# Vercy AI instruction - YAML 1.2 (JSON-compatible) { "vercy": "1.0-draft", "publication": { "status": "published", "adjudicationStatus": "reviewable-draft", "publishableCanonical": false, "generatedAt": "2026-10-06T21:12:34Z", "synthesisSha256": "96105a8929ea5c0ab8a802d7a6a5ed62499a1a99c567b0076a1bfd49f9ca509e", "providerMode": "single-provider-waiver", "providers": [ "Codex" ], "waivedProviders": [ "Claude", "Grok" ] }, "metaModel": { "id": "WM-LIV-015", "registryId": "vr.wm-liv-015", "name": "Phenotype / Trait", "version": "0.1.0", "previousVersions": [], "entryKind": "entity", "family": "World Models", "category": "Physical world and living systems", "industry": [ "Cross-industry" ], "domain": [ "PHY.LIV.PHN" ], "tags": [ "phenotype", "trait", "phy.liv.phn" ], "status": "published" }, "canonicalUrl": "https://ver.cy/models/wm-liv-015-phenotype-trait/", "sourceUrl": "https://github.com/ver-cy/world-models/tree/feat/mega-model-registry/research/runs/wm-liv-015", "model": { "registry_id": "vr.wm-liv-015", "model_id": "WM-LIV-015", "name": "Phenotype / Trait", "entry_kind": "entity", "purpose": "Describe a traceable assertion about a biological trait for a specified subject and context, preserving the distinction between a trait concept, evidence and an asserted result.", "scope_statement": "One root is a phenotype or trait assertion record with its own identity and revisions. It references a reusable trait definition and a specified organism, specimen or biological observation unit. Observations, calculations, imported reports and predictions remain explicitly typed. The root is neither an organism nor a universal trait dictionary nor an entire patient or trial dossier.", "in_scope": [ "Assertion identity and subject resolution; trait and variable references with versioned meaning.", "Result form, assessment status, method, time, anatomy, developmental stage, environment and uncertainty.", "Evidence links, correction lineage, local record governance and qualified exchange projections." ], "out_of_scope": [ "Master organism, taxon, specimen, population, genome, disease and study lifecycles.", "Clinical diagnosis, treatment, breeding or selection decisions, genetic causation and biological interventions.", "Authoring a universal ontology, executing instruments, association analysis or inferring sensitive traits from unrelated personal data." ], "boundary_notes": [ { "neighbor": "WM-LIV-002 Organism Individual", "distinction": "Registry parent is contextual association, not is-a inheritance: an assertion is about an organism and is not an organism. The relation ledger contains no rows for this model. Require a subject binding; individual binding is conditional because a specimen or biological plot can be the immediate subject.", "source_refs": [ "SRC-004", "SRC-007" ] }, { "neighbor": "Trait vocabularies and observation variables", "distinction": "Reuse versioned definitions. The root stores a reference and a meaning snapshot, not authority to redefine the source ontology. A label match does not prove equivalence.", "source_refs": [ "SRC-003", "SRC-004", "SRC-005" ] }, { "neighbor": "WM-LIV-023 Clinical / Biological Specimen and WM-LIV-003 Population", "distinction": "Keep immediate subject, source organism and aggregation level distinct. Sample findings and plot summaries cannot automatically be attributed to each contributing organism. Pure environmental observations are outside this biological assertion model.", "source_refs": [ "SRC-004", "SRC-007" ] }, { "neighbor": "WM-LIV-012 Genomic Sequence / Variant and WM-LIV-021 Disease / Biological Condition", "distinction": "Carry optional externally governed links to interpretations. A feature, measurement or association is not a diagnosis or proof that a variant causes a trait.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] }, { "neighbor": "Study, instrument, policy and provenance services", "distinction": "Keep external identifiers and subject-specific context only. Local functions manipulate records; they do not operate devices, perform experiments, authorize disclosure or implement external audit infrastructure.", "source_refs": [ "SRC-004", "SRC-007", "SRC-008", "SRC-009" ] } ] }, "sources": [ { "id": "SRC-001", "title": "PhenotypicFeature - Phenopacket schema", "organization": "Global Alliance for Genomics and Health", "url": "https://phenopacket-schema.readthedocs.io/en/latest/phenotype.html", "version_or_date": "2.0 documentation; mutable latest URL read 2026-10-07", "source_type": "schema", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:11:17Z", "relevance": "Feature type, explicit exclusion, onset, resolution, modifiers and evidence. These are exchange fields, not a diagnosis or permission to collect data." }, { "id": "SRC-002", "title": "Measurement - Phenopacket schema", "organization": "Global Alliance for Genomics and Health", "url": "https://phenopacket-schema.readthedocs.io/en/latest/measurement.html", "version_or_date": "2.0 documentation; mutable latest URL read 2026-10-07", "source_type": "schema", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:11:17Z", "relevance": "Assay and typed result, observed time and procedure; numerical, ordinal and categorical measurement are distinguished from a phenotype conclusion." }, { "id": "SRC-003", "title": "How does the HPO define phenotype?", "organization": "Human Phenotype Ontology consortium", "url": "https://obophenotype.github.io/human-phenotype-ontology/clinicians/what-is-phenotype/", "version_or_date": "Undated clinician guide read 2026-10-07; ontology release not pinned", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 2, "accessed_at": "2026-10-06T21:11:17Z", "relevance": "The broad biological use of phenotype differs from the clinical focus on abnormalities; term selection and detailed component descriptions matter." }, { "id": "SRC-004", "title": "MIAPPE checklist and data model", "organization": "MIAPPE community", "url": "https://raw.githubusercontent.com/MIAPPE/MIAPPE/master/MIAPPE_Checklist_Data_Model.tsv", "version_or_date": "Mutable master checklist read 2026-10-07; release and commit not pinned", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:11:17Z", "relevance": "Observation units, samples, observed variables, methods, scales, environment and experimental factors. Plant scope only; no universal individual-level requirement." }, { "id": "SRC-005", "title": "Crop Ontology Pages - Trait Dictionary V5", "organization": "Planteome project", "url": "https://wiki.planteome.org/index.php/Crop_Ontology_Pages", "version_or_date": "Historical wiki content, oldid 1791 linked; read 2026-10-07", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 2, "accessed_at": "2026-10-06T21:11:17Z", "relevance": "Separate trait, method, scale and variable identifiers; computational methods and lossy projections. Historical mapping examples are not current implementation conformance." }, { "id": "SRC-006", "title": "The Unified Code for Units of Measure", "organization": "UCUM Organization", "url": "https://ucum.org/ucum", "version_or_date": "Version 2.2; 2024-06-17", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:11:17Z", "relevance": "Machine-readable unit semantics and dimensional compatibility. Unit equivalence alone does not establish biological comparability." }, { "id": "SRC-007", "title": "Semantic Sensor Network Ontology", "organization": "World Wide Web Consortium", "url": "https://www.w3.org/TR/2017/REC-vocab-ssn-20171019/", "version_or_date": "W3C Recommendation 2017-10-19; pinned historical edition", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:11:17Z", "relevance": "Observation, property, feature of interest, sample, procedure and result; phenomenon time differs from result time. Conceptual alignment only." }, { "id": "SRC-008", "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": "W3C Recommendation 2013-04-30; pinned historical edition", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:11:17Z", "relevance": "Attribution, derivation, revision and invalidation links support assertion lineage; they do not certify accuracy