# Vercy AI instruction - YAML 1.2 (JSON-compatible) { "vercy": "1.0-draft", "publication": { "status": "published", "adjudicationStatus": "reviewable-draft", "publishableCanonical": false, "generatedAt": "2026-09-07T10:15:46Z", "synthesisSha256": "0fb1b92fb79593cce058a25b0179b1b8ae103ede8466cdd10a16248b794cc37e", "providerMode": "single-provider-waiver", "providers": [ "Codex" ], "waivedProviders": [ "Claude", "Grok" ] }, "metaModel": { "id": "WM-LIV-023", "registryId": "vr.wm-liv-023", "name": "Clinical / Biological Specimen", "version": "0.3.0-research.1", "previousVersions": [], "entryKind": "entity", "family": "World Models", "category": "Physical world and living systems", "industry": [ "Cross-industry" ], "domain": [ "PHY.LIV.SPM" ], "tags": [ "clinical", "biological", "specimen", "phy.liv.spm" ], "status": "published" }, "canonicalUrl": "https://ver.cy/models/wm-liv-023-clinical-biological-specimen/", "sourceUrl": "https://github.com/ver-cy/world-models/tree/feat/mega-model-registry/research/runs/wm-liv-023", "model": { "registry_id": "vr.wm-liv-023", "model_id": "WM-LIV-023", "name": "Clinical / Biological Specimen", "entry_kind": "entity", "purpose": "Represent one governed physical material specimen and its source-qualified collection, derivation, condition, custody, quality, use and disposition history.", "scope_statement": "Owns one physical specimen identity, accession and label bindings, profile and material classification; source references; direct material state and quantity; actual collection context; containers, additives and seals; parent-child, split, aliquot, pool, extraction, culture and transformation lineage; processing methods, devices, reagents and quantity effects; storage position and environment; transport and custody transitions; preanalytical variables, observations, quality, contamination, sufficiency and fitness assessments; availability, reservation, allocation, consumption, destruction and disposition; consent, permit and benefit-sharing bindings; provenance, correction, access, retention and loss-aware projections. Source organisms, people, environments, body sites, collection procedures, devices, containers, repositories, requests, observations, analyses, results, datasets, consent records, permits, agreements and decisions remain external.", "in_scope": [ "Physical specimen identity, material profile, source references, direct properties, quantity and collection context", "Derivation, processing, containers, storage, transport, custody, quality, use and disposition history", "Rights, consent and permit bindings, provenance, correction, access, retention and loss-aware interoperability" ], "out_of_scope": [ "Owning organism, person, environment, place, body site, procedure, device, container, repository, request, observation, assay, analysis, result, dataset, consent, permit, agreement or decision lifecycles", "Inferring donor identity, disease, diagnosis, consent, ownership, fitness, quality or contamination status without source-qualified evidence", "Protected disclosure, custody transfer, destructive use, physical disposal, external-system mutation or identity merge without authority" ], "boundary_notes": [ { "neighbor": "WM-LIV-002 Organism Individual", "distinction": "The registered parent is retained as a common source reference. A specimen can also derive from another specimen, mixed organisms, environmental material, a place, substance or product, so organism parentage is not universal.", "source_refs": [ "SRC-001", "SRC-010", "SRC-011", "SRC-013", "SRC-015" ] }, { "neighbor": "WM-LIV-024 Biobank / Sample Repository", "distinction": "A repository owns collection policy, facilities, inventory services and holdings. It contains or controls specimens but does not become their physical identity or erase earlier custody.", "source_refs": [ "SRC-004", "SRC-006", "SRC-007", "SRC-009", "SRC-017" ] }, { "neighbor": "WM-MAT-007 Laboratory Analysis", "distinction": "An analysis consumes or observes specimen material and produces results or data. The specimen retains physical and derivation identity independently from request, assay and result.", "source_refs": [ "SRC-001", "SRC-003", "SRC-010", "SRC-012", "SRC-016" ] }, { "neighbor": "Collection event and procedure", "distinction": "The actual event creates or obtains the specimen from a source and is distinct from the order, planned procedure and physical material that remains afterward.", "source_refs": [ "SRC-001", "SRC-002", "SRC-005", "SRC-013", "SRC-016" ] }, { "neighbor": "Container, label, accession and storage position", "distinction": "These identify, contain or locate the specimen under a source system. Re-labeling, re-containerization or relocation never silently changes material identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-005", "SRC-014" ] }, { "neighbor": "Derived specimen and pool", "distinction": "Every aliquot, split, extract, culture or transformed output receives a new identity. A pool retains membership, contribution and quantity lineage to all source specimens.", "source_refs": [ "SRC-001", "SRC-009", "SRC-012", "SRC-013", "SRC-016", "SRC-020" ] }, { "neighbor": "Consent, permit, agreement and ownership", "distinction": "Consent, lawful basis, collection permit, MTA, ABS terms and ownership or control are external governance records. Possession or custody does not prove title or permitted use.", "source_refs": [ "SRC-017", "SRC-018", "SRC-019", "SRC-022" ] } ] }, "sources": [ { "id": "SRC-001", "title": "FHIR R5 Specimen", "organization": "Health Level Seven International", "url": "https://hl7.org/fhir/R5/specimen.html", "version_or_date": "FHIR R5 5.0.0, Trial Use maturity 2", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines a sample for analysis with identifiers, accession, status, type, subject, collection, processing, containers, parent and request links." }, { "id": "SRC-002", "title": "Requirements for the collection and transport of samples for medical laboratory examinations", "organization": "International Organization for Standardization", "url": "https://www.iso.org/standard/80035.html", "version_or_date": "ISO 20658:2023 edition 1", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines clinical pre-examination requirements for request, patient preparation and identification, collection and transport." }, { "id": "SRC-003", "title": "Medical laboratories: Requirements for quality and competence", "organization": "International Organization for Standardization", "url": "https://www.iso.org/standard/76677.html", "version_or_date": "ISO 15189:2022 edition 4", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines medical-laboratory quality and competence requirements including pre-examination processes and point-of-care testing." }, { "id": "SRC-004", "title": "Biotechnology: Biobanking general requirements", "organization": "International Organization for Standardization", "url": "https://www.iso.org/standard/67888.html", "version_or_date": "ISO 20387:2018 edition 1; revision in progress", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines competence, impartiality, consistent operation and quality control for biological material and associated data in biobanks." }, { "id": "SRC-005", "title": "Laboratory quality management system handbook", "organization": "World Health Organization", "url": "https://www.who.int/publications-detail-redirect/9789241548274", "version_or_date": "WHO handbook, 2011", "source_type": "public-authority", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Covers sample collection, labeling, acceptance, rejection, transport, storage, disposal and laboratory quality management." }, { "id": "SRC-006", "title": "NCI Best Practices for Biospecimen Resources", "organization": "National Cancer Institute", "url": "https://biospecimens.cancer.gov/bestpractices/overview.asp", "version_or_date": "Best-practices portal updated 26 September 2023", "source_type": "public-authority", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines operational, technical, ethical, legal and policy principles for biospecimen collection, processing and storage." }, { "id": "SRC-007", "title": "ISBER Best Practices for Repositories", "organization": "International Society for Biological and Environmental Repositories", "url": "https://www.isber.org/page/BPR", "version_or_date": "Fifth edition, December 2023", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Provides global evidence- and consensus-based practices for biological and environmental repositories." }, { "id": "SRC-008", "title": "Standard PREanalytical Code", "organization": "International Society for Biological and Environmental Repositories", "url": "https://cdn.ymaws.com/www.isber.org/resource/resmgr/isber_2019/pdf/standard_preanalytical_code_.pdf", "version_or_date": "SPREC 3.0, 2018", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines coded critical preanalytical variables for fluid and solid biospecimens." }, { "id": "SRC-009", "title": "Minimum Information About BIobank data Sharing", "organization": "BBMRI-ERIC", "url": "https://miabis.bbmri-eric.eu/README", "version_or_date": "MIABIS Core 3.0 and individual-level components, accessed 7 September 2026", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines interoperable biobank, collection, resource, network, donor, sample and event information." }, { "id": "SRC-010", "title": "BioSample Documentation", "organization": "National Center for Biotechnology Information", "url": "https://www.ncbi.nlm.nih.gov/biosample/docs/", "version_or_date": "Living documentation, accessed 7 September 2026", "source_type": "registry", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines physical biological source materials, structured attributes, provenance and links to derived archive data." }, { "id": "SRC-011", "title": "BioSample Packages", "organization": "National Center for Biotechnology Information", "url": "https://www.ncbi.nlm.nih.gov/biosample/docs/packages/", "version_or_date": "Standard and MIxS packages through version 6.0, accessed 7 September 2026", "source_type": "schema", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines versioned sample-type packages and required attributes for human, animal, plant, microbial and environmental contexts." }, { "id": "SRC-012", "title": "Phenopacket Schema Biosample", "organization": "Global Alliance for Genomics and Health", "url": "https://phenopacket-schema.readthedocs.io/en/stable/biosample.html", "version_or_date": "Phenopacket Schema 2.0 stable documentation", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines a biological material unit, individual and parent derivation links, tissue, sample type, collection time, pathology and processing references." }, { "id": "SRC-013", "title": "Darwin Core List of Terms", "organization": "Biodiversity Information Standards", "url": "https://dwc.tdwg.org/list/", "version_or_date": "Darwin Core vocabulary 2026-05-26", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines MaterialEntity, MaterialSample, identifiers, sampling events, locations, taxa, preparation and biodiversity provenance." }, { "id": "SRC-014", "title": "GGBN Data Standard", "organization": "Global Genome Biodiversity Network", "url": "https://www.ggbn.org/ggbn_portal/site/wf?p=GGBN_Data_Standard", "version_or_date": "GGBN Data Standard v1, 4 October 2016", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines material-sample type, preparation, quality, concentration, volume, weight, storage and permit or transfer facts for biodiversity repositories." }, { "id": "SRC-015", "title": "Minimum Information about any Sequence", "organization": "Genomic Standards Consortium", "url": "https://genomicsstandardsconsortium.github.io/mixs/", "version_or_date": "Living MIxS documentation, accessed 7 September 2026", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines checklists and environmental extensions for contextual metadata about sequenced samples." }, { "id": "SRC-016", "title": "Ontology for Biomedical Investigations", "organization": "OBI Consortium", "url": "https://github.com/obi-ontology/obi", "version_or_date": "Living ontology repository, accessed 7 September 2026", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines specimens, assays, devices, material processing, study designs and investigation relationships." }, { "id": "SRC-017", "title": "Declaration of Taipei on Health Databases and Biobanks", "organization": "World Medical Association", "url": "https://www.wma.net/policies-post/wma-declaration-of-taipei-on-ethical-considerations-regarding-health-databases-and-biobanks/", "version_or_date": "2016 revision; further revision in progress", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines consent, privacy, withdrawal, governance, access, transfer, retention and destruction principles for identifiable human material and data." }, { "id": "SRC-018", "title": "Nagoya Protocol on Access and Benefit-sharing", "organization": "Convention on Biological Diversity", "url": "https://www.cbd.int/abs/doc/protocol/nagoya-protocol-en.pdf", "version_or_date": "Adopted 2010; in force 12 October 2014", "source_type": "legislation", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines access, prior informed consent, mutually agreed terms, compliance and benefit-sharing for genetic resources." }, { "id": "SRC-019", "title": "General Data Protection Regulation", "organization": "European Union", "url": "https://eur-lex.europa.eu/eli/reg/2016/679/2016-05-04/eng", "version_or_date": "Regulation (EU) 2016/679 consolidated official text", "source_type": "legislation", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines