target": "WM-LIV-023 Clinical / Biological Specimen", "relation": "REFERENCE", "purpose": "Proposed binding, not a frozen registry edge. Keep material identity, processing and storage external, including whole-body material records.", "required": false, "source_refs": [ "SRC-003", "SRC-006" ] }, { "target": "WM-MAT-008 Observation / Measurement Record", "relation": "REFERENCE", "purpose": "Proposed binding, not a frozen registry edge. Link observation evidence and summarize qualified properties; instruments and observation lifecycle stay external.", "required": false, "source_refs": [ "SRC-003" ] }, { "target": "WM-LIV-015 Phenotype / Trait", "relation": "REFERENCE", "purpose": "Proposed binding, not a frozen registry edge. Reference trait definitions; individual trait assertions do not define the trait ontology.", "required": false, "source_refs": [ "SRC-002", "SRC-003" ] }, { "target": "WM-PER-001 Person", "relation": "REFERENCE", "purpose": "Proposed binding, not a frozen registry edge. Optional privacy-controlled biological projection; social and legal identity are not owned here.", "required": false, "source_refs": [ "SRC-002", "SRC-005" ] }, { "target": "WM-LIV-021 Disease / Biological Condition", "relation": "REFERENCE", "purpose": "Proposed binding, not a frozen registry edge. Reference expert condition assertions only; do not infer diagnosis or prescribe treatment.", "required": false, "source_refs": [ "SRC-002", "SRC-003" ] } ], "serviceLayers": { "dimension": { "owner_package_requirements": [ "Name a role-based scientific record steward and authoritative identity master", "Declare biological individuality criterion, taxonomic scope and profile version", "Define privacy, welfare, biosafety, disclosure and retention authorities before instance use" ], "namespace_guidance": "Use vr.wm-liv-002 for the model and an adopting-Dimension namespace for instances; keep organism, assertion, encounter and material identifiers distinct.", "registry_links": [ "vr.wm-liv-002", "Proposed neighbors in composition require version and master-system bindings before use" ] }, "canon_and_patch": { "canonicalization_rules": [ "Keep source assertions, original units, uncertainty and competing identifications; choose an as-of projection with a stated rule", "Never canonicalize a record merge into a biological identity claim without reviewed evidence" ], "patch_rules": [ "Append corrections with attribution, reason and superseded revision; check optimistic concurrency", "Do not overwrite uncertain times or promote taxon expectations into individual facts" ], "compatibility_rules": [ "Version changes to individuality, missingness, units or identity mappings require migration review", "Preserve legacy aliases as qualified mappings only; no registered legacy model exists for this run" ] }, "artifact_rules": { "identity_priority": [ "Authoritative master-system identifier with issuer namespace", "Governed global identifier or IRI", "Dimension-assigned UUID or ULID" ], "timestamp_rule": "Known instants use RFC 3339 with seconds and explicit offset or Z. Separate biological event time, observation time, result time and ingestion time. Preserve date-only, estimated age and interval values with precision; never invent seconds or an offset for unknown times.", "serial_naming_rule": "Use stable artifact identity plus revision; human labels may include sequence numbers but dates are not identity.", "integrity_rule": "Record digest, media type, source reference and revision for evidence; integrity does not prove identity, truth, consent or legal title." }, "policies": [ "These service rules and hierarchy are local design proposals informed by the cited evidence, not requirements imposed by those sources", "Apply welfare and biosafety review to physical interactions; the model contains policy references only", "Human-linked biological or genomic data require a qualified privacy and consent profile before use", "Minimize sensitive locations and linkage clues in recipient views; retain the reason for withholding", "Unknown, absent, not collected, disputed and not applicable are distinct; non-detection does not prove death", "No brand or company is designated as record owner; stewardship roles are assigned by the adopting Dimension" ], "crud": { "read": [ "Resolve recipient role and purpose at bundle, layer, finding and artifact level; do not follow restricted evidence links by default" ], "create": [ "Require identity master and boundary criterion; uncertain matching stays a candidate record until reviewed" ], "update": [ "Append attributed assertion revisions with effective time and concurrency checks; do not mutate referenced masters" ], "delete": [ "Retire or tombstone duplicate local records with reviewed redirects; never interpret record retirement as death", "Apply Dimension retention and authorized payload erasure including sensitive media and cached exports; keep only permitted minimal provenance", "Referenced sample, observation and person masters own their retention execution; local deletion neither destroys an organism nor deletes their records" ] }, "roles": [ { "name": "Record steward", "responsibilities": [ "Maintain individual identity, boundary profile and reversible record corrections" ] }, { "name": "Observer", "responsibilities": [ "Submit attributed evidence with method, time and uncertainty" ] }, { "name": "Scientific reviewer", "responsibilities": [ "Review identity