or impose perpetual retention." }, { "id": "SRC-009", "title": "Framework for responsible sharing of genomic and health-related data", "organization": "Global Alliance for Genomics and Health", "url": "https://www.ga4gh.org/product/framework-for-responsible-sharing-of-genomic-and-health-related-data/", "version_or_date": "Product overview read 2026-10-07; linked full framework not reviewed", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 2, "accessed_at": "2026-10-06T21:11:17Z", "relevance": "Overview supports privacy, human rights, non-discrimination and procedural fairness. Local access and retention rules below are proposed safeguards, not legal conclusions." } ], "structure": { "bundles": [ { "id": "b-identity", "name": "Assertion and subject", "description": "Establish the claim record and its biological referent.", "rationale": "This concern prevents an assertion from losing establish the claim record and its biological referent.", "source_refs": [ "SRC-004", "SRC-007", "SRC-008" ], "layers": [ { "id": "l-assertion", "name": "Assertion identity", "description": "A persistent record identifies a claim; neither a date nor an ontology code identifies the individual claim.", "source_refs": [ "SRC-007", "SRC-008" ], "findings": [ { "id": "f-assertion", "name": "Assertion identity", "description": "A persistent record identifies a claim; neither a date nor an ontology code identifies the individual claim.", "source_refs": [ "SRC-007", "SRC-008" ], "questions": [ { "id": "q-assertion-1", "text": "Which master identifier and revision identify this assertion?", "kind": "identity", "answer_data": [ "assertion-id", "Authoritative assertion ID, issuing namespace, revision and aliases." ] }, { "id": "q-assertion-2", "text": "Is the asserted result observed, calculated, reported by another party or predicted?", "kind": "classification", "answer_data": [ "assertion-mode", "Explicit acquisition mode; predicted results never masquerade as measurements." ] }, { "id": "q-assertion-3", "text": "Which scientific or clinical steward is responsible for this local assertion?", "kind": "ownership", "answer_data": [ "steward", "Responsible role and master-system reference, separate from subject identity." ] } ], "data_elements": [ { "id": "d-assertion-1", "name": "assertion-id", "description": "Authoritative assertion ID, issuing namespace, revision and aliases.", "value_kind": "identifier", "cardinality": "1", "required": true, "source_refs": [ "SRC-007", "SRC-008" ] }, { "id": "d-assertion-2", "name": "assertion-mode", "description": "Explicit acquisition mode; predicted results never masquerade as measurements.", "value_kind": "code", "cardinality": "1", "required": true, "source_refs": [ "SRC-007", "SRC-008" ] }, { "id": "d-assertion-3", "name": "steward", "description": "Responsible role and master-system reference, separate from subject identity.", "value_kind": "reference", "cardinality": "1", "required": true, "source_refs": [ "SRC-007", "SRC-008" ] } ], "artifacts": [ { "id": "a-assertion", "name": "Assertion identity record", "description": "Versioned evidence projection for this finding; may be a section of the assertion package rather than a separate file.", "media_or_form": [ "Structured record or evidence reference" ], "serial": true, "identity_strategy": "Authoritative master-system artifact ID first; governed IRI second; adopting-Dimension UUID or ULID last. Keep stable logical ID and separate revision and content digest. Dates are metadata only.", "source_refs": [ "SRC-007", "SRC-008" ] } ], "inline_only_rationale": null } ] }, { "id": "l-subject", "name": "Subject and resolution", "description": "Bind a claim to its immediate biological subject and record the permitted inference scope. Unresolved identity blocks acceptance.", "source_refs": [ "SRC-004", "SRC-007" ], "findings": [ { "id": "f-subject", "name": "Subject and resolution", "description": "Bind a claim to its immediate biological subject and record the permitted inference scope. Unresolved identity blocks acceptance.", "source_refs": [ "SRC-004", "SRC-007" ], "questions": [ { "id": "q-subject-1", "text": "Which organism, specimen or biological observation unit is the immediate subject?", "kind": "relationship", "answer_data": [ "subject-binding", "Subject ID, subject kind, master system and resolution state." ] }, { "id": "q-subject-2", "text": "Which source organism or population links support a sample or pooled result?", "kind": "composition", "answer_data": [ "origin-links", "Source links and pooling or aggregation level, without invented individual values." ] }, { "id": "q-subject-3", "text": "Which anatomical location or observation-unit position does this assertion concern?", "kind": "spatial", "answer_data": [ "subject-location", "Anatomical reference, laterality or plant-part index and scoped location; allow unknown." ] } ], "data_elements": [ { "id": "d-subject-1", "name": "subject-binding", "description": "Subject ID, subject kind, master system and resolution state.", "value_kind": "reference", "cardinality": "1", "required": true, "source_refs": [ "SRC-004", "SRC-007" ] }, { "id": "d-subject-2", "name": "origin-links", "description": "Source links and pooling or aggregation level, without invented individual values.", "value_kind": "collection", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-004", "SRC-007" ] }, { "id": "d-subject-3", "name": "subject-location", "description": "Anatomical reference, laterality or plant-part index and scoped location; allow unknown.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-004", "SRC-007" ] } ], "artifacts": [ { "id": "a-subject", "name": "Subject and resolution record", "description": "Versioned evidence projection for this finding; may be a section of the assertion package rather than a separate file.", "media_or_form": [ "Structured record or evidence reference" ], "serial": true, "identity_strategy": "Authoritative master-system artifact ID first; governed IRI second; adopting-Dimension UUID or ULID last. Keep stable logical ID and separate revision and content digest. Dates are metadata only.", "source_refs": [ "SRC-004", "SRC-007" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "b-meaning", "name": "Trait and procedure", "description": "Preserve the concept and the procedure used to assess it.", "rationale": "This concern prevents an assertion from losing preserve the concept and the procedure used to assess it.", "source_refs": [ "SRC-003", "SRC-004", "SRC-005", "SRC-007" ], "layers": [ { "id": "l-trait", "name": "Trait meaning", "description": "The assertion references the trait concept and preserves the source terminology scope. A clinical abnormality vocabulary does not exhaust biological traits.", "source_refs": [ "SRC-003", "SRC-005" ], "findings": [ { "id": "f-trait", "name": "Trait meaning", "description": "The assertion references the trait concept and preserves the source terminology scope. A clinical abnormality vocabulary does not exhaust biological traits.", "source_refs": [ "SRC-003", "SRC-005" ], "questions": [ { "id": "q-trait-1", "text": "Which trait concept, definition and terminology release supply the meaning?", "kind": "definition", "answer_data": [ "trait-definition", "Concept ID, preferred label, definition reference and release; mark local concepts." ] }, { "id": "q-trait-2", "text": "Is this a normal characteristic, an abnormal feature or a profile-specific classification?", "kind": "classification", "answer_data": [ "trait-class", "Classification and profile rationale; no automatic diagnosis." ] }, { "id": "q-trait-3", "text": "Which evidence supports a local-to-reference term mapping and its exactness?", "kind": "interoperability", "answer_data": [ "term-mapping", "Source and target releases, exact or broader or narrower mapping, reviewer and unresolved state." ] } ], "data_elements": [ { "id": "d-trait-1", "name": "trait-definition", "description": "Concept ID, preferred label, definition reference and release; mark local concepts.