personal, genetic and health data protections, lawful bases, purpose limitation, minimization and data-subject rights." }, { "id": "SRC-020", "title": "PROV-O: The PROV Ontology", "organization": "World Wide Web Consortium", "url": "https://www.w3.org/TR/prov-o/", "version_or_date": "W3C Recommendation, 30 April 2013", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines entity, activity, agent, derivation, attribution, revision and invalidation provenance." }, { "id": "SRC-021", "title": "Data Quality Vocabulary", "organization": "World Wide Web Consortium", "url": "https://www.w3.org/TR/vocab-dqv/", "version_or_date": "W3C Working Group Note, 15 December 2016", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines quality measurements, annotations, policies, standards and provenance." }, { "id": "SRC-022", "title": "ODRL Information Model 2.2", "organization": "World Wide Web Consortium", "url": "https://www.w3.org/TR/odrl-model/", "version_or_date": "W3C Recommendation, 15 February 2018", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines permissions, prohibitions, duties, constraints and policy parties." }, { "id": "SRC-023", "title": "Date and Time on the Internet", "organization": "Internet Engineering Task Force", "url": "https://www.rfc-editor.org/rfc/rfc3339.html", "version_or_date": "RFC 3339, July 2002", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines timestamps with seconds and an explicit numeric offset or Z." }, { "id": "SRC-024", "title": "JSON Canonicalization Scheme", "organization": "Internet Engineering Task Force", "url": "https://www.rfc-editor.org/rfc/rfc8785.html", "version_or_date": "RFC 8785, June 2020", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-07T10:21:00Z", "relevance": "Defines deterministic JSON canonicalization for hashing, comparison and signing." } ], "structure": { "bundles": [ { "id": "specimen-identity-boundary-type-and-source", "name": "Specimen identity, boundary, type and source", "description": "Groups the governed Resource Consumption concern for specimen identity, boundary, type and source.", "rationale": "Identify one physical material entity and its source without confusing records, labels or containers with the material.", "source_refs": [ "SRC-001", "SRC-009", "SRC-010", "SRC-013", "SRC-014", "SRC-020", "SRC-024", "SRC-011", "SRC-012", "SRC-015", "SRC-016" ], "layers": [ { "id": "physical-identity-identifiers-accession-and-mastership", "name": "Physical identity, identifiers, accession and mastership", "description": "Groups Resource Consumption context for physical identity, identifiers, accession and mastership without importing neighboring master lifecycles.", "source_refs": [ "SRC-001", "SRC-009", "SRC-010", "SRC-013", "SRC-014", "SRC-020", "SRC-024" ], "findings": [ { "id": "specimen-identifier-accession-barcode-alias-label-and-master-system", "name": "Specimen identifier, accession, barcode, alias, label and master system", "description": "Records specimen identifier, accession, barcode, alias, label and master system as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-009", "SRC-010", "SRC-013", "SRC-014", "SRC-020", "SRC-024" ], "questions": [ { "id": "specimen-identifier-accession-barcode-alias-label-and-master-system-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish specimen identifier, accession, barcode, alias, label and master system?", "kind": "identity", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "specimen-identifier-accession-barcode-alias-label-and-master-system-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies specimen identifier, accession, barcode, alias, label and master system?", "kind": "authority", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "specimen-identifier-accession-barcode-alias-label-and-master-system-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect specimen identifier, accession, barcode, alias, label and master system?", "kind": "security", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "specimen-identifier-accession-barcode-alias-label-and-master-system-data", "name": "Specimen identifier, accession, barcode, alias, label and master system data", "description": "Typed specimen values and external references required to answer the governed questions for specimen identifier, accession, barcode, alias, label and master system.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-009", "SRC-010", "SRC-013", "SRC-014", "SRC-020", "SRC-024" ] } ], "artifacts": [ { "id": "specimen-identifier-accession-barcode-alias-label-and-master-system-artifact", "name": "Specimen identifier, accession, barcode, alias, label and master system evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting specimen identifier, accession, barcode, alias, label and master system.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-009", "SRC-010", "SRC-013", "SRC-014", "SRC-020", "SRC-024" ] } ], "inline_only_rationale": null }, { "id": "physical-entity-record-container-position-and-digital-representation-boundary", "name": "Physical entity, record, container, position and digital representation boundary", "description": "Records physical entity, record, container, position and digital representation boundary as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-009", "SRC-010", "SRC-013", "SRC-014", "SRC-020", "SRC-024" ], "questions": [ { "id": "physical-entity-record-container-position-and-digital-representation-boundary-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish physical entity, record, container, position and digital representation boundary?", "kind": "classification", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "physical-entity-record-container-position-and-digital-representation-boundary-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies physical entity, record, container, position and digital representation boundary?", "kind": "requirement", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "physical-entity-record-container-position-and-digital-representation-boundary-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect physical entity, record, container, position and digital representation boundary?", "kind": "privacy", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "physical-entity-record-container-position-and-digital-representation-boundary-data", "name": "Physical entity, record, container, position and digital representation boundary data", "description": "Typed specimen values and external references required to answer the governed questions for physical entity, record, container, position and digital representation boundary.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-009", "SRC-010", "SRC-013", "SRC-014", "SRC-020", "SRC-024" ] } ], "artifacts": [ { "id": "physical-entity-record-container-position-and-digital-representation-boundary-artifact", "name": "Physical entity, record, container, position and digital representation boundary evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting physical entity, record, container, position and digital representation boundary.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-009", "SRC-010", "SRC-013", "SRC-014", "SRC-020", "SRC-024" ] } ], "inline_only_rationale": null } ] }, { "id": "specimen-kind-profile-source-and-biological-context", "name": "Specimen kind, profile, source and biological context", "description": "Groups Resource Consumption context for specimen kind, profile, source and biological context without importing neighboring master lifecycles.", "source_refs": [ "SRC-001", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016" ], "findings": [ { "id": "clinical-research-veterinary-plant-microbial-environmental-food-and-biodiversity-profile", "name": "Clinical, research, veterinary, plant, microbial, environmental, food and biodiversity profile", "description": "Records clinical, research, veterinary, plant, microbial, environmental, food and biodiversity profile as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016" ], "questions": [ { "id": "clinical-research-veterinary-plant-microbial-environmental-food-and-biodiversity-profile-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish clinical, research, veterinary, plant, microbial, environmental, food and biodiversity profile?", "kind": "classification", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "clinical-research-veterinary-plant-microbial-environmental-food-and-biodiversity-profile-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies clinical, research, veterinary, plant, microbial, environmental, food and biodiversity profile?", "kind": "constraint", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "clinical-research-veterinary-plant-microbial-environmental-food-and-biodiversity-profile-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect clinical, research, veterinary, plant, microbial, environmental, food and biodiversity profile?", "kind": "retention", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "clinical-research-veterinary-plant-microbial-environmental-food-and-biodiversity-profile-data", "name": "Clinical, research, veterinary, plant, microbial, environmental, food and biodiversity profile data", "description": "Typed specimen values and external references required to answer the governed questions for clinical, research, veterinary, plant, microbial, environmental, food and biodiversity profile.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016" ] } ], "artifacts": [ { "id": "clinical-research-veterinary-plant-microbial-environmental-food-and-biodiversity-profile-artifact", "name": "Clinical, research, veterinary, plant, microbial, environmental, food and biodiversity profile evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting clinical, research, veterinary, plant, microbial, environmental, food and biodiversity profile.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016" ] } ], "inline_only_rationale": null }, { "id": "source-subject-donor-taxon-anatomy-location-disease-and-encounter-reference", "name": "Source subject, donor, taxon, anatomy, location, disease and encounter reference", "description": "Records source subject, donor, taxon, anatomy, location, disease and encounter reference as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016" ], "questions": [ { "id": "source-subject-donor-taxon-anatomy-location-disease-and-encounter-reference-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish source subject, donor, taxon, anatomy, location, disease and encounter reference?", "kind": "relationship", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "source-subject-donor-taxon-anatomy-location-disease-and-encounter-reference-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies source subject, donor, taxon, anatomy, location, disease and encounter reference?", "kind": "process", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "source-subject-donor-taxon-anatomy-location-disease-and-encounter-reference-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect source subject, donor, taxon, anatomy, location, disease and encounter reference?", "kind": "access", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "source-subject-donor-taxon-anatomy-location-disease-and-encounter-reference-data", "name": "Source subject, donor, taxon, anatomy, location, disease and encounter reference data", "description": "Typed specimen values and external references required to answer the governed questions for source subject, donor, taxon, anatomy, location, disease and encounter reference.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016" ] } ], "artifacts": [ { "id": "source-subject-donor-taxon-anatomy-location-disease-and-encounter-reference-artifact", "name": "Source subject, donor, taxon, anatomy, location, disease and encounter reference evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting source subject, donor, taxon, anatomy, location, disease and encounter reference.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "collection-physical-properties-container-and-label", "name": "Collection, physical properties, container and label", "description": "Groups the governed Resource Consumption concern for collection, physical properties, container and label.", "rationale": "Record actual sampling context and the direct material state established at collection or receipt.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-005", "SRC-009", "SRC-012", "SRC-013", "SRC-015", "SRC-016", "SRC-023", "SRC-008", "SRC-014" ], "layers": [ { "id": "collection-event-method-actor-place-and-time", "name": "Collection event, method, actor, place and time", "description": "Groups Resource Consumption context for collection event, method, actor, place and time without importing neighboring master lifecycles.