disputes, taxon determinations and ambiguous individuality" ] }, { "name": "Disclosure reviewer", "responsibilities": [ "Approve purpose-bound views, exceptions and sensitivity controls" ] }, { "name": "Custodian", "responsibilities": [ "Attest scoped custody facts without asserting legal title solely from possession" ] } ], "access": { "default_rule": "Deny sensitive evidence by default until a role, purpose and applicable policy grant access; public views are explicitly approved projections.", "scopes": [ "bundle", "layer", "finding", "artifact" ], "exceptions": [ "A qualified reviewer may authorize a time-limited, purpose-bound exception with documented basis; no implicit waiver through links" ], "audit_requirements": [ "Reference the adopting Dimension's audit master for access, corrections, identity merges and exports", "Log policy and actor references while minimizing identifiers and precise location payloads" ] }, "agents_bootstrap": { "filename": "AGENTS.md", "required_fields": [ "Name", "Type", "Specification URL", "Storage type URL", "Interface URL", "Processes URL" ], "read_order": [ "Read AGENTS.md, owner and Dimension policies", "Read spec.yaml and visible research holds", "Resolve versioned neighbor bindings and evidence access before populating assertions" ] } }, "coverage": { "claim": "Source-grounded proposed structure for one explicitly bounded organism individual. A separate frozen no-tools local self-audit found no critical conflict. This remains a noncanonical reviewable draft with independent-review, source/version, specialist-profile and executable-conformance holds.", "confidence": "medium", "checklist": [ { "dimension": "identity", "status": "covered", "notes": "Master identity, individual boundary, recognition and disputed aliases." }, { "dimension": "lifecycle", "status": "covered", "notes": "Origin, development, as-of vitality and death evidence; record retirement remains separate." }, { "dimension": "relationships", "status": "covered", "notes": "Qualified lineage, population and material references; external masters retain their lifecycles." }, { "dimension": "temporal", "status": "covered", "notes": "Event, observation, result and recorded times; imprecision and stale state." }, { "dimension": "provenance", "status": "covered", "notes": "Attributed evidence, revision and inference distinctions." }, { "dimension": "ownership", "status": "covered", "notes": "Role-qualified stewardship and custody; no automatic title or ownership of human subjects." }, { "dimension": "validation", "status": "gap", "notes": "Research schema validation is available; executable instance schemas and biological fixture suite remain unimplemented." }, { "dimension": "access", "status": "covered", "notes": "Recipient-specific disclosure and linkage-risk review." }, { "dimension": "retention and deletion", "status": "covered", "notes": "Policy-dependent erasure, holds and minimal tombstones; no physical disposal." }, { "dimension": "interoperability", "status": "gap", "notes": "Conceptual alignments only; release-pinned adapters and round-trip tests remain deferred." }, { "dimension": "physical properties", "status": "covered", "notes": "Units, body scope, method, conditions, uncertainty and external observations." }, { "dimension": "behavior and capabilities", "status": "covered", "notes": "Observed action, conditional inference and permission are distinct." }, { "dimension": "biological individuality", "status": "gap", "notes": "Generic criterion required; taxon-specific colony, clone, symbiosis and fusion/fission decisions await expert profiles." } ], "known_omissions": [ "Independent second-provider review is absent; the subsequent local audit cannot replace it", "Complete pinned source/version verification and direct HTTP measurements are pending coordinator execution", "Nested instance schemas, vocabulary bindings, mappings and adversarial fixtures are not implemented", "Specialist individuality, human privacy, welfare, biosafety, permit and jurisdiction profiles require qualified review; no operational guidance is supplied" ], "conflicts": [], "regional_assumptions": [ "No universal legal ownership, permit or consent rule is asserted", "Human-focused schema examples are selectively aligned, not forced onto all organisms", "Generic scope covers identified organisms only; aggregations need an explicit alternative boundary" ], "adversarial_checks": [ "Reject a pooled sample or taxonomically homogeneous culture as automatic proof of one individual", "Keep tag reuse and identical genotype from silently merging records", "Distinguish organism continuity from specimen persistence and record revision", "Reject non-detection as automatic death and stale location as current presence", "Check whether linked media or identifiers reveal a generalized location", "Do not confuse observed behavior, possible capability and authorized handling" ] }, "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": "The root denotes one individual with continuity across observations and assertion revisions. An explicit individuality criterion excludes ambiguous groups and samples; neighboring masters own their separate lifecycles. The registry standalone-mm label is a record category, not a conflicting research entry kind." }, "decisions": [ { "concept": "Persistent individual boundary", "disposition": "accepted", "rationale": "A declared individual persists across observations, determinations