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-003", "SRC-005" ] }, { "id": "d-trait-2", "name": "trait-class", "description": "Classification and profile rationale; no automatic diagnosis.", "value_kind": "code", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-003", "SRC-005" ] }, { "id": "d-trait-3", "name": "term-mapping", "description": "Source and target releases, exact or broader or narrower mapping, reviewer and unresolved state.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-003", "SRC-005" ] } ], "artifacts": [ { "id": "a-trait", "name": "Trait meaning record", "description": "Versioned evidence projection for this finding; may be a section of the assertion package rather than a separate file.", "media_or_form": [ "Structured record or evidence reference" ], "serial": true, "identity_strategy": "Authoritative master-system artifact ID first; governed IRI second; adopting-Dimension UUID or ULID last. Keep stable logical ID and separate revision and content digest. Dates are metadata only.", "source_refs": [ "SRC-003", "SRC-005" ] } ], "inline_only_rationale": null } ] }, { "id": "l-variable", "name": "Method and variable definition", "description": "Separate what is assessed from the method and scale that operationalize it. Computational procedures remain visible.", "source_refs": [ "SRC-004", "SRC-005", "SRC-007" ], "findings": [ { "id": "f-variable", "name": "Method and variable definition", "description": "Separate what is assessed from the method and scale that operationalize it. Computational procedures remain visible.", "source_refs": [ "SRC-004", "SRC-005", "SRC-007" ], "questions": [ { "id": "q-variable-1", "text": "Which method version and variable definition were applied?", "kind": "process", "answer_data": [ "method-binding", "Trait, method and scale IDs plus protocol reference and declared deviations." ] }, { "id": "q-variable-2", "text": "Which observer, instrument or software version produced the evidence?", "kind": "provenance", "answer_data": [ "producer", "Role or device reference, software version and calibration or scoring qualification reference when relevant." ] }, { "id": "q-variable-3", "text": "Which method limitations or conditions prevent comparison with another assertion?", "kind": "constraint", "answer_data": [ "method-limits", "Applicability, detection limits, non-comparable protocols and relevant uncertainty references." ] } ], "data_elements": [ { "id": "d-variable-1", "name": "method-binding", "description": "Trait, method and scale IDs plus protocol reference and declared deviations.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-004", "SRC-005", "SRC-007" ] }, { "id": "d-variable-2", "name": "producer", "description": "Role or device reference, software version and calibration or scoring qualification reference when relevant.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-004", "SRC-005", "SRC-007" ] }, { "id": "d-variable-3", "name": "method-limits", "description": "Applicability, detection limits, non-comparable protocols and relevant uncertainty references.", "value_kind": "collection", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-004", "SRC-005", "SRC-007" ] } ], "artifacts": [ { "id": "a-variable", "name": "Method and variable definition record", "description": "Versioned evidence projection for this finding; may be a section of the assertion package rather than a separate file.", "media_or_form": [ "Structured record or evidence reference" ], "serial": true, "identity_strategy": "Authoritative master-system artifact ID first; governed IRI second; adopting-Dimension UUID or ULID last. Keep stable logical ID and separate revision and content digest. Dates are metadata only.", "source_refs": [ "SRC-004", "SRC-005", "SRC-007" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "b-value", "name": "Result and assessment", "description": "Express a result without losing its scale or missingness semantics.", "rationale": "This concern prevents an assertion from losing express a result without losing its scale or missingness semantics.", "source_refs": [ "SRC-001", "SRC-002", "SRC-005", "SRC-006" ], "layers": [ { "id": "l-result", "name": "Typed result", "description": "Preserve the original representation and its scale. Local conversion is a separately attributed derivation, never an overwrite.", "source_refs": [ "SRC-002", "SRC-005", "SRC-006" ], "findings": [ { "id": "f-result", "name": "Typed result", "description": "Preserve the original representation and its scale. Local conversion is a separately attributed derivation, never an overwrite.", "source_refs": [ "SRC-002", "SRC-005", "SRC-006" ], "questions": [ { "id": "q-result-1", "text": "What value, category or coupled component set was recorded?", "kind": "measurement", "answer_data": [ "result-value", "Discriminated result type and value, including component codes where needed." ] }, { "id": "q-result-2", "text": "Which unit or ordered category definitions give the result its scale?", "kind": "measurement", "answer_data": [ "result-scale", "Unit code and vocabulary version or category set with explicit ordering; dimensionless is explicit." ] }, { "id": "q-result-3", "text": "Which conversion, rounding or censoring rule was applied to the original value?", "kind": "validation", "answer_data": [ "result-transform", "Original value, comparator, transform and precision; incompatible dimensions produce refusal." ] } ], "data_elements": [ { "id": "d-result-1", "name": "result-value", "description": "Discriminated result type and value, including component codes where needed.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-002", "SRC-005", "SRC-006" ] }, { "id": "d-result-2", "name": "result-scale", "description": "Unit code and vocabulary version or category set with explicit ordering; dimensionless is explicit.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-002", "SRC-005", "SRC-006" ] }, { "id": "d-result-3", "name": "result-transform", "description": "Original value, comparator, transform and precision; incompatible dimensions produce refusal.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-002", "SRC-005", "SRC-006" ] } ], "artifacts": [ { "id": "a-result", "name": "Typed result record", "description": "Versioned evidence projection for this finding; may be a section of the assertion package rather than a separate file.", "media_or_form": [ "Structured record or evidence reference" ], "serial": true, "identity_strategy": "Authoritative master-system artifact ID first; governed IRI second; adopting-Dimension UUID or ULID last. Keep stable logical ID and separate revision and content digest. Dates are metadata only.", "source_refs": [ "SRC-002", "SRC-005", "SRC-006" ] } ], "inline_only_rationale": null } ] }, { "id": "l-assessment", "name": "Assessment and missingness", "description": "A local assessment state distinguishes presence, explicit absence, uncertainty, not assessed and unavailable. The latter states must not be coerced into an external boolean.", "source_refs": [ "SRC-001", "SRC-002" ], "findings": [ { "id": "f-assessment", "name": "Assessment and missingness", "description": "A local assessment state distinguishes presence, explicit absence, uncertainty, not assessed and unavailable. The latter states must not be coerced into an external boolean.", "source_refs": [ "SRC-001", "SRC-002" ], "questions": [ { "id": "q-assessment-1", "text": "Was the feature present, explicitly absent, uncertain, not assessed or unavailable?", "kind": "state", "answer_data": [ "assessment-state", "Declared local state with missingness reason; zero is a value, not missing." ] }, { "id": "q-assessment-2", "text": "Which examination or report supports an explicit negative finding?", "kind": "evidence", "answer_data": [ "negative-support", "Assessment evidence and scope; omission alone provides no negative evidence." ] }, { "id": "q-assessment-3", "text": "Which severity, modifiers or reference range qualify this specific assertion?", "kind": "quality", "answer_data": [ "qualifiers", "Versioned qualifier terms or applicable range with context; do not imply universal normality." ] } ], "data_elements": [ { "id": "d-assessment-1", "name": "assessment-state", "description": "Declared local state with missingness reason; zero is a value, not missing.", "value_kind": "code", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002" ] }, { "id": "d-assessment-2", "name": "negative-support", "description": "Assessment evidence and scope; omission alone provides no negative evidence.", "value_kind": "reference", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-002" ] }, { "id": "d-assessment-3", "name": "qualifiers", "description": "Versioned qualifier terms or applicable range with context; do not imply universal normality.