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-005", "SRC-009", "SRC-012", "SRC-013", "SRC-015", "SRC-016", "SRC-023" ], "findings": [ { "id": "planned-versus-actual-collection-request-procedure-reason-protocol-and-collector", "name": "Planned versus actual collection, request, procedure, reason, protocol and collector", "description": "Records planned versus actual collection, request, procedure, reason, protocol and collector as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-005", "SRC-009", "SRC-012", "SRC-013", "SRC-015", "SRC-016", "SRC-023" ], "questions": [ { "id": "planned-versus-actual-collection-request-procedure-reason-protocol-and-collector-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish planned versus actual collection, request, procedure, reason, protocol and collector?", "kind": "event", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "planned-versus-actual-collection-request-procedure-reason-protocol-and-collector-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies planned versus actual collection, request, procedure, reason, protocol and collector?", "kind": "event", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "planned-versus-actual-collection-request-procedure-reason-protocol-and-collector-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect planned versus actual collection, request, procedure, reason, protocol and collector?", "kind": "exception", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "planned-versus-actual-collection-request-procedure-reason-protocol-and-collector-data", "name": "Planned versus actual collection, request, procedure, reason, protocol and collector data", "description": "Typed specimen values and external references required to answer the governed questions for planned versus actual collection, request, procedure, reason, protocol and collector.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-005", "SRC-009", "SRC-012", "SRC-013", "SRC-015", "SRC-016", "SRC-023" ] } ], "artifacts": [ { "id": "planned-versus-actual-collection-request-procedure-reason-protocol-and-collector-artifact", "name": "Planned versus actual collection, request, procedure, reason, protocol and collector evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting planned versus actual collection, request, procedure, reason, protocol and collector.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-005", "SRC-009", "SRC-012", "SRC-013", "SRC-015", "SRC-016", "SRC-023" ] } ], "inline_only_rationale": null }, { "id": "collection-time-body-site-location-device-method-and-source-condition", "name": "Collection time, body site, location, device, method and source condition", "description": "Records collection time, body site, location, device, method and source condition as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-005", "SRC-009", "SRC-012", "SRC-013", "SRC-015", "SRC-016", "SRC-023" ], "questions": [ { "id": "collection-time-body-site-location-device-method-and-source-condition-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish collection time, body site, location, device, method and source condition?", "kind": "temporal", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "collection-time-body-site-location-device-method-and-source-condition-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies collection time, body site, location, device, method and source condition?", "kind": "measurement", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "collection-time-body-site-location-device-method-and-source-condition-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect collection time, body site, location, device, method and source condition?", "kind": "interoperability", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "collection-time-body-site-location-device-method-and-source-condition-data", "name": "Collection time, body site, location, device, method and source condition data", "description": "Typed specimen values and external references required to answer the governed questions for collection time, body site, location, device, method and source condition.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-005", "SRC-009", "SRC-012", "SRC-013", "SRC-015", "SRC-016", "SRC-023" ] } ], "artifacts": [ { "id": "collection-time-body-site-location-device-method-and-source-condition-artifact", "name": "Collection time, body site, location, device, method and source condition evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting collection time, body site, location, device, method and source condition.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-005", "SRC-009", "SRC-012", "SRC-013", "SRC-015", "SRC-016", "SRC-023" ] } ], "inline_only_rationale": null } ] }, { "id": "material-type-quantity-container-additive-and-seal", "name": "Material type, quantity, container, additive and seal", "description": "Groups Resource Consumption context for material type, quantity, container, additive and seal without importing neighboring master lifecycles.", "source_refs": [ "SRC-001", "SRC-002", "SRC-005", "SRC-008", "SRC-012", "SRC-014", "SRC-016" ], "findings": [ { "id": "tissue-fluid-cell-organism-molecule-mixture-physical-state-and-composition", "name": "Tissue, fluid, cell, organism, molecule, mixture, physical state and composition", "description": "Records tissue, fluid, cell, organism, molecule, mixture, physical state and composition as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-002", "SRC-005", "SRC-008", "SRC-012", "SRC-014", "SRC-016" ], "questions": [ { "id": "tissue-fluid-cell-organism-molecule-mixture-physical-state-and-composition-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish tissue, fluid, cell, organism, molecule, mixture, physical state and composition?", "kind": "composition", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "tissue-fluid-cell-organism-molecule-mixture-physical-state-and-composition-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies tissue, fluid, cell, organism, molecule, mixture, physical state and composition?", "kind": "evidence", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "tissue-fluid-cell-organism-molecule-mixture-physical-state-and-composition-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect tissue, fluid, cell, organism, molecule, mixture, physical state and composition?", "kind": "decision", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "tissue-fluid-cell-organism-molecule-mixture-physical-state-and-composition-data", "name": "Tissue, fluid, cell, organism, molecule, mixture, physical state and composition data", "description": "Typed specimen values and external references required to answer the governed questions for tissue, fluid, cell, organism, molecule, mixture, physical state and composition.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-005", "SRC-008", "SRC-012", "SRC-014", "SRC-016" ] } ], "artifacts": [ { "id": "tissue-fluid-cell-organism-molecule-mixture-physical-state-and-composition-artifact", "name": "Tissue, fluid, cell, organism, molecule, mixture, physical state and composition evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting tissue, fluid, cell, organism, molecule, mixture, physical state and composition.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-002", "SRC-005", "SRC-008", "SRC-012", "SRC-014", "SRC-016" ] } ], "inline_only_rationale": null }, { "id": "mass-volume-count-concentration-dimensions-container-additive-seal-and-label", "name": "Mass, volume, count, concentration, dimensions, container, additive, seal and label", "description": "Records mass, volume, count, concentration, dimensions, container, additive, seal and label as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-002", "SRC-005", "SRC-008", "SRC-012", "SRC-014", "SRC-016" ], "questions": [ { "id": "mass-volume-count-concentration-dimensions-container-additive-seal-and-label-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish mass, volume, count, concentration, dimensions, container, additive, seal and label?", "kind": "measurement", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "mass-volume-count-concentration-dimensions-container-additive-seal-and-label-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies mass, volume, count, concentration, dimensions, container, additive, seal and label?", "kind": "quality", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "mass-volume-count-concentration-dimensions-container-additive-seal-and-label-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect mass, volume, count, concentration, dimensions, container, additive, seal and label?", "kind": "identity", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "mass-volume-count-concentration-dimensions-container-additive-seal-and-label-data", "name": "Mass, volume, count, concentration, dimensions, container, additive, seal and label data", "description": "Typed specimen values and external references required to answer the governed questions for mass, volume, count, concentration, dimensions, container, additive, seal and label.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-005", "SRC-008", "SRC-012", "SRC-014", "SRC-016" ] } ], "artifacts": [ { "id": "mass-volume-count-concentration-dimensions-container-additive-seal-and-label-artifact", "name": "Mass, volume, count, concentration, dimensions, container, additive, seal and label evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting mass, volume, count, concentration, dimensions, container, additive, seal and label.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-002", "SRC-005", "SRC-008", "SRC-012", "SRC-014", "SRC-016" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "processing-derivation-pooling-and-quantity-lineage", "name": "Processing, derivation, pooling and quantity lineage", "description": "Groups the governed Resource Consumption concern for processing, derivation, pooling and quantity lineage.", "rationale": "Preserve every material transformation, input, output and quantity effect.", "source_refs": [ "SRC-001", "SRC-006", "SRC-007", "SRC-009", "SRC-012", "SRC-013", "SRC-014", "SRC-016", "SRC-020", "SRC-003", "SRC-005", "SRC-008" ], "layers": [ { "id": "parent-child-split-aliquot-pool-extraction-and-culture-lineage", "name": "Parent-child, split, aliquot, pool, extraction and culture lineage", "description": "Groups Resource Consumption context for parent-child, split, aliquot, pool, extraction and culture lineage without importing neighboring master lifecycles.", "source_refs": [ "SRC-001", "SRC-006", "SRC-007", "SRC-009", "SRC-012", "SRC-013", "SRC-014", "SRC-016", "SRC-020" ], "findings": [ { "id": "parent-input-child-output-derivation-kind-order-and-identity", "name": "Parent input, child output, derivation kind, order and identity", "description": "Records parent input, child output, derivation kind, order and identity as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-006", "SRC-007", "SRC-009", "SRC-012", "SRC-013", "SRC-014", "SRC-016", "SRC-020" ], "questions": [ { "id": "parent-input-child-output-derivation-kind-order-and-identity-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish parent input, child output, derivation kind, order and identity?", "kind": "relationship", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "parent-input-child-output-derivation-kind-order-and-identity-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies parent input, child output, derivation kind, order and identity?", "kind": "validation", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "parent-input-child-output-derivation-kind-order-and-identity-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect parent input, child output, derivation kind, order and identity?", "kind": "classification", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "parent-input-child-output-derivation-kind-order-and-identity-data", "name": "Parent input, child output, derivation kind, order and identity data", "description": "Typed specimen values and external references required to answer the governed questions for parent input, child output, derivation kind, order and identity.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-006", "SRC-007", "SRC-009", "SRC-012", "SRC-013", "SRC-014", "SRC-016", "SRC-020" ] } ], "artifacts": [ { "id": "parent-input-child-output-derivation-kind-order-and-identity-artifact", "name": "Parent input, child output, derivation kind, order and identity evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting parent input, child output, derivation kind, order and identity.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-006", "SRC-007", "SRC-009", "SRC-012", "SRC-013", "SRC-014", "SRC-016", "SRC-020" ] } ], "inline_only_rationale": null }, { "id": "split-aliquot-pool-composite-extract-culture-fixation-and-transformation", "name": "Split, aliquot, pool, composite, extract, culture, fixation and transformation", "description": "Records split, aliquot, pool, composite, extract, culture, fixation and transformation as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-006", "SRC-007", "SRC-009", "SRC-012", "SRC-013", "SRC-014", "SRC-016", "SRC-020" ], "questions": [ { "id": "split-aliquot-pool-composite-extract-culture-fixation-and-transformation-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish split, aliquot, pool, composite, extract, culture, fixation and transformation?", "kind": "process", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "split-aliquot-pool-composite-extract-culture-fixation-and-transformation-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies split, aliquot, pool, composite, extract, culture, fixation and transformation?", "kind": "security", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "split-aliquot-pool-composite-extract-culture-fixation-and-transformation-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect split, aliquot, pool, composite, extract, culture, fixation and transformation?", "kind": "composition", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "split-aliquot-pool-composite-extract-culture-fixation-and-transformation-data", "name": "Split, aliquot, pool, composite, extract, culture, fixation and transformation data", "description": "Typed specimen values and external references required to answer the governed questions for split, aliquot, pool, composite, extract, culture, fixation and transformation.