and record revisions. The registry standalone-mm category does not conflict with the research entity kind." }, { "concept": "Broader Darwin Core class", "disposition": "qualified", "rationale": "The source permits groups, but the result explicitly narrows admission and requires an individuality criterion. Ambiguous colonies, cultures and collective samples are deferred rather than silently treated as individuals." }, { "concept": "Identity and recognition", "disposition": "accepted", "rationale": "Issuer-qualified identities, lost marks, tag reuse and competing matches are handled explicitly. Shared genotype, appearance or a sample accession cannot independently authorize a merge." }, { "concept": "Taxonomy and relationships", "disposition": "accepted as references", "rationale": "Determinations are revisable assertions. Taxon definitions, pedigree graphs, population dynamics and material lifecycles remain in referenced masters; all new bindings are marked proposed." }, { "concept": "Legacy and relation contract", "disposition": "accepted", "rationale": "The frozen registry has no legacy alias or existing specification and the relationship ledger has no matching rows. Supplement neighbors are not silently promoted into mandatory composition." }, { "concept": "Life status and uncertain time", "disposition": "accepted", "rationale": "Origin is separate from first encounter and registration. Non-detection does not prove death; stale status and partial dates remain qualified rather than being converted into invented exact times." }, { "concept": "Measurements and behavior", "disposition": "qualified", "rationale": "The result requires observation context, units and uncertainty and separates sample measurements from whole-organism properties. Capabilities remain conditional local assertions, not prescribed biological or handling procedures." }, { "concept": "Custody and human projections", "disposition": "limited", "rationale": "Possession, record stewardship, lawful ownership and authority are distinguished. Human ownership is excluded, and biological projections depend on a qualified privacy profile while person and health masters remain external." }, { "concept": "Sample source attribution", "disposition": "accepted", "rationale": "Pooled or environmental material cannot establish a single donor. Source links require evidence and can remain uncertain; sample processing and storage are outside this model." }, { "concept": "Local functions", "disposition": "accepted as unimplemented proposals", "rationale": "All six functions require authority, evidence and revision checks, include refusal paths and produce local records. None performs physical interaction, clinical diagnosis, sample processing or external transmission." }, { "concept": "Disclosure and retention", "disposition": "accepted with policy dependency", "rationale": "Recipient views address linkage leaks as well as coordinates. History preservation is qualified by authorized payload erasure and minimal permitted provenance, avoiding an unconditional indefinite-retention rule." }, { "concept": "Evidence and conformance", "disposition": "held", "rationale": "The seven source readings support conceptual distinctions, not complete runtime mappings. Candidate object groups are not executable nested schemas, and acceptance fixtures are questions rather than completed tests." }, { "concept": "Independent review and HTTP measurement", "disposition": "waived and held", "rationale": "This is a separate local Codex self-audit of frozen evidence, not independent review. No direct HTTP request was attempted, so zero measured successes must not be reported as source failures or live verification." } ], "publicationHolds": [ "Independent external review is absent under the owner-authorized single-provider waiver. Claude and Grok were skipped with zero attempts; the separate local Codex no-tools self-audit is not independent second-provider review.", "Source and version verification remains incomplete. Seven URLs yielded readable web-tool content, but direct HTTP was not attempted under the owner-reported sandbox block; no response statuses or body hashes were measured. The coordinator must run check_sources.py outside the sandbox and review version pins and claim support.", "Specialist biological individuality, human privacy, welfare, biosafety, custody, permit and jurisdiction profiles require qualified review before operational use. The generic draft cannot decide ambiguous colony, clone, fusion, fission or culture boundaries.", "Nested instance schemas, version-pinned neighbor bindings, vocabulary mappings, loss checks and executable adversarial fixtures are incomplete. No runtime implementation or external-standard conformance is certified.", "Independent external review was explicitly waived by the repository owner; this codex-only result remains a reviewable draft." ], "deferredResearch": [ "Restore independent second-provider review before canonical promotion.", "Run coordinator HTTP checks, pin living documentation releases and independently assess claim support and applicable licenses.", "Develop taxon-specific individuality and human-data profiles plus nested schemas and fixtures for tag reuse, non-detection, pooled samples, fusion/fission, stale location and disclosure linkage." ] }, "statistics": { "sources": 7, "bundles": 6, "layers": 12, "findings": 12, "questions": 48, "artifacts": 12, "functions": 6 } }