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-002" ] } ], "artifacts": [ { "id": "a-assessment", "name": "Assessment and missingness record", "description": "Versioned evidence projection for this finding; may be a section of the assertion package rather than a separate file.", "media_or_form": [ "Structured record or evidence reference" ], "serial": true, "identity_strategy": "Authoritative master-system artifact ID first; governed IRI second; adopting-Dimension UUID or ULID last. Keep stable logical ID and separate revision and content digest. Dates are metadata only.", "source_refs": [ "SRC-001", "SRC-002" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "b-setting", "name": "Time and context", "description": "Qualify the assertion by temporal and biological circumstances.", "rationale": "This concern prevents an assertion from losing qualify the assertion by temporal and biological circumstances.", "source_refs": [ "SRC-001", "SRC-004", "SRC-007" ], "layers": [ { "id": "l-time", "name": "Time and repetition", "description": "Separate when a trait applies from acquisition and record creation. Repeated measurements are new assertions; corrections are revisions.", "source_refs": [ "SRC-001", "SRC-004", "SRC-007" ], "findings": [ { "id": "f-time", "name": "Time and repetition", "description": "Separate when a trait applies from acquisition and record creation. Repeated measurements are new assertions; corrections are revisions.", "source_refs": [ "SRC-001", "SRC-004", "SRC-007" ], "questions": [ { "id": "q-time-1", "text": "When did the asserted feature apply and when was the evidence acquired?", "kind": "temporal", "answer_data": [ "time-context", "Phenomenon interval or age, acquisition time and ingestion time; preserve uncertainty and original precision." ] }, { "id": "q-time-2", "text": "What onset or resolution is supported without inferring it from first or last entry?", "kind": "lifecycle", "answer_data": [ "course", "Onset and resolution evidence, age or developmental stage and unknown bounds." ] }, { "id": "q-time-3", "text": "Which series and replicate identifiers distinguish repeats from corrections?", "kind": "relationship", "answer_data": [ "series-links", "Series ID, replicate ID and prior assertion or revision relation; timestamps are not identity." ] } ], "data_elements": [ { "id": "d-time-1", "name": "time-context", "description": "Phenomenon interval or age, acquisition time and ingestion time; preserve uncertainty and original precision.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-004", "SRC-007" ] }, { "id": "d-time-2", "name": "course", "description": "Onset and resolution evidence, age or developmental stage and unknown bounds.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-004", "SRC-007" ] }, { "id": "d-time-3", "name": "series-links", "description": "Series ID, replicate ID and prior assertion or revision relation; timestamps are not identity.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-004", "SRC-007" ] } ], "artifacts": [ { "id": "a-time", "name": "Time and repetition record", "description": "Versioned evidence projection for this finding; may be a section of the assertion package rather than a separate file.", "media_or_form": [ "Structured record or evidence reference" ], "serial": true, "identity_strategy": "Authoritative master-system artifact ID first; governed IRI second; adopting-Dimension UUID or ULID last. Keep stable logical ID and separate revision and content digest. Dates are metadata only.", "source_refs": [ "SRC-001", "SRC-004", "SRC-007" ] } ], "inline_only_rationale": null } ] }, { "id": "l-context", "name": "Biological and environmental context", "description": "Conditions qualify biological interpretation without proving causation. Environmental measurements are referenced from their own records.", "source_refs": [ "SRC-004", "SRC-007" ], "findings": [ { "id": "f-context", "name": "Biological and environmental context", "description": "Conditions qualify biological interpretation without proving causation. Environmental measurements are referenced from their own records.", "source_refs": [ "SRC-004", "SRC-007" ], "questions": [ { "id": "q-context-1", "text": "What taxonomic and developmental context governs interpretation of this assertion?", "kind": "classification", "answer_data": [ "biological-context", "Taxon reference, age or stage vocabulary and relevant subject attributes under access policy." ] }, { "id": "q-context-2", "text": "Which environment, study or treatment records describe the observation conditions?", "kind": "relationship", "answer_data": [ "condition-links", "Study, environment and factor references with their scope and time, without copying their lifecycle." ] }, { "id": "q-context-3", "text": "Which context is unknown, confounded or incompatible with the intended comparison?", "kind": "exception", "answer_data": [ "context-gaps", "Missing covariates, stated confounding and limits; no inference of genetic causation." ] } ], "data_elements": [ { "id": "d-context-1", "name": "biological-context", "description": "Taxon reference, age or stage vocabulary and relevant subject attributes under access policy.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-004", "SRC-007" ] }, { "id": "d-context-2", "name": "condition-links", "description": "Study, environment and factor references with their scope and time, without copying their lifecycle.", "value_kind": "collection", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-004", "SRC-007" ] }, { "id": "d-context-3", "name": "context-gaps", "description": "Missing covariates, stated confounding and limits; no inference of genetic causation.", "value_kind": "collection", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-004", "SRC-007" ] } ], "artifacts": [ { "id": "a-context", "name": "Biological and environmental context record", "description": "Versioned evidence projection for this finding; may be a section of the assertion package rather than a separate file.", "media_or_form": [ "Structured record or evidence reference" ], "serial": true, "identity_strategy": "Authoritative master-system artifact ID first; governed IRI second; adopting-Dimension UUID or ULID last. Keep stable logical ID and separate revision and content digest. Dates are metadata only.", "source_refs": [ "SRC-004", "SRC-007" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "b-lineage", "name": "Evidence and record continuity", "description": "Trace support and controlled revisions without equating record state with biology.", "rationale": "This concern prevents an assertion from losing trace support and controlled revisions without equating record state with biology.", "source_refs": [ "SRC-001", "SRC-005", "SRC-008" ], "layers": [ { "id": "l-evidence", "name": "Evidence and derivation", "description": "Link claims to evidence with explicit lineage. Evidence identity, availability and scientific adequacy are separate properties.", "source_refs": [ "SRC-001", "SRC-005", "SRC-008" ], "findings": [ { "id": "f-evidence", "name": "Evidence and derivation", "description": "Link claims to evidence with explicit lineage. Evidence identity, availability and scientific adequacy are separate properties.", "source_refs": [ "SRC-001", "SRC-005", "SRC-008" ], "questions": [ { "id": "q-evidence-1", "text": "Which primary records or derived artifacts support the assertion?", "kind": "provenance", "answer_data": [ "evidence-links", "Evidence ID, provenance role, locator and restricted availability state." ] }, { "id": "q-evidence-2", "text": "Which inputs and computation support a derived or predicted result?", "kind": "process", "answer_data": [ "derivation", "Input assertion references, formula or model version and attribution; mark prediction separately." ] }, { "id": "q-evidence-3", "text": "Which uncertainty, conflicting observation or scoring limitation remains unresolved?", "kind": "quality", "answer_data": [ "quality-review", "Uncertainty type, review status, contrary evidence and reviewer; no unsupported numerical confidence." ] } ], "data_elements": [ { "id": "d-evidence-1", "name": "evidence-links", "description": "Evidence ID, provenance role, locator and restricted availability state.", "value_kind": "collection", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-005", "SRC-008" ] }, { "id": "d-evidence-2", "name": "derivation", "description": "Input assertion references, formula or model version and attribution; mark prediction separately.