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-006", "SRC-007", "SRC-009", "SRC-012", "SRC-013", "SRC-014", "SRC-016", "SRC-020" ] } ], "artifacts": [ { "id": "split-aliquot-pool-composite-extract-culture-fixation-and-transformation-artifact", "name": "Split, aliquot, pool, composite, extract, culture, fixation and transformation evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting split, aliquot, pool, composite, extract, culture, fixation and transformation.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-006", "SRC-007", "SRC-009", "SRC-012", "SRC-013", "SRC-014", "SRC-016", "SRC-020" ] } ], "inline_only_rationale": null } ] }, { "id": "processing-method-device-reagent-actor-and-quantity-balance", "name": "Processing method, device, reagent, actor and quantity balance", "description": "Groups Resource Consumption context for processing method, device, reagent, actor and quantity balance without importing neighboring master lifecycles.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-016" ], "findings": [ { "id": "processing-step-protocol-version-actor-device-reagent-lot-parameter-and-time", "name": "Processing step, protocol version, actor, device, reagent lot, parameter and time", "description": "Records processing step, protocol version, actor, device, reagent lot, parameter and time as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-016" ], "questions": [ { "id": "processing-step-protocol-version-actor-device-reagent-lot-parameter-and-time-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish processing step, protocol version, actor, device, reagent lot, parameter and time?", "kind": "provenance", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "processing-step-protocol-version-actor-device-reagent-lot-parameter-and-time-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies processing step, protocol version, actor, device, reagent lot, parameter and time?", "kind": "privacy", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "processing-step-protocol-version-actor-device-reagent-lot-parameter-and-time-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect processing step, protocol version, actor, device, reagent lot, parameter and time?", "kind": "relationship", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "processing-step-protocol-version-actor-device-reagent-lot-parameter-and-time-data", "name": "Processing step, protocol version, actor, device, reagent lot, parameter and time data", "description": "Typed specimen values and external references required to answer the governed questions for processing step, protocol version, actor, device, reagent lot, parameter and time.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-016" ] } ], "artifacts": [ { "id": "processing-step-protocol-version-actor-device-reagent-lot-parameter-and-time-artifact", "name": "Processing step, protocol version, actor, device, reagent lot, parameter and time evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting processing step, protocol version, actor, device, reagent lot, parameter and time.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-016" ] } ], "inline_only_rationale": null }, { "id": "input-output-yield-loss-residue-consumption-and-quantity-reconciliation", "name": "Input, output, yield, loss, residue, consumption and quantity reconciliation", "description": "Records input, output, yield, loss, residue, consumption and quantity reconciliation as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-016" ], "questions": [ { "id": "input-output-yield-loss-residue-consumption-and-quantity-reconciliation-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish input, output, yield, loss, residue, consumption and quantity reconciliation?", "kind": "validation", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "input-output-yield-loss-residue-consumption-and-quantity-reconciliation-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies input, output, yield, loss, residue, consumption and quantity reconciliation?", "kind": "retention", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "input-output-yield-loss-residue-consumption-and-quantity-reconciliation-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect input, output, yield, loss, residue, consumption and quantity reconciliation?", "kind": "state", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "input-output-yield-loss-residue-consumption-and-quantity-reconciliation-data", "name": "Input, output, yield, loss, residue, consumption and quantity reconciliation data", "description": "Typed specimen values and external references required to answer the governed questions for input, output, yield, loss, residue, consumption and quantity reconciliation.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-016" ] } ], "artifacts": [ { "id": "input-output-yield-loss-residue-consumption-and-quantity-reconciliation-artifact", "name": "Input, output, yield, loss, residue, consumption and quantity reconciliation evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting input, output, yield, loss, residue, consumption and quantity reconciliation.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-016" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "storage-transport-location-custody-and-integrity", "name": "Storage, transport, location, custody and integrity", "description": "Groups the governed Resource Consumption concern for storage, transport, location, custody and integrity.", "rationale": "Track material conditions and responsibility throughout movement and holding.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-020", "SRC-023", "SRC-002", "SRC-017", "SRC-018" ], "layers": [ { "id": "storage-position-environment-duration-and-excursion", "name": "Storage position, environment, duration and excursion", "description": "Groups Resource Consumption context for storage position, environment, duration and excursion without importing neighboring master lifecycles.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-020", "SRC-023" ], "findings": [ { "id": "facility-unit-device-rack-box-slot-position-and-effective-location", "name": "Facility, unit, device, rack, box, slot, position and effective location", "description": "Records facility, unit, device, rack, box, slot, position and effective location as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-020", "SRC-023" ], "questions": [ { "id": "facility-unit-device-rack-box-slot-position-and-effective-location-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish facility, unit, device, rack, box, slot, position and effective location?", "kind": "spatial", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "facility-unit-device-rack-box-slot-position-and-effective-location-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies facility, unit, device, rack, box, slot, position and effective location?", "kind": "access", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "facility-unit-device-rack-box-slot-position-and-effective-location-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect facility, unit, device, rack, box, slot, position and effective location?", "kind": "lifecycle", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "facility-unit-device-rack-box-slot-position-and-effective-location-data", "name": "Facility, unit, device, rack, box, slot, position and effective location data", "description": "Typed specimen values and external references required to answer the governed questions for facility, unit, device, rack, box, slot, position and effective location.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-020", "SRC-023" ] } ], "artifacts": [ { "id": "facility-unit-device-rack-box-slot-position-and-effective-location-artifact", "name": "Facility, unit, device, rack, box, slot, position and effective location evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting facility, unit, device, rack, box, slot, position and effective location.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-020", "SRC-023" ] } ], "inline_only_rationale": null }, { "id": "temperature-atmosphere-humidity-light-duration-freeze-thaw-and-excursion", "name": "Temperature, atmosphere, humidity, light, duration, freeze-thaw and excursion", "description": "Records temperature, atmosphere, humidity, light, duration, freeze-thaw and excursion as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-020", "SRC-023" ], "questions": [ { "id": "temperature-atmosphere-humidity-light-duration-freeze-thaw-and-excursion-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish temperature, atmosphere, humidity, light, duration, freeze-thaw and excursion?", "kind": "state", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "temperature-atmosphere-humidity-light-duration-freeze-thaw-and-excursion-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies temperature, atmosphere, humidity, light, duration, freeze-thaw and excursion?", "kind": "exception", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "temperature-atmosphere-humidity-light-duration-freeze-thaw-and-excursion-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect temperature, atmosphere, humidity, light, duration, freeze-thaw and excursion?", "kind": "temporal", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "temperature-atmosphere-humidity-light-duration-freeze-thaw-and-excursion-data", "name": "Temperature, atmosphere, humidity, light, duration, freeze-thaw and excursion data", "description": "Typed specimen values and external references required to answer the governed questions for temperature, atmosphere, humidity, light, duration, freeze-thaw and excursion.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-020", "SRC-023" ] } ], "artifacts": [ { "id": "temperature-atmosphere-humidity-light-duration-freeze-thaw-and-excursion-artifact", "name": "Temperature, atmosphere, humidity, light, duration, freeze-thaw and excursion evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting temperature, atmosphere, humidity, light, duration, freeze-thaw and excursion.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-020", "SRC-023" ] } ], "inline_only_rationale": null } ] }, { "id": "transport-packaging-handover-and-chain-of-custody", "name": "Transport, packaging, handover and chain of custody", "description": "Groups Resource Consumption context for transport, packaging, handover and chain of custody without importing neighboring master lifecycles.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-014", "SRC-017", "SRC-018", "SRC-020" ], "findings": [ { "id": "transport-leg-origin-destination-carrier-packaging-monitor-and-cold-chain", "name": "Transport leg, origin, destination, carrier, packaging, monitor and cold chain", "description": "Records transport leg, origin, destination, carrier, packaging, monitor and cold chain as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-014", "SRC-017", "SRC-018", "SRC-020" ], "questions": [ { "id": "transport-leg-origin-destination-carrier-packaging-monitor-and-cold-chain-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish transport leg, origin, destination, carrier, packaging, monitor and cold chain?", "kind": "process", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "transport-leg-origin-destination-carrier-packaging-monitor-and-cold-chain-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies transport leg, origin, destination, carrier, packaging, monitor and cold chain?", "kind": "interoperability", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "transport-leg-origin-destination-carrier-packaging-monitor-and-cold-chain-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect transport leg, origin, destination, carrier, packaging, monitor and cold chain?", "kind": "spatial", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "transport-leg-origin-destination-carrier-packaging-monitor-and-cold-chain-data", "name": "Transport leg, origin, destination, carrier, packaging, monitor and cold chain data", "description": "Typed specimen values and external references required to answer the governed questions for transport leg, origin, destination, carrier, packaging, monitor and cold chain.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-014", "SRC-017", "SRC-018", "SRC-020" ] } ], "artifacts": [ { "id": "transport-leg-origin-destination-carrier-packaging-monitor-and-cold-chain-artifact", "name": "Transport leg, origin, destination, carrier, packaging, monitor and cold chain evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting transport leg, origin, destination, carrier, packaging, monitor and cold chain.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-014", "SRC-017", "SRC-018", "SRC-020" ] } ], "inline_only_rationale": null }, { "id": "custodian-possessor-controller-owner-handover-receipt-seal-and-discrepancy", "name": "Custodian, possessor, controller, owner, handover, receipt, seal and discrepancy", "description": "Records custodian, possessor, controller, owner, handover, receipt, seal and discrepancy as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-014", "SRC-017", "SRC-018", "SRC-020" ], "questions": [ { "id": "custodian-possessor-controller-owner-handover-receipt-seal-and-discrepancy-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish custodian, possessor, controller, owner, handover, receipt, seal and discrepancy?", "kind": "ownership", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "custodian-possessor-controller-owner-handover-receipt-seal-and-discrepancy-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies custodian, possessor, controller, owner, handover, receipt, seal and discrepancy?", "kind": "decision", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "custodian-possessor-controller-owner-handover-receipt-seal-and-discrepancy-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect custodian, possessor, controller, owner, handover, receipt, seal and discrepancy?", "kind": "provenance", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "custodian-possessor-controller-owner-handover-receipt-seal-and-discrepancy-data", "name": "Custodian, possessor, controller, owner, handover, receipt, seal and discrepancy data", "description": "Typed specimen values and external references required to answer the governed questions for custodian, possessor, controller, owner, handover, receipt, seal and discrepancy.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-014", "SRC-017", "SRC-018", "SRC-020" ] } ], "artifacts": [ { "id": "custodian-possessor-controller-owner-handover-receipt-seal-and-discrepancy-artifact", "name": "Custodian, possessor, controller, owner, handover, receipt, seal and discrepancy evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting custodian, possessor, controller, owner, handover, receipt, seal and discrepancy.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-014", "SRC-017", "SRC-018", "SRC-020" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "preanalytics-quality-fitness-availability-and-disposition", "name": "Preanalytics, quality, fitness, availability and disposition", "description": "Groups the governed Resource Consumption concern for preanalytics, quality, fitness, availability and disposition.", "rationale": "Qualify sample integrity and control material use without inventing permanent truth.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-021", "SRC-001", "SRC-004", "SRC-009", "SRC-017" ], "layers": [ { "id": "preanalytical-variables-quality-observation-and-nonconformance", "name": "Preanalytical variables, quality observation and nonconformance", "description": "Groups Resource Consumption context for preanalytical variables, quality observation and nonconformance without importing neighboring master lifecycles.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-021" ], "findings": [ { "id": "ischemia-delay-centrifugation-fixation-processing-storage-and-freeze-thaw-profile", "name": "Ischemia, delay, centrifugation, fixation, processing, storage and freeze-thaw profile", "description": "Records ischemia, delay, centrifugation, fixation, processing, storage and freeze-thaw profile as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-021" ], "questions": [ { "id": "ischemia-delay-centrifugation-fixation-processing-storage-and-freeze-thaw-profile-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish ischemia, delay, centrifugation, fixation, processing, storage and freeze-thaw profile?", "kind": "quality", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "ischemia-delay-centrifugation-fixation-processing-storage-and-freeze-thaw-profile-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies ischemia, delay, centrifugation, fixation, processing, storage and freeze-thaw profile?", "kind": "identity", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "ischemia-delay-centrifugation-fixation-processing-storage-and-freeze-thaw-profile-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect ischemia, delay, centrifugation, fixation, processing, storage and freeze-thaw profile?", "kind": "ownership", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "ischemia-delay-centrifugation-fixation-processing-storage-and-freeze-thaw-profile-data", "name": "Ischemia, delay, centrifugation, fixation, processing, storage and freeze-thaw profile data", "description": "Typed specimen values and external references required to answer the governed questions for ischemia, delay, centrifugation, fixation, processing, storage and freeze-thaw profile.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-021" ] } ], "artifacts": [ { "id": "ischemia-delay-centrifugation-fixation-processing-storage-and-freeze-thaw-profile-artifact", "name": "Ischemia, delay, centrifugation, fixation, processing, storage and freeze-thaw profile evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting ischemia, delay, centrifugation, fixation, processing, storage and freeze-thaw profile.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-021" ] } ], "inline_only_rationale": null }, { "id": "integrity-purity-concentration-contamination-volume-sufficiency-method-and-uncertainty", "name": "Integrity, purity, concentration, contamination, volume, sufficiency, method and uncertainty", "description": "Records integrity, purity, concentration, contamination, volume, sufficiency, method and uncertainty as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-021" ], "questions": [ { "id": "integrity-purity-concentration-contamination-volume-sufficiency-method-and-uncertainty-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish integrity, purity, concentration, contamination, volume, sufficiency, method and uncertainty?", "kind": "measurement", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "integrity-purity-concentration-contamination-volume-sufficiency-method-and-uncertainty-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies integrity, purity, concentration, contamination, volume, sufficiency, method and uncertainty?", "kind": "classification", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "integrity-purity-concentration-contamination-volume-sufficiency-method-and-uncertainty-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect integrity, purity, concentration, contamination, volume, sufficiency, method and uncertainty?", "kind": "authority", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "integrity-purity-concentration-contamination-volume-sufficiency-method-and-uncertainty-data", "name": "Integrity, purity, concentration, contamination, volume, sufficiency, method and uncertainty data", "description": "Typed specimen values and external references required to answer the governed questions for integrity, purity, concentration, contamination, volume, sufficiency, method and uncertainty.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-021" ] } ], "artifacts": [ { "id": "integrity-purity-concentration-contamination-volume-sufficiency-method-and-uncertainty-artifact", "name": "Integrity, purity, concentration, contamination, volume, sufficiency, method and uncertainty evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting integrity, purity, concentration, contamination, volume, sufficiency, method and uncertainty.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-002", "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-014", "SRC-021" ] } ], "inline_only_rationale": null } ] }, { "id": "fitness-acceptance-allocation-use-depletion-and-disposition", "name": "Fitness, acceptance, allocation, use, depletion and disposition", "description": "Groups Resource Consumption context for fitness, acceptance, allocation, use, depletion and disposition without importing neighboring master lifecycles.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-009", "SRC-017", "SRC-021" ], "findings": [ { "id": "purpose-qualified-fitness-acceptance-rejection-restriction-and-release", "name": "Purpose-qualified fitness, acceptance, rejection, restriction and release", "description": "Records purpose-qualified fitness, acceptance, rejection, restriction and release as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-009", "SRC-017", "SRC-021" ], "questions": [ { "id": "purpose-qualified-fitness-acceptance-rejection-restriction-and-release-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish purpose-qualified fitness, acceptance, rejection, restriction and release?", "kind": "decision", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "purpose-qualified-fitness-acceptance-rejection-restriction-and-release-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies purpose-qualified fitness, acceptance, rejection, restriction and release?", "kind": "composition", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "purpose-qualified-fitness-acceptance-rejection-restriction-and-release-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect purpose-qualified fitness, acceptance, rejection, restriction and release?", "kind": "requirement", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "purpose-qualified-fitness-acceptance-rejection-restriction-and-release-data", "name": "Purpose-qualified fitness, acceptance, rejection, restriction and release data", "description": "Typed specimen values and external references required to answer the governed questions for purpose-qualified fitness, acceptance, rejection, restriction and release.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-009", "SRC-017", "SRC-021" ] } ], "artifacts": [ { "id": "purpose-qualified-fitness-acceptance-rejection-restriction-and-release-artifact", "name": "Purpose-qualified fitness, acceptance, rejection, restriction and release evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting purpose-qualified fitness, acceptance, rejection, restriction and release.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-009", "SRC-017", "SRC-021" ] } ], "inline_only_rationale": null }, { "id": "available-reserved-allocated-partly-consumed-depleted-destroyed-returned-and-disposed", "name": "Available, reserved, allocated, partly consumed, depleted, destroyed, returned and disposed", "description": "Records available, reserved, allocated, partly consumed, depleted, destroyed, returned and disposed as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-009", "SRC-017", "SRC-021" ], "questions": [ { "id": "available-reserved-allocated-partly-consumed-depleted-destroyed-returned-and-disposed-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish available, reserved, allocated, partly consumed, depleted, destroyed, returned and disposed?", "kind": "lifecycle", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "available-reserved-allocated-partly-consumed-depleted-destroyed-returned-and-disposed-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies available, reserved, allocated, partly consumed, depleted, destroyed, returned and disposed?", "kind": "relationship", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "available-reserved-allocated-partly-consumed-depleted-destroyed-returned-and-disposed-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect available, reserved, allocated, partly consumed, depleted, destroyed, returned and disposed?", "kind": "constraint", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "available-reserved-allocated-partly-consumed-depleted-destroyed-returned-and-disposed-data", "name": "Available, reserved, allocated, partly consumed, depleted, destroyed, returned and disposed data", "description": "Typed specimen values and external references required to answer the governed questions for available, reserved, allocated, partly consumed, depleted, destroyed, returned and disposed.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-009", "SRC-017", "SRC-021" ] } ], "artifacts": [ { "id": "available-reserved-allocated-partly-consumed-depleted-destroyed-returned-and-disposed-artifact", "name": "Available, reserved, allocated, partly consumed, depleted, destroyed, returned and disposed evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting available, reserved, allocated, partly consumed, depleted, destroyed, returned and disposed.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-009", "SRC-017", "SRC-021" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "governance-rights-provenance-lifecycle-and-exchange", "name": "Governance, rights, provenance, lifecycle and exchange", "description": "Groups the governed Resource Consumption concern for governance, rights, provenance, lifecycle and exchange.", "rationale": "Enforce lawful and ethical use while preserving correction history and loss-aware projections.", "source_refs": [ "SRC-004", "SRC-006", "SRC-007", "SRC-009", "SRC-014", "SRC-017", "SRC-018", "SRC-019", "SRC-022", "SRC-001", "SRC-002", "SRC-003", "SRC-005", "SRC-008", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-015", "SRC-016", "SRC-020", "SRC-021", "SRC-023", "SRC-024" ], "layers": [ { "id": "consent-lawful-basis-permit-benefit-sharing-access-and-retention", "name": "Consent, lawful basis, permit, benefit sharing, access and retention", "description": "Groups Resource Consumption context for consent, lawful basis, permit, benefit sharing, access and retention without importing neighboring master lifecycles.", "source_refs": [ "SRC-004", "SRC-006", "SRC-007", "SRC-009", "SRC-014", "SRC-017", "SRC-018", "SRC-019", "SRC-022" ], "findings": [ { "id": "consent-withdrawal-purpose-lawful-basis-privacy-recontact-and-return-of-results", "name": "Consent, withdrawal, purpose, lawful basis, privacy, recontact and return of results", "description": "Records consent, withdrawal, purpose, lawful basis, privacy, recontact and return of results as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-004", "SRC-006", "SRC-007", "SRC-009", "SRC-014", "SRC-017", "SRC-018", "SRC-019", "SRC-022" ], "questions": [ { "id": "consent-withdrawal-purpose-lawful-basis-privacy-recontact-and-return-of-results-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish consent, withdrawal, purpose, lawful basis, privacy, recontact and return of results?", "kind": "privacy", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "consent-withdrawal-purpose-lawful-basis-privacy-recontact-and-return-of-results-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies consent, withdrawal, purpose, lawful basis, privacy, recontact and return of results?", "kind": "state", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "consent-withdrawal-purpose-lawful-basis-privacy-recontact-and-return-of-results-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect consent, withdrawal, purpose, lawful basis, privacy, recontact and return of results?", "kind": "process", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "consent-withdrawal-purpose-lawful-basis-privacy-recontact-and-return-of-results-data", "name": "Consent, withdrawal, purpose, lawful basis, privacy, recontact and return of results data", "description": "Typed specimen values and external references required to answer the governed questions for consent, withdrawal, purpose, lawful basis, privacy, recontact and return of results.