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-005", "SRC-008" ] }, { "id": "d-evidence-3", "name": "quality-review", "description": "Uncertainty type, review status, contrary evidence and reviewer; no unsupported numerical confidence.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-005", "SRC-008" ] } ], "artifacts": [ { "id": "a-evidence", "name": "Evidence and derivation record", "description": "Versioned evidence projection for this finding; may be a section of the assertion package rather than a separate file.", "media_or_form": [ "Structured record or evidence reference" ], "serial": true, "identity_strategy": "Authoritative master-system artifact ID first; governed IRI second; adopting-Dimension UUID or ULID last. Keep stable logical ID and separate revision and content digest. Dates are metadata only.", "source_refs": [ "SRC-001", "SRC-005", "SRC-008" ] } ], "inline_only_rationale": null } ] }, { "id": "l-revision", "name": "Correction and withdrawal", "description": "The proposed local lifecycle uses draft, reviewed, superseded and withdrawn states. Record withdrawal differs from biological resolution.", "source_refs": [ "SRC-008" ], "findings": [ { "id": "f-revision", "name": "Correction and withdrawal", "description": "The proposed local lifecycle uses draft, reviewed, superseded and withdrawn states. Record withdrawal differs from biological resolution.", "source_refs": [ "SRC-008" ], "questions": [ { "id": "q-revision-1", "text": "Which review state and supersession relation apply to this record revision?", "kind": "lifecycle", "answer_data": [ "record-state", "State, predecessor and successor references with responsible reviewer." ] }, { "id": "q-revision-2", "text": "Who may correct a subject binding or value and on what evidence?", "kind": "authority", "answer_data": [ "correction-authority", "Role, correction reason, evidence and expected prior revision; concurrent changes conflict." ] }, { "id": "q-revision-3", "text": "Which retention rule permits disposal of payloads and what minimal linkage may remain?", "kind": "retention", "answer_data": [ "disposition", "Policy reference, disposition decision and lawful minimal tombstone; history does not justify unlimited retention." ] } ], "data_elements": [ { "id": "d-revision-1", "name": "record-state", "description": "State, predecessor and successor references with responsible reviewer.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-008" ] }, { "id": "d-revision-2", "name": "correction-authority", "description": "Role, correction reason, evidence and expected prior revision; concurrent changes conflict.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-008" ] }, { "id": "d-revision-3", "name": "disposition", "description": "Policy reference, disposition decision and lawful minimal tombstone; history does not justify unlimited retention.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-008" ] } ], "artifacts": [ { "id": "a-revision", "name": "Correction and withdrawal record", "description": "Versioned evidence projection for this finding; may be a section of the assertion package rather than a separate file.", "media_or_form": [ "Structured record or evidence reference" ], "serial": true, "identity_strategy": "Authoritative master-system artifact ID first; governed IRI second; adopting-Dimension UUID or ULID last. Keep stable logical ID and separate revision and content digest. Dates are metadata only.", "source_refs": [ "SRC-008" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "b-use", "name": "Exchange and governed use", "description": "Carry semantic losses and permission limits into every projection.", "rationale": "This concern prevents an assertion from losing carry semantic losses and permission limits into every projection.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005", "SRC-008", "SRC-009" ], "layers": [ { "id": "l-exchange", "name": "Exchange and interpretation links", "description": "Mappings are proposed alignments. A target format may omit local states or qualifiers; export must report that loss.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ], "findings": [ { "id": "f-exchange", "name": "Exchange and interpretation links", "description": "Mappings are proposed alignments. A target format may omit local states or qualifiers; export must report that loss.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ], "questions": [ { "id": "q-exchange-1", "text": "Which target profile and version can represent this assertion without changing its meaning?", "kind": "interoperability", "answer_data": [ "export-profile", "Selected Phenopackets or plant profile, mapping version and unsupported fields." ] }, { "id": "q-exchange-2", "text": "What round-trip or comparison evidence demonstrates preservation of subject, state, unit and time?", "kind": "validation", "answer_data": [ "mapping-check", "Fixture reference and differences, with no conformance claim before testing." ] }, { "id": "q-exchange-3", "text": "Which external disease, genotype or breeding interpretation is linked and with what qualification?", "kind": "relationship", "answer_data": [ "interpretation-links", "External master reference, association or interpretation role and provenance; no local clinical or selection decision." ] } ], "data_elements": [ { "id": "d-exchange-1", "name": "export-profile", "description": "Selected Phenopackets or plant profile, mapping version and unsupported fields.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ] }, { "id": "d-exchange-2", "name": "mapping-check", "description": "Fixture reference and differences, with no conformance claim before testing.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ] }, { "id": "d-exchange-3", "name": "interpretation-links", "description": "External master reference, association or interpretation role and provenance; no local clinical or selection decision.", "value_kind": "collection", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ] } ], "artifacts": [ { "id": "a-exchange", "name": "Exchange and interpretation links record", "description": "Versioned evidence projection for this finding; may be a section of the assertion package rather than a separate file.", "media_or_form": [ "Structured record or evidence reference" ], "serial": true, "identity_strategy": "Authoritative master-system artifact ID first; governed IRI second; adopting-Dimension UUID or ULID last. Keep stable logical ID and separate revision and content digest. Dates are metadata only.