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-004", "SRC-006", "SRC-007", "SRC-009", "SRC-014", "SRC-017", "SRC-018", "SRC-019", "SRC-022" ] } ], "artifacts": [ { "id": "consent-withdrawal-purpose-lawful-basis-privacy-recontact-and-return-of-results-artifact", "name": "Consent, withdrawal, purpose, lawful basis, privacy, recontact and return of results evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting consent, withdrawal, purpose, lawful basis, privacy, recontact and return of results.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-004", "SRC-006", "SRC-007", "SRC-009", "SRC-014", "SRC-017", "SRC-018", "SRC-019", "SRC-022" ] } ], "inline_only_rationale": null }, { "id": "collection-permit-mta-abs-benefit-sharing-license-access-retention-and-hold", "name": "Collection permit, MTA, ABS, benefit sharing, license, access, retention and hold", "description": "Records collection permit, mta, abs, benefit sharing, license, access, retention and hold as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-004", "SRC-006", "SRC-007", "SRC-009", "SRC-014", "SRC-017", "SRC-018", "SRC-019", "SRC-022" ], "questions": [ { "id": "collection-permit-mta-abs-benefit-sharing-license-access-retention-and-hold-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish collection permit, mta, abs, benefit sharing, license, access, retention and hold?", "kind": "access", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "collection-permit-mta-abs-benefit-sharing-license-access-retention-and-hold-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies collection permit, mta, abs, benefit sharing, license, access, retention and hold?", "kind": "lifecycle", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "collection-permit-mta-abs-benefit-sharing-license-access-retention-and-hold-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect collection permit, mta, abs, benefit sharing, license, access, retention and hold?", "kind": "event", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "collection-permit-mta-abs-benefit-sharing-license-access-retention-and-hold-data", "name": "Collection permit, MTA, ABS, benefit sharing, license, access, retention and hold data", "description": "Typed specimen values and external references required to answer the governed questions for collection permit, mta, abs, benefit sharing, license, access, retention and hold.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-004", "SRC-006", "SRC-007", "SRC-009", "SRC-014", "SRC-017", "SRC-018", "SRC-019", "SRC-022" ] } ], "artifacts": [ { "id": "collection-permit-mta-abs-benefit-sharing-license-access-retention-and-hold-artifact", "name": "Collection permit, MTA, ABS, benefit sharing, license, access, retention and hold evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting collection permit, mta, abs, benefit sharing, license, access, retention and hold.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-004", "SRC-006", "SRC-007", "SRC-009", "SRC-014", "SRC-017", "SRC-018", "SRC-019", "SRC-022" ] } ], "inline_only_rationale": null } ] }, { "id": "provenance-correction-audit-quality-and-standards-projection", "name": "Provenance, correction, audit, quality and standards projection", "description": "Groups Resource Consumption context for provenance, correction, audit, quality and standards projection without importing neighboring master lifecycles.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ], "findings": [ { "id": "source-actor-method-system-correction-duplicate-merge-split-and-audit", "name": "Source, actor, method, system, correction, duplicate, merge, split and audit", "description": "Records source, actor, method, system, correction, duplicate, merge, split and audit as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ], "questions": [ { "id": "source-actor-method-system-correction-duplicate-merge-split-and-audit-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish source, actor, method, system, correction, duplicate, merge, split and audit?", "kind": "provenance", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "source-actor-method-system-correction-duplicate-merge-split-and-audit-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies source, actor, method, system, correction, duplicate, merge, split and audit?", "kind": "temporal", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "source-actor-method-system-correction-duplicate-merge-split-and-audit-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect source, actor, method, system, correction, duplicate, merge, split and audit?", "kind": "measurement", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "source-actor-method-system-correction-duplicate-merge-split-and-audit-data", "name": "Source, actor, method, system, correction, duplicate, merge, split and audit data", "description": "Typed specimen values and external references required to answer the governed questions for source, actor, method, system, correction, duplicate, merge, split and audit.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ] } ], "artifacts": [ { "id": "source-actor-method-system-correction-duplicate-merge-split-and-audit-artifact", "name": "Source, actor, method, system, correction, duplicate, merge, split and audit evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting source, actor, method, system, correction, duplicate, merge, split and audit.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ] } ], "inline_only_rationale": null }, { "id": "fhir-miabis-biosample-phenopacket-darwin-core-ggbn-mixs-obi-and-json-projection", "name": "FHIR, MIABIS, BioSample, Phenopacket, Darwin Core, GGBN, MIxS, OBI and JSON projection", "description": "Records fhir, miabis, biosample, phenopacket, darwin core, ggbn, mixs, obi and json projection as a source-qualified Clinical / Biological Specimen assertion while source subjects, collection events, containers, repositories, analyses, results, consent and decisions retain external mastership.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ], "questions": [ { "id": "fhir-miabis-biosample-phenopacket-darwin-core-ggbn-mixs-obi-and-json-projection-q01", "text": "Which specimen identity, physical boundary, material kind, source context and direct properties establish fhir, miabis, biosample, phenopacket, darwin core, ggbn, mixs, obi and json projection?", "kind": "interoperability", "answer_data": [ "authoritative specimen identifier, accession, label aliases, profile and master system", "physical entity boundary, source subject or environment, taxon, anatomy, material type and state", "quantity, unit, composition, container, additive, seal and explicit unknowns" ] }, { "id": "fhir-miabis-biosample-phenopacket-darwin-core-ggbn-mixs-obi-and-json-projection-q02", "text": "Which collection, processing, storage, transport, custody, measurement and actor history qualifies fhir, miabis, biosample, phenopacket, darwin core, ggbn, mixs, obi and json projection?", "kind": "spatial", "answer_data": [ "actual event, protocol, method, actor, place, device, reagent, parameters and RFC 3339 clocks", "typed input-output lineage, parent and child identifiers, quantity balance and transformation order", "storage and transport environment, custody, location, excursions, observations, uncertainty and nonconformance" ] }, { "id": "fhir-miabis-biosample-phenopacket-darwin-core-ggbn-mixs-obi-and-json-projection-q03", "text": "Which quality, fitness, lifecycle, access, retention, correction and interoperability rules affect fhir, miabis, biosample, phenopacket, darwin core, ggbn, mixs, obi and json projection?", "kind": "evidence", "answer_data": [ "purpose-qualified quality, acceptance, rejection, reservation, allocation, consumption and disposition", "consent or lawful basis, permit, MTA, ABS, purpose, role, jurisdiction, retention and audit", "immutable corrections, duplicate or split history, source and target profiles, validation and semantic-loss report" ] } ], "data_elements": [ { "id": "fhir-miabis-biosample-phenopacket-darwin-core-ggbn-mixs-obi-and-json-projection-data", "name": "FHIR, MIABIS, BioSample, Phenopacket, Darwin Core, GGBN, MIxS, OBI and JSON projection data", "description": "Typed specimen values and external references required to answer the governed questions for fhir, miabis, biosample, phenopacket, darwin core, ggbn, mixs, obi and json projection.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ] } ], "artifacts": [ { "id": "fhir-miabis-biosample-phenopacket-darwin-core-ggbn-mixs-obi-and-json-projection-artifact", "name": "FHIR, MIABIS, BioSample, Phenopacket, Darwin Core, GGBN, MIxS, OBI and JSON projection evidence manifest", "description": "Digest-addressed manifest of specimen identity, material state, events, lineage, quantity, conditions, governance and provenance supporting fhir, miabis, biosample, phenopacket, darwin core, ggbn, mixs, obi and json projection.", "media_or_form": [ "application/json", "application/ld+json", "application/yaml", "text/markdown", "image/barcode", "external reference" ], "serial": true, "identity_strategy": "Authoritative specimen or accession identifier first, then source-qualified immutable assertion identifier, then Dimension UUID or ULID; never use donor name, label text, timestamp, container or storage position alone.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ] } ], "inline_only_rationale": null } ] } ] } ] }, "functions": [ { "id": "register-specimen", "name": "Register specimen", "description": "Create stable identity for one physical specimen and bind its profile, source reference and master authority.", "inputs": [ "specimen proposal", "source context", "master authority" ], "outputs": [ "specimen identifier", "initial revision" ], "preconditions": [ "active Dimension", "physical boundary explicit" ], "effects": [ "unknowns are explicit and no donor, diagnosis or consent is fabricated" ], "source_refs": [ "SRC-001", "SRC-009", "SRC-010", "SRC-013" ] }, { "id": "record-collection", "name": "Record collection", "description": "Append the actual collection event with source, method, actor, place, device, protocol and time.", "inputs": [ "specimen reference", "collection event", "source reference" ], "outputs": [ "collection assertion" ], "preconditions": [ "collector authority", "source matching complete" ], "effects": [ "planned request and actual collection remain distinct" ], "source_refs": [ "SRC-001", "SRC-002", "SRC-005", "SRC-009", "SRC-013" ] }, { "id": "assign-container-and-label", "name": "Assign container and label", "description": "Bind a container, additive, seal and label to the specimen without replacing material identity.", "inputs": [ "specimen revision", "container reference", "label assertion" ], "outputs": [ "qualified containment and label links" ], "preconditions": [ "identifier collision checked" ], "effects": [ "container, barcode and specimen identities remain separate" ], "source_refs": [ "SRC-001", "SRC-002", "SRC-005", "SRC-014" ] }, { "id": "derive-specimen", "name": "Derive specimen", "description": "Create child identities for split, aliquot, pool, extract, culture or transformed outputs and preserve every input.", "inputs": [ "input specimens", "derivation kind", "output proposals" ], "outputs": [ "child specimens", "derivation graph" ], "preconditions": [ "inputs resolvable", "method authorized" ], "effects": [ "parents remain immutable and output quantity is reconciled" ], "source_refs": [ "SRC-001", "SRC-009", "SRC-012", "SRC-013", "SRC-016", "SRC-020" ] }, { "id": "record-processing", "name": "Record processing", "description": "Append processing steps, devices, reagents, parameters, actors, clocks and quantity effects.", "inputs": [ "specimen revision", "process execution", "measurements" ], "outputs": [ "processing assertion", "quantity reconciliation" ], "preconditions": [ "protocol pinned", "actors attributable" ], "effects": [ "input state and all outputs remain traceable" ], "source_refs": [ "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-016" ] }, { "id": "store-and-move-specimen", "name": "Store and move specimen", "description": "Record effective location, environmental conditions, moves, excursions and freeze-thaw events.", "inputs": [ "specimen revision", "placement or move", "condition observations" ], "outputs": [ "location and condition assertions" ], "preconditions": [ "facility and device resolvable" ], "effects": [ "history is append-only and current location is derived" ], "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-007", "SRC-014", "SRC-020" ] }, { "id": "transfer-custody", "name": "Transfer custody", "description": "Record an attributable handover, receipt, seal state and discrepancy without inferring ownership.", "inputs": [ "specimen revision", "sender", "receiver", "handover evidence" ], "outputs": [ "custody transition" ], "preconditions": [ "both parties and authority resolvable" ], "effects": [ "custody, possession, control