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ] } ], "inline_only_rationale": null } ] }, { "id": "l-governance", "name": "Use and disclosure constraints", "description": "Proposed local safeguards require purpose and authority checks. A data format or de-identified label is not sharing permission.", "source_refs": [ "SRC-008", "SRC-009" ], "findings": [ { "id": "f-governance", "name": "Use and disclosure constraints", "description": "Proposed local safeguards require purpose and authority checks. A data format or de-identified label is not sharing permission.", "source_refs": [ "SRC-008", "SRC-009" ], "questions": [ { "id": "q-governance-1", "text": "Which policy governs subject identifiability, permitted purpose and secondary use?", "kind": "privacy", "answer_data": [ "use-policy", "Applicable policy and authority or consent reference where required; jurisdiction review remains external." ] }, { "id": "q-governance-2", "text": "Which recipient may read which assertion fields and supporting artifacts?", "kind": "access", "answer_data": [ "disclosure-scope", "Recipient role, purpose, field and artifact scope, expiry and refusal for insufficient authority." ] }, { "id": "q-governance-3", "text": "Which disclosure risks or exceptional access requests require steward review?", "kind": "security", "answer_data": [ "risk-review", "Sensitive combinations, location precision, linkage risk and time-limited exception evidence; audit reference only." ] } ], "data_elements": [ { "id": "d-governance-1", "name": "use-policy", "description": "Applicable policy and authority or consent reference where required; jurisdiction review remains external.", "value_kind": "reference", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-008", "SRC-009" ] }, { "id": "d-governance-2", "name": "disclosure-scope", "description": "Recipient role, purpose, field and artifact scope, expiry and refusal for insufficient authority.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-008", "SRC-009" ] }, { "id": "d-governance-3", "name": "risk-review", "description": "Sensitive combinations, location precision, linkage risk and time-limited exception evidence; audit reference only.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-008", "SRC-009" ] } ], "artifacts": [ { "id": "a-governance", "name": "Use and disclosure constraints record", "description": "Versioned evidence projection for this finding; may be a section of the assertion package rather than a separate file.", "media_or_form": [ "Structured record or evidence reference" ], "serial": true, "identity_strategy": "Authoritative master-system artifact ID first; governed IRI second; adopting-Dimension UUID or ULID last. Keep stable logical ID and separate revision and content digest. Dates are metadata only.", "source_refs": [ "SRC-008", "SRC-009" ] } ], "inline_only_rationale": null } ] } ] } ] }, "functions": [ { "id": "fn-register", "name": "Register an assertion draft", "description": "Proposed, unimplemented local operation. Create a local assertion after resolving its subject and trait references.", "inputs": [ "Subject binding, trait definition, acquisition mode, assessment state and evidence references" ], "outputs": [ "Draft assertion with stable ID or explicit refusal" ], "preconditions": [ "No identity collision; subject is biological and resolved; collection authority recorded" ], "effects": [ "Creates a draft only; does not observe or alter an organism" ], "source_refs": [ "SRC-001", "SRC-004", "SRC-007" ] }, { "id": "fn-qualify", "name": "Qualify a result", "description": "Proposed, unimplemented local operation. Attach the original scale, method and context; preserve imported ambiguity.", "inputs": [ "Existing draft revision, original value and method-scale context" ], "outputs": [ "Qualified revision or incompatibility report" ], "preconditions": [ "Editor authority and matching expected revision; missing information is explicitly marked" ], "effects": [ "Adds metadata and preserves raw values; does not assert comparability" ], "source_refs": [ "SRC-002", "SRC-005", "SRC-006" ] }, { "id": "fn-link", "name": "Link supporting evidence", "description": "Proposed, unimplemented local operation. Record a cited observation or derivation without certifying it as true.", "inputs": [ "Evidence master IDs, input assertion IDs, producer and lineage role" ], "outputs": [ "Evidence links or unresolved-reference refusal" ], "preconditions": [ "Read authority for referenced data; input versions known; no circular self-support" ], "effects": [ "Updates local evidence index without importing restricted payloads" ], "source_refs": [ "SRC-001", "SRC-008" ] }, { "id": "fn-review", "name": "Record a semantic review", "description": "Proposed, unimplemented local operation. Record reviewer findings about subject, scale, missingness and temporal consistency.", "inputs": [ "Assertion revision, profile rules and reviewer findings" ], "outputs": [ "Reviewed record or unresolved-issues report" ], "preconditions": [ "Qualified reviewer role; evidence accessible or limitations explicitly recorded" ], "effects": [ "Marks local review status only; no clinical diagnosis, prediction or selection action" ], "source_refs": [ "SRC-001", "SRC-002", "SRC-004" ] }, { "id": "fn-supersede", "name": "Supersede or withdraw an assertion", "description": "Proposed, unimplemented local operation. Link a correction or withdrawal to its predecessor under the retention policy.", "inputs": [ "Prior revision, reason, replacement where applicable and authorization" ], "outputs": [ "New revision or concurrency refusal" ], "preconditions": [ "Expected revision matches; correction supported; disposition policy checked" ], "effects": [ "Preserves permitted lineage while marking predecessor state; no biological state change" ], "source_refs": [ "SRC-008", "SRC-009" ] }, { "id": "fn-project", "name": "Prepare an exchange projection", "description": "Proposed, unimplemented local operation. Produce a local recipient-scoped representation and a semantic loss report.", "inputs": [ "Assertion revision, target profile version and disclosure authorization reference" ], "outputs": [ "Local projection and loss report or refusal" ], "preconditions": [ "Recipient and purpose allowed; no unsupported state coercion; profile selected" ], "effects": [ "Creates a local artifact only; does not transmit data or grant access" ], "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005", "SRC-009" ] } ], "composition": [ { "target": "WM-LIV-002", "relation": "REFERENCE", "purpose": "Conditional organism subject or source binding; registry parent is not inheritance.", "required": false, "source_refs": [ "SRC-004", "SRC-007" ] }, { "target": "WM-LIV-023", "relation": "REFERENCE", "purpose": "Immediate specimen and provenance reference; specimen custody remains external.", "required": false, "source_refs": [ "SRC-004", "SRC-007" ] }, { "target": "WM-LIV-003", "relation": "REFERENCE", "purpose": "Population or pooled-subject context; never assign its summary to every individual.", "required": false, "source_refs": [ "SRC-004", "SRC-007" ] }, { "target": "WM-LIV-001", "relation": "REFERENCE", "purpose": "Taxonomic interpretation context with externally governed identity.", "required": false, "source_refs": [ "SRC-004" ] }, { "target": "WM-LIV-012", "relation": "REFERENCE", "purpose": "Optional genomic interpretation link, without variant assessment or causation inference.", "required": false, "source_refs": [ "SRC-003" ] }, { "target": "WM-LIV-021", "relation": "REFERENCE", "purpose": "Optional disease interpretation link, without making a diagnosis.", "required": false, "source_refs": [ "SRC-001", "SRC-003" ] }, { "target": "GA4GH Phenopackets 2.0", "relation": "ALIGN", "purpose": "Profile-dependent exchange of feature assertions and measurements; test missing-state projection.", "required": false, "source_refs": [ "SRC-001", "SRC-002" ] }, { "target": "MIAPPE and Crop Ontology", "relation": "ALIGN", "purpose": "Plant method, scale, unit and context alignment; pin releases before implementation.", "required": false, "source_refs": [ "SRC-004", "SRC-005" ] }, { "target": "SOSA/SSN and PROV-O", "relation": "ALIGN", "purpose": "Conceptual observation and lineage references; no RDF conformance claimed.", "required": false, "source_refs": [ "SRC-007", "SRC-008" ] } ], "serviceLayers": { "dimension": { "owner_package_requirements": [ "Name a scientific, clinical or environmental steward and the authoritative assertion master system.", "Bind subject identifiers, selected domain profile, vocabulary releases and method versions.", "Declare purpose, access rules, correction authority and retention schedule before storing sensitive