and ownership remain separate" ], "source_refs": [ "SRC-002", "SRC-006", "SRC-007", "SRC-017", "SRC-018", "SRC-020" ] }, { "id": "assess-quality-and-fitness", "name": "Assess quality and fitness", "description": "Append method- and purpose-qualified integrity, contamination, sufficiency, acceptance or rejection assessments.", "inputs": [ "specimen revision", "observations", "intended use" ], "outputs": [ "quality and fitness assertions" ], "preconditions": [ "method, threshold and uncertainty present" ], "effects": [ "assessment never rewrites intrinsic material history" ], "source_refs": [ "SRC-003", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-021" ] }, { "id": "allocate-consume-and-dispose", "name": "Allocate, consume and dispose", "description": "Reserve, allocate, partially consume, deplete, return, destroy or dispose material with quantity and authority controls.", "inputs": [ "specimen revision", "requested action", "authorization" ], "outputs": [ "lifecycle event", "remaining quantity" ], "preconditions": [ "consent, permit, retention and hold evaluated" ], "effects": [ "destructive actions preserve evidence and never cascade to source subjects or data" ], "source_refs": [ "SRC-004", "SRC-006", "SRC-007", "SRC-017", "SRC-018", "SRC-019", "SRC-022" ] }, { "id": "project-authorized-view", "name": "Project authorized view", "description": "Produce a minimum-necessary standards projection with identity, privacy and semantic-loss controls.", "inputs": [ "specimen revision", "recipient purpose", "target profile" ], "outputs": [ "authorized projection", "conformance and loss report" ], "preconditions": [ "access granted", "target release pinned" ], "effects": [ "disclosure is audited and canonical material identity is preserved" ], "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-007", "SRC-008", "SRC-009", "SRC-010", "SRC-011", "SRC-012", "SRC-013", "SRC-014", "SRC-015", "SRC-016", "SRC-017", "SRC-018", "SRC-019", "SRC-020", "SRC-021", "SRC-022", "SRC-023", "SRC-024" ] } ], "composition": [ { "target": "WM-LIV-002 Organism Individual", "relation": "REFERENCE", "purpose": "Resolve a common organism or donor source without treating that parent as universal or importing its lifecycle.", "required": false, "source_refs": [ "SRC-001", "SRC-010", "SRC-011", "SRC-012", "SRC-013" ] }, { "target": "WM-LIV-024 Biobank / Sample Repository", "relation": "REFERENCE", "purpose": "Resolve repository holding, governance and storage context without replacing physical specimen identity.", "required": false, "source_refs": [ "SRC-004", "SRC-006", "SRC-007", "SRC-009", "SRC-017" ] }, { "target": "WM-MAT-007 Laboratory Analysis", "relation": "REFERENCE", "purpose": "Resolve downstream analysis and results while preserving specimen material and quantity lineage.", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-010", "SRC-012", "SRC-016" ] }, { "target": "Source subject, collection event, place, container, device, observation, consent, permit, agreement, evidence and decision masters", "relation": "REFERENCE", "purpose": "Resolve external context without importing neighboring identities or lifecycle.", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-013", "SRC-017", "SRC-018", "SRC-019" ] }, { "target": "HL7 FHIR R5 Specimen", "relation": "ALIGN", "purpose": "Project clinical exchange identifiers, accession, status, type, subject, collection, processing, container, parent and request links.", "required": false, "source_refs": [ "SRC-001" ] }, { "target": "ISO 20658:2023, ISO 15189:2022 and WHO laboratory quality guidance", "relation": "ALIGN", "purpose": "Project clinical pre-examination, quality, collection, labeling, acceptance, transport, storage and disposal controls.", "required": false, "source_refs": [ "SRC-002", "SRC-003", "SRC-005" ] }, { "target": "ISO 20387:2018, NCI Best Practices, ISBER Best Practices and SPREC 3.0", "relation": "ALIGN", "purpose": "Project biobank competence, quality, ethical governance and preanalytical variables with licensed or advisory limitations.", "required": false, "source_refs": [ "SRC-004", "SRC-006", "SRC-007", "SRC-008" ] }, { "target": "MIABIS, NCBI BioSample and GA4GH Phenopacket Biosample", "relation": "ALIGN", "purpose": "Project biobank, archive and clinical-genomics sample metadata and derivation context.", "required": false, "source_refs": [ "SRC-009", "SRC-010", "SRC-011", "SRC-012" ] }, { "target": "Darwin Core 2026-05-26, GGBN v1, MIxS and OBI", "relation": "ALIGN", "purpose": "Project biodiversity, environmental, sequence-context and biomedical-investigation specimen views.", "required": false, "source_refs": [ "SRC-013", "SRC-014", "SRC-015", "SRC-016" ] }, { "target": "WMA Taipei, Nagoya Protocol, GDPR and ODRL 2.2", "relation": "ALIGN", "purpose": "Project consent, lawful basis, access, benefit sharing, transfer, privacy, rights and duties.", "required": false, "source_refs": [ "SRC-017", "SRC-018", "SRC-019", "SRC-022" ] }, { "target": "W3C PROV-O and DQV", "relation": "ALIGN", "purpose": "Project derivation, revision, attribution, invalidation and quality measurement semantics.", "required": false, "source_refs": [ "SRC-020", "SRC-021" ] }, { "target": "RFC 3339 and RFC 8785", "relation": "ALIGN", "purpose": "Project unambiguous clocks and deterministic JSON serialization.", "required": false, "source_refs": [ "SRC-023", "SRC-024" ] } ], "serviceLayers": { "dimension": { "owner_package_requirements": [ "Declare Dimension owner, specimen master, source-subject masters, collection and processing authorities, repository stewards, quality reviewers, access approvers and auditors.", "Register specimen-type, identifier, collection, container, processing, storage, transport, quality, consent, permit, retention and projection profiles.", "Register organism, person, environment, place, container, device, request, procedure, repository, analysis, result, consent, agreement, evidence and decision masters separately.", "Pin clinical, research, veterinary, plant, microbial, environmental, biodiversity, food, jurisdictional and exchange profiles." ], "namespace_guidance": "Mint only Dimension-owned specimen, derivation, processing, placement, custody, quality and lifecycle assertion identifiers locally; preserve donor, organism, place, accession, container, repository, permit, analysis and result identifiers as typed external references.", "registry_links": [ "https://ver.cy/models/", "https://ver.cy/model-agent-protocol.md", "Dimension-local specimen, biological identity, location, custody, consent, permit, quality, retention and provenance registries" ] }, "canon_and_patch": { "canonicalization_rules": [ "Canonicalize by registry ID, model version, authoritative physical-specimen identifier, profile, source-qualified boundary and immutable revision; never by donor name, accession display, barcode text, timestamp, container, position or hash alone.", "Keep physical specimen, digital record, label, accession, container, source subject, collection event, repository holding, observation, assay, analysis, result, consent and decision distinct." ], "patch_rules": [ "Additive extensions declare target node, specimen profile, authority, source, method, units, protocol and terminology releases, access, effective time and interoperability impact.", "Breaking identity, derivation, quantity, custody, status or time changes require a new immutable revision, successor mapping, migration report, compatibility declaration and continued resolution of prior identifiers." ], "compatibility_rules": [ "Consumers may ignore unknown additive fields only when specimen identity, physical boundary, source links, derivation, quantity, event clocks, custody and access meaning remain intact.", "FHIR, MIABIS, NCBI BioSample, Phenopackets, Darwin Core, GGBN, MIxS and OBI mappings pin source and target releases and declare transformed, inferred, omitted or non-round-trippable values." ] }, "artifact_rules": { "identity_priority": [ "Authoritative master-system specimen identifier or accession bound to one physical material entity.", "Source-qualified immutable identifier for collection, derivation, processing, custody, quality or lifecycle assertion.", "Adopting-Dimension UUID or ULID when no authoritative external identifier exists." ], "timestamp_rule": "Record event timestamps in RFC 3339 with seconds and an explicit numeric offset or Z; keep collection, receipt, accession, processing, storage, movement, custody, observation, reservation, consumption, destruction, correction and ingestion times distinct.", "serial_naming_rule": "Name serial artifacts as {specimen-id}--{artifact-kind}--{revision-or-assertion-id}; never use donor name, sample label, date, barcode, container, position, filename or digest alone as identity.", "integrity_rule": "Store digest, media type, byte length, issuer, specimen and source identity, profile and rules versions, units, method, clocks, provenance, validation, sensitivity, consent or lawful basis, permit, purpose, access marking and semantic-loss declaration." }, "policies": [ "The adopting Dimension declares who may register specimens, collect, label, process, derive, move, hold, assess, allocate, disclose, consume, destroy, correct and tombstone records.", "Every usable specimen requires stable physical identity, explicit source context or unknown, material and profile classification, collection or derivation provenance, quantity and unit, status, custody and applicable governance.", "Agents never infer donor identity, disease, diagnosis, consent, ownership, fitness, quality or absence of contamination from a label, specimen type, accession, container or repository record.", "Organisms, people, environments, places, containers, devices, collection procedures, repositories, analyses, observations, results, datasets, consents, permits, agreements and decisions remain external masters.", "Agents may validate identifiers, units, lineage, quantity balance and deterministic projections under delegation; collection, custody transfer, protected disclosure, destructive use, disposal and identity merge require accountable authority." ], "crud": { "read": [ "Resolve active Dimension, purpose, role, specimen identity and profile, source links, status, location, custody, quality, consent or lawful basis, permit, sensitivity, retention and access; return the minimum necessary projection." ], "create": [ "Create a stable physical-specimen identity, profile, source context or explicit unknown, master authority, collection or derivation provenance and initial quantity before downstream processing is recorded." ], "update": [ "Append an immutable collection, label, derivation, processing, placement, custody, quality, allocation, lifecycle or correction assertion with actor, authority, reason, source, method, RFC 3339 effective time and predecessor." ], "delete": [ "Apply consent, permit, MTA, ABS, biosafety, clinical, legal, audit, retention and hold rules; tombstone eligible records or physically dispose material while preserving material provenance and non-cascading external masters." ] }, "roles": [ { "name": "Dimension owner", "responsibilities": [ "Own namespace, mastership, delegation, access, retention and federation rules." ] }, { "name": "Specimen registrar or accessioner", "responsibilities": [ "Own physical identity, accession, label reconciliation, status and record continuity." ] }, { "name": "Collector or source steward", "responsibilities": [ "Own actual collection, source matching, method, consent or permit checks and collection evidence." ] }, { "name": "Laboratory processor", "responsibilities": [ "Own processing, derivation, devices, reagents, parameters and quantity accounting." ] }, { "name": "Repository or storage custodian", "responsibilities": [ "Own placement, environmental monitoring, inventory, custody and retrieval evidence." ] }, { "name": "Quality or biosafety reviewer", "responsibilities": [ "Own method-qualified integrity, contamination, acceptance, fitness and nonconformance assessments." ] }, { "name": "Data or access authority", "responsibilities": [ "Own consent or lawful basis, permits, benefit sharing, purpose, disclosure, retention and transfer decisions." ] }, { "name": "Reviewer or auditor", "responsibilities": [ "Review identity, lineage, quantity, conditions, custody, lifecycle and disclosure without rewriting originals." ] } ], "access": { "default_rule": "Deny protected human, genetic, sensitive-location, endangered-species or commercially restricted specimen context and mutation unless active Dimension, role, purpose, consent or lawful basis, permit, MTA, jurisdiction and field policy grant the action; expose the minimum necessary projection.", "scopes": [ "bundle", "layer", "finding", "artifact" ], "exceptions": [ "Emergency, public-health, biosafety or legally compelled access must be grounded, time-limited, purpose-bound, attributable, independently reviewed and unable to erase immutable provenance or legal-hold evidence." ], "audit_requirements": [ "Log actor, role, purpose, specimen and source identity, action, decision, policy and standard versions, RFC 3339 timestamp with offset, affected material and fields, recipient, source evidence and outcome for privileged mutation, transfer, consumption, destruction or disclosure." ] }, "agents_bootstrap": { "filename": "AGENTS.md", "required_fields": [ "Name", "Type", "Specification URL", "Storage type URL", "Interface URL", "Processes URL" ], "read_order": [ "Read the nearest Dimension-owner AGENTS.md, active specimen and source masters, profile, biosafety, consent, permit, MTA, access, retention and