observations.", "Require a biological subject binding; individual, specimen and population model dependencies are conditional, not globally mandatory." ], "namespace_guidance": "Use a governed assertion namespace distinct from trait vocabulary and subject namespaces. Preserve source IDs and version pins; local extensions cannot redefine external terms.", "registry_links": [ "vr.wm-liv-015", "WM-LIV-002", "WM-LIV-023", "WM-LIV-003" ] }, "canon_and_patch": { "canonicalization_rules": [ "Canonical within an adopting Dimension means the designated record master, not a universally true phenotype. This research is a noncanonical reviewable draft.", "Keep one stable assertion ID, revisions and separate identities for repeated measurements. Preserve original value, scale, missingness and subject level." ], "patch_rules": [ "Require expected revision, authorized role, reason and evidence for a correction; reject stale concurrent writes.", "Changing subject or polarity requires explicit correction review; never silently rewrite upstream source data." ], "compatibility_rules": [ "Pin vocabulary, scale and profile versions. Broader or narrower term mappings are not exact equivalence.", "Unknown, not assessed and unavailable do not map to false or absent. Report lossy conversions and reject unsupported exports." ] }, "artifact_rules": { "identity_priority": [ "Authoritative master-system identifier", "Governed global identifier or IRI", "UUID or ULID assigned by the adopting Dimension" ], "timestamp_rule": "Exact timestamps use RFC 3339 with seconds and explicit offset or Z. Distinguish phenomenon/event time, observation or acquisition time, result time and ingestion time. Preserve date-only, age, stage, uncertain interval or unknown values as typed temporal data; never fabricate seconds or an offset for imprecise evidence.", "serial_naming_rule": "Use stable assertion and artifact IDs with separate revision tokens; dates alone never identify a serial record.", "integrity_rule": "Record content digest, media type, source locator and provenance for retained payloads. A digest proves byte continuity only. Access checks apply to locators and digests as well as payloads." }, "policies": [ "Local design rule: do not use trait data for discriminatory rankings, unsupported diagnosis, genetic determinism or automated selection actions.", "Local design rule: assess identifiability and linkage risk before disclosure; a pseudonym, public vocabulary term or exchange format does not confer access rights.", "Follow the adopting jurisdiction and institutional policy for authority, consent where applicable, retention and exceptional access; no legal compliance claim is made here.", "Dangerous biological subjects remain at policy and reference level; no experiment, intervention or device operation is authorized." ], "crud": { "read": [ "Resolve authorized view, source versions and quality flags; withheld evidence remains explicitly unavailable." ], "create": [ "Create a draft with master ID, subject binding, trait definition, acquisition mode, assessment state and steward; do not invent missing measurements." ], "update": [ "Use conditional revision writes and attributed corrections; repeated observations create new assertions." ], "delete": [ "The adopting-Dimension records service executes retention and disposition for local assertion payloads under policy and holds. Preserve only a lawful minimal tombstone or supersession link; remove sensitive content from caches and derived artifacts within that policy. Referenced organism, specimen, ontology and disease records are never cascade-deleted." ] }, "roles": [ { "name": "Data steward", "responsibilities": [ "Sets local scope, mastership and disposition policy." ] }, { "name": "Observer or importer", "responsibilities": [ "Records method, source, uncertainty and acquisition mode without inventing facts." ] }, { "name": "Domain reviewer", "responsibilities": [ "Checks trait meaning, subject scope, evidence and corrections; clinical judgments stay in the responsible clinical system." ] }, { "name": "Access custodian", "responsibilities": [ "Approves recipient-purpose scope and exceptions under the applicable policy." ] }, { "name": "Projection maintainer", "responsibilities": [ "Pins mapping versions and reports losses and unsupported fields." ] } ], "access": { "default_rule": "Deny sensitive instance access unless the policy grants the requester and purpose an explicit scope; public specification availability grants no instance access.", "scopes": [ "bundle", "layer", "finding", "artifact" ], "exceptions": [ "Require documented, time-limited approval for exceptional access; unknown authority produces refusal." ], "audit_requirements": [ "Send read, correction, export preparation and disposition event references to the adopting audit service; this model does not implement its log lifecycle." ] }, "agents_bootstrap": { "filename": "AGENTS.md", "required_fields": [ "Name", "Type", "Specification URL", "Storage type URL", "Interface URL", "Processes URL" ], "read_order": [ "Read AGENTS.md and the nearest owner and Dimension policy.", "Read the pinned specification, holds and subject and terminology bindings.", "Inspect assertion, result, evidence and recipient permissions before any permitted local operation." ] } }, "coverage": { "claim": "Source-grounded proposed structure for a biological phenotype or trait assertion record using selected human clinical and plant research evidence. A separate frozen no-tools local self-audit found no critical contradiction. Independent review, live source/version verification, domain profiles and executable conformance remain holds; this is a noncanonical reviewable draft, not universal coverage or an operational clinical system.", "confidence": "medium", "checklist": [ { "dimension": "identity", "status": "covered", "notes": "Distinct claim, subject, trait and artifact IDs." }, { "dimension": "lifecycle", "status": "covered", "notes": "Proposed record review, revision and withdrawal; biological resolution remains separate." }, { "dimension": "relationships", "status": "covered", "notes": "Conditional master references and explicit inference scope." }, { "dimension": "temporal", "status": "covered", "notes": "Partial dates and ages retained without fabricated exact timestamps." }, { "dimension": "provenance", "status": "covered", "notes": "Attribution, inputs and evidence availability are explicit." }, { "dimension": "ownership", "status": "covered", "notes": "Neutral steward and external master boundaries." }, { "dimension": "validation", "status": "covered", "notes": "Semantic research rules are specified; executable instance constraints are a gap." }, { "dimension": "access", "status": "covered", "notes": "Recipient and purpose scoped projections with refusal paths." }, { "dimension": "retention and deletion", "status": "covered", "notes": "Adopting service performs policy-governed disposal; no cascade deletion." }, { "dimension": "interoperability", "status": "covered", "notes": "Conceptual alignments and explicit loss reports; adapters remain untested." }, { "dimension": "direct properties", "status": "covered", "notes": "Value, category, scale, qualifiers and state; no physical properties of the assertion record itself." }, { "dimension": "recognition and observation", "status": "covered", "notes": "Measured, calculated, reported and predicted modes stay distinct." }, { "dimension": "capabilities and actions", "status": "covered", "notes": "Six proposed local record operations; no intervention or decision execution." }, { "dimension": "species and sector profiles", "status": "gap", "notes": "Strongest evidence is human clinical and plant research; animal, microbial and ecological specializations remain unvalidated." }, { "dimension": "independent review", "status": "gap", "notes": "Claude and Grok skipped under owner waiver; separate local no-tools audit is not independent review." }, { "dimension": "live source verification", "status": "gap", "notes": "Browser content reviewed; direct HTTP status and complete release pinning remain unchecked in this sandbox." } ], "known_omissions": [ "Executable nested instance schemas, controlled-state validation, source profile mappings and adversarial round-trip fixtures.", "Pinned neighbor model versions, vocabulary releases, licenses and independently checked source availability.", "Animal, microbial, ecological and species-specific reference ranges and measurement uncertainty profiles.", "Jurisdiction-specific privacy, consent, retention, data sovereignty and clinical or breeding governance review." ], "conflicts": [], "regional_assumptions": [ "No jurisdiction supplies universal rules here. Governance policies are proposed safeguards and require local review.", "Human clinical abnormality vocabularies and plant experimental metadata have different scopes; neither is universal across organisms." ], "adversarial_checks": [ "Missing and zero results cannot be normalized to explicit absence.", "Sample, plot or population assertions cannot silently become individual claims.", "A prediction or derived feature cannot be relabeled as a raw measurement.", "Unit conversion cannot establish biological comparability or erase method differences.", "Record withdrawal and ontology deprecation cannot establish biological resolution.", "An ontology term or phenotype-to-variant link cannot establish diagnosis, inheritance or causation." ] }, "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 stable root is an assertion record that can be reviewed, revised or withdrawn. A referenced trait concept, the biological bearer, an acquisition event and a result are distinct. The registry standalone-mm describes the record plane, not the subject-kind enum. The organism parent supplies contextual association rather than is-a inheritance; no strict relation-ledger rows were found." }, "decisions": [ { "concept": "Assertion root versus trait dictionary", "disposition": "accepted", "rationale": "Names, scope, questions and functions consistently use a persistent assertion root while reusing trait and variable definitions by reference. The two are not merged into one identifier or lifecycle." }, { "concept": "Organism parent and subject level", "disposition": "qualified", "rationale": "The registry parent is not valid biological inheritance for an assertion. Conditional organism, specimen and population references preserve immediate subject level; the core requires a resolved biological subject even though no single neighbor is globally required." }, { "concept": "Pure environment and pooled findings", "disposition": "bounded", "rationale": "The admitted plant standard has broader observation-unit scope than this biological model. The explicit exclusion of pure environmental observations is coherent, and pooling cannot silently create individual values." }, { "concept": "Trait and operational variable", "disposition": "separated", "rationale": "The trait meaning and method-scale binding are separate findings. Terminology scope, release, mapping exactness and local concepts remain visible rather than treating a shared label as semantic identity." }, { "concept": "Observed, derived, reported and predicted results", "disposition": "accepted with labeling", "rationale": "The supplement's observed-only claim is rejected. The candidate preserves acquisition mode and computational lineage without authorizing prediction or presenting a prediction as a raw measurement." }, { "concept": "Missingness, polarity and zero", "disposition": "accepted", "rationale": "The local assessment state distinguishes explicit absence, uncertainty, unavailable and not assessed. A negative assertion requires supporting assessment evidence, and unsupported boolean projections must be refused." }, { "concept": "Value scales and comparability", "disposition": "qualified", "rationale": "Original values, category order, coupled components and conversion history are retained. Unit compatibility alone cannot establish comparable biological methods, subjects or conditions." }, { "concept": "Temporal precision and record continuity", "disposition": "accepted", "rationale": "Typed ages, stages and uncertain dates are preserved without fabricated seconds. Repeats have separate identities; corrections are revisions; record withdrawal does not imply that a biological feature resolved." }, { "concept": "Genetic and diagnostic interpretation", "disposition": "delegated", "rationale": "The external links are conditional and qualified. Neither a phenotype code, a disease link nor a variant association supplies a local diagnosis, causation conclusion or breeding decision." }, { "concept": "Six local record operations", "disposition": "accepted as proposed", "rationale": "Inputs, outputs, authority preconditions, refusal paths and effects stay within record maintenance. No function performs measurement, intervention, diagnosis, external transmission or permission expansion." }, { "concept": "Evidence and scientific adequacy", "disposition": "separated", "rationale": "Evidence identity, access, attribution and unresolved quality are represented separately. A digest, source link or provenance graph cannot certify the truth of an assertion." }, { "concept": "Privacy and retention", "disposition": "accepted with policy dependency", "rationale": "The rules are explicitly proposed safeguards with adopting-policy dependencies. History retention is limited by lawful disposition; no cascade deletion reaches referenced biological records, and pseudonyms do not grant access." }, { "concept": "Candidate schema and mapping coverage", "disposition": "deferred", "rationale": "Candidate data groups and alignments are not executable instance schemas. Subject-level, missingness, time and unit round-trip fixtures and pinned model bindings remain required before operational claims." }, { "concept": "Source authority and independence", "disposition": "limited", "rationale": "Official browser content supports selected distinctions, but mutable documentation and historical mappings need version review. Direct HTTP checks were not run, rather than measured as failed requests. The local self-audit does not replace an independent provider." } ], "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 an independent second-provider review.", "Live source and version verification remains incomplete. Nine admitted source pages were reviewed through the browsing tool, but direct HTTP checks were not run due to the sandbox restriction: zero attempts, zero measured HTTP 200 responses and no response hashes. The coordinator must run check_sources.py outside the sandbox. Mutable documentation, ontology releases, licenses and historical mapping applicability still require verification.", "Species, study, clinical, breeding and jurisdiction profiles require qualified review. Human clinical and plant evidence does not establish animal, microbial or ecological completeness; privacy, consent, retention and data sovereignty rules are not legal determinations.", "Nested instance schemas, pinned neighbor bindings, terminology validation, uncertainty profiles and tested Phenopackets/MIAPPE/ontology mappings remain incomplete. Proposed local operations are unimplemented; no runtime, clinical, scientific-validity or external-standard conformance certification is claimed.", "Independent external review was explicitly waived by the repository owner; this codex-only result remains a reviewable draft." ], "deferredResearch": [ "Pin and independently verify source editions, ontology and scale releases, source licenses and adopting model bindings.", "Build executable profiles and adversarial fixtures for negative versus missing results, repeated versus corrected observations, unit conversion, pooled subjects, uncertain time and restricted evidence.", "Validate species-specific and jurisdiction-specific uses with domain and data-governance reviewers before operational adoption.", "Restore independent external review before any canonical or publishable-draft promotion." ] }, "statistics": { "sources": 9, "bundles": 6, "layers": 12, "findings": 12, "questions": 36, "artifacts": 12, "functions": 6 } }