jurisdiction rules.", "Read this model AGENTS.md, pinned spec.yaml and required collection, processing, repository, quality, analysis, evidence and decision instructions before mutation." ] } }, "coverage": { "claim": "WM-LIV-023 covers one governed physical clinical or biological specimen, source context, direct material properties, collection, containers, processing, derivation, quantity, storage, transport, custody, quality, use, disposition, rights, provenance and loss-aware interoperability. Specimen-type, assay, biosafety, species, jurisdictional and independent-review questions remain deferred.", "confidence": "medium", "checklist": [ { "dimension": "identity", "status": "covered", "notes": "Physical specimen, record, accession, label, container, position, source, parent and child identities remain distinct." }, { "dimension": "classification and definition", "status": "covered", "notes": "Clinical, research, veterinary, plant, microbial, environmental, food and biodiversity profiles plus material types are explicit." }, { "dimension": "direct properties", "status": "covered", "notes": "Material, physical state, composition, mass, volume, count, concentration, dimensions, container, additive and seal are source-qualified." }, { "dimension": "recognition and observation", "status": "covered", "notes": "Agents distinguish specimens through authoritative identity, labels, physical boundaries, source links, container and custody evidence rather than a name alone." }, { "dimension": "capabilities and possible actions", "status": "covered", "notes": "Collect, label, derive, process, store, move, transfer, assess, allocate, consume, destroy and project actions expose authority and effects." }, { "dimension": "lifecycle", "status": "covered", "notes": "Available, reserved, allocated, partly consumed, depleted, destroyed, returned, disposed, corrected, merged and split states preserve history." }, { "dimension": "relationships", "status": "covered", "notes": "Source, parent-child, pool, container, repository, analysis, observation, consent, permit, agreement and result links are typed." }, { "dimension": "temporal", "status": "covered", "notes": "Collection, receipt, accession, processing, storage, movement, custody, observation, reservation, use, destruction and correction clocks remain distinct." }, { "dimension": "spatial", "status": "covered", "notes": "Source location, collection site, facility, unit, device, rack, box, slot, transport origin and destination are time-qualified." }, { "dimension": "provenance", "status": "covered", "notes": "Sources, actors, protocols, methods, devices, reagents, events, derivations, custody, observations, corrections and projections are linked." }, { "dimension": "ownership", "status": "covered", "notes": "Donor, source, owner, controller, custodian, possessor, collector, processor, repository and user roles are not conflated." }, { "dimension": "validation", "status": "covered", "notes": "Identity collision, source match, label, lineage, quantity balance, time order, location, temperature, seal, quality and projection checks are explicit." }, { "dimension": "access", "status": "covered", "notes": "Consent or lawful basis, permits, MTA, ABS, purpose, role, jurisdiction, sensitivity, minimum projection and audit are represented." }, { "dimension": "retention and deletion", "status": "covered", "notes": "Reservation, consumption, destruction, withdrawal, biosafety, legal hold, record continuity and non-cascading tombstones are explicit." }, { "dimension": "interoperability", "status": "covered", "notes": "FHIR, MIABIS, BioSample, Phenopackets, Darwin Core, GGBN, MIxS and OBI projections pin releases and disclose loss." } ], "known_omissions": [ "Specimen-type, disease, assay, preservation, biosafety, dangerous-goods, species, clinical, biodiversity and jurisdiction profiles require expert review.", "Source organisms, people, environments, places, devices, containers, procedures, repositories, observations, analyses, results, consents, permits, agreements, datasets and decisions remain neighboring masters.", "Automated collection, diagnosis, fitness approval, access grant, custody transfer, destructive use and disposal remain outside unreviewed agent authority." ], "conflicts": [ "Clinical specimen, biospecimen, biological sample, material sample, preserved specimen, isolate, aliquot and extract overlap across standards but have different boundaries and profiles.", "Specimen identifier, accession, barcode, label, container identifier, storage position and digital record identifier cannot be collapsed into one universal identity.", "FHIR, MIABIS, BioSample, Phenopackets, Darwin Core, GGBN, MIxS and OBI differ in scope, granularity, lifecycle and required provenance." ], "regional_assumptions": [ "Human clinical requirements do not govern all veterinary, plant, microbial, environmental, food or biodiversity specimens.", "ISO standards and ISBER practices include licensed or advisory material; exact releases and allowed use must be pinned before conformance claims.", "Consent, privacy, access, benefit sharing, collection permits, biosafety, transport, retention and disposal depend on jurisdiction, species, material and purpose." ], "adversarial_checks": [ "Reject a specimen without stable physical identity, master authority, material boundary, profile and collection or derivation provenance.", "Reject donor name, sample label, accession display, barcode, container, storage position, timestamp or hash as universal material identity.", "Reject child, aliquot, extract, culture or pool that overwrites parents, loses contributor identities or fails quantity reconciliation.", "Reject planned request treated as actual collection or current location treated as custody or ownership.", "Reject unqualified quality, fitness, contamination absence or diagnosis inferred from specimen type, label or repository metadata.", "Reject consumption, destruction, disposal, merge, split or correction that erases prior material, quantity, evidence, consent, permit or custody history.", "Reject protected human, genetic, sensitive-location or regulated-biological context disclosed without purpose, authority, minimum-necessary scope and audit." ] }, "researchAdjudication": { "providerMode": "single-provider-waiver", "activeProviders": [ "codex" ], "waivedProviders": [ "claude", "grok" ], "providerPolicy": { "contract_version": "1.0.0", "mode": "single-provider-waiver", "effective_at": "2026-09-06T00:00:00Z", "scope": "Canonical single-stream subject-model research after the six-workstream consolidation", "active_providers": [ "codex" ], "waived_providers": [ { "provider": "claude", "authorized_by": "repository owner", "authorized_at": "2026-09-06T00:00:00Z", "reason": "Claude produced no result on prior 1800-second and 900-second attempts and again timed out on bounded 600-second Sonnet and 300-second Haiku passes. The owner prioritized completion over provider availability." }, { "provider": "grok", "authorized_by": "repository owner", "authorized_at": "2026-09-06T00:00:00Z", "reason": "The repository owner authorized completion without Grok when Grok is unavailable, slow or schema-invalid. Grok may still be attempted as a bounded supplemental reviewer, but its failure never blocks a valid Claude plus no-tools result." } ], "review_rule": "Codex may complete source-grounded fallback research after bounded Claude and Grok attempts fail. It requires a separate no-tools adversarial audit and remains reviewable-draft with a visible absence-of-external-review hold.", "supplemental_provider_attempts": [ { "provider": "claude", "required": false, "maximum_attempts": 1, "failure_policy": "record-and-continue", "admission_rule": "Use only a locally schema-valid result whose sources and boundaries survive adjudication." }, { "provider": "grok", "required": false, "maximum_attempts": 1, "failure_policy": "record-and-continue", "admission_rule": "Use only a locally schema-valid result whose sources and boundaries survive adjudication." } ] }, "boundaryDecision": { "entry_kind": "entity", "status": "confirmed-after-review", "rationale": "The root is one identifiable physical material entity. Collection and transformation events, assertions and external records describe its lifecycle but do not make it an aggregate or replace material identity." }, "decisions": [ { "concept": "Physical specimen boundary", "disposition": "accepted-as-entity", "rationale": "One specimen is a physical material entity distinct from its digital record, accession, label, container, position and repository holding." }, { "concept": "WM-LIV-002 parent signal", "disposition": "retained-as-optional-source-reference", "rationale": "An organism is a common source but not universal because specimens may derive from another specimen, mixed organisms, environmental material, places, substances or products." }, { "concept": "WM-LIV-024 incoming containment", "disposition": "reframed-as-repository-reference", "rationale": "A biobank or repository can hold, control and manage a specimen without owning its physical identity or erasing earlier custody." }, { "concept": "WM-MAT-007 outgoing analysis relation", "disposition": "accepted-as-downstream-reference", "rationale": "Analysis may observe or consume material and generate results, but specimen and analysis lifecycles remain separate." }, { "concept": "Derived specimen identity", "disposition": "accepted-with-new-identity", "rationale": "Every split, aliquot, extract, culture or transformed output receives a new identifier and preserves parent, method, actor, clocks and quantity lineage." }, { "concept": "Pooling", "disposition": "accepted-with-many-input-lineage", "rationale": "A pool is a new specimen whose contributor identities, quantities and derivation evidence remain resolvable." }, { "concept": "Quality and fitness", "disposition": "accepted-as-qualified-assessments", "rationale": "Integrity, purity, contamination, sufficiency and fitness depend on method, time, threshold and intended use and are not timeless intrinsic truth." }, { "concept": "Custody, location and ownership", "disposition": "kept-distinct", "rationale": "Current placement, possession, custody, control, legal ownership and permitted use have different authorities and evidence." }, { "concept": "Clinical and broader biological profiles", "disposition": "accepted-with-explicit-profile-discriminator", "rationale": "Human clinical, research, veterinary, plant, microbial, environmental, biodiversity and food specimens share a root but require distinct source, quality, safety and governance rules." }, { "concept": "Provider waiver and local no-tools audit", "disposition": "accepted-with-mandatory-hold", "rationale": "One bounded Claude Sonnet attempt and one bounded Grok attempt timed out. Codex separately audits the frozen validated result and comparison without acquiring new facts, so assurance remains reviewable-draft." } ], "publicationHolds": [ "Absence-of-external-review hold: the bounded Claude Sonnet and Grok attempts timed out before producing admissible results; no external result was admitted.", "Boundary hold: source organisms, people, environments, places, body sites, procedures, devices, containers, repositories, requests, observations, analyses, results, datasets, consents, permits, agreements and decisions remain external masters.", "Identity hold: every specimen requires stable physical identity; accessions, barcodes, labels, containers, positions, timestamps and digital rows are not universal material identity.", "Profile hold: human clinical, veterinary, plant, microbial, environmental, biodiversity, food, tumor, liquid-biopsy, tissue, cell, nucleic-acid and other profiles require specialist review.", "Quality hold: fitness, integrity, contamination, quantity and sufficiency require method, units, time, uncertainty, threshold and intended-use qualification.", "Licensed-standard hold: ISO and ISBER detail is licensed or advisory; production conformance must use authorized copies and exact releases.", "Rights hold: consent or lawful basis, permits, MTA, Nagoya applicability, benefit sharing, purpose, jurisdiction and withdrawal rules require accountable review.", "Safety hold: infectious, toxic, radioactive, genetically modified, dangerous-goods and biosecurity profiles require applicable specialist controls.", "Interoperability hold: source and target releases, mapping direction, transformation, inference, omissions and round-trip loss must be declared for every projection.", "Completeness hold: the 24-source draft is broad but does not claim universal specimen, laboratory, biobank, biodiversity, legal, safety or operational coverage.", "Independent external review was explicitly waived by the repository owner; this codex-only result remains a reviewable draft." ], "deferredResearch": [ "Develop specimen-type, assay, preservation, biosafety, dangerous-goods, disease, species and jurisdiction profiles with domain experts.", "Resolve detailed sibling boundaries for source subjects, sampling events, containers, repositories, inventory, analyses, observations, results, evidence, consent, permits, agreements and decisions.", "Pin production crosswalks to exact FHIR, ISO, ISBER, MIABIS, BioSample, Phenopacket, Darwin Core, GGBN, MIxS and OBI releases and execute conformance suites.", "Obtain independent laboratory, pathology, biobank, biodiversity, veterinary, privacy, legal, biosafety, logistics, security and records review." ] }, "statistics": { "sources": 24, "bundles": 6, "layers": 12, "findings": 24, "questions": 72, "artifacts": 24, "functions": 10 } }