# Vercy AI instruction - YAML 1.2 (JSON-compatible) { "vercy": "1.0-draft", "publication": { "status": "published", "adjudicationStatus": "reviewable-draft", "publishableCanonical": false, "generatedAt": "2026-10-06T21:13:09Z", "synthesisSha256": "f25d170ccdc0dd1de166b3082fdb0a4d3fb931398e5da52f834a83063f3dfdbd", "providerMode": "single-provider-waiver", "providers": [ "Codex" ], "waivedProviders": [ "Claude", "Grok" ] }, "metaModel": { "id": "WM-LIV-014", "registryId": "vr.wm-liv-014", "name": "Protein / Biomolecule", "version": "0.1.0", "previousVersions": [], "entryKind": "entity", "family": "World Models", "category": "Physical world and living systems", "industry": [ "Cross-industry" ], "domain": [ "PHY.LIV.MOL" ], "tags": [ "protein", "biomolecule", "phy.liv.mol" ], "status": "published" }, "canonicalUrl": "https://ver.cy/models/wm-liv-014-protein-biomolecule/", "sourceUrl": "https://github.com/ver-cy/world-models/tree/feat/mega-model-registry/research/runs/wm-liv-014", "model": { "registry_id": "vr.wm-liv-014", "model_id": "WM-LIV-014", "name": "Protein / Biomolecule", "entry_kind": "entity", "purpose": "Represent one scoped molecular kind with scientific master references, form definitions and evidence-qualified properties, structures and biological claims.", "scope_statement": "One molecular kind at a declared identity resolution, primarily protein and peptide forms with a bounded nonprotein chemical profile. Local assertions describe the subject without mastering specimens, experiments, genes, pathways or external databases. The root is an entity record about a kind, not a taxonomic classifier or an individual physical molecule.", "in_scope": [ "Scoped molecular identity, accessions and ambiguity-aware crosswalks.", "Sequence or chemical definitions, form differences and qualified properties.", "Structure, recognition, function, context and interaction evidence references.", "Local assertion provenance, curation continuity and governed exchange." ], "out_of_scope": [ "Physical specimen, batch, reagent inventory, custody and experimental execution.", "Gene, transcript, genome, organism and pathway lifecycle or process simulation.", "Molecular engineering, production, optimization, clinical decisions and regulatory approvals.", "A complete chemical ontology, all biomolecule subclasses, raw experimental archives or external master curation." ], "boundary_notes": [ { "neighbor": "WM-LIV-002", "distinction": "Registry parent is contextual only, not entity inheritance; a molecule kind is not an organism individual.", "source_refs": [ "SRC-002", "SRC-005" ] }, { "neighbor": "WM-LIV-013", "distinction": "Encoding reference does not make a protein the same subject as its gene.", "source_refs": [ "SRC-002" ] }, { "neighbor": "WM-LIV-023", "distinction": "A specimen is a physical occurrence with custody; this root describes a molecular kind.", "source_refs": [ "SRC-005", "SRC-010" ] }, { "neighbor": "WM-MAT-001", "distinction": "Shared chemical identity may refer to the same external master; substance and material lifecycle is not copied here.", "source_refs": [ "SRC-003" ] }, { "neighbor": "Structure archive record", "distinction": "One entry can describe multiple entities and representations; entry identity cannot substitute for the molecular subject.", "source_refs": [ "SRC-005", "SRC-007" ] } ] }, "sources": [ { "id": "SRC-001", "title": "Accession", "organization": "UniProt Consortium", "url": "https://www.uniprot.org/help/accession_numbers", "version_or_date": "Page modified 2026-06-12 in indexed text; direct browser open returned fallback", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 2, "accessed_at": "2026-10-06T21:12:00Z", "relevance": "Primary and secondary accession identity; merges and splits require qualified mappings." }, { "id": "SRC-002", "title": "How do I get the nucleotide sequence that corresponds to the UniProtKB sequence?", "organization": "UniProt Consortium", "url": "https://www.uniprot.org/help/canonical_nucleotide", "version_or_date": "Page modified 2023-08-21 in indexed text; direct browser open returned fallback", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 2, "accessed_at": "2026-10-06T21:12:00Z", "relevance": "Canonical protein sequence and nucleotide or gene references are not interchangeable." }, { "id": "SRC-003", "title": "About ChEBI", "organization": "EMBL-EBI", "url": "https://www.ebi.ac.uk/chebi/about", "version_or_date": "Living documentation accessed 2026-10-07; release not pinned", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:12:00Z", "relevance": "Chemical identity, class and role, structure representations, charge, mass and provenance." }, { "id": "SRC-004", "title": "Proteomics Standards Initiative ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms", "organization": "HUPO Proteomics Standards Initiative and Consortium for Top-Down Proteomics", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7612572/", "version_or_date": "2022 primary standards-author paper; indexed text reviewed; full open challenged", "source_type": "scientific", "primary_source": true, "authority_tier": 2, "accessed_at": "2026-10-06T21:12:00Z", "relevance": "Sequence forms, modification localization and ambiguity. Syntax is an alignment, not proof of observed existence." }, { "id": "SRC-005", "title": "PDBx/mmCIF User Guide", "organization": "Worldwide Protein Data Bank", "url": "https://mmcif.wwpdb.org/docs/user-guide/guide.html", "version_or_date": "Dictionary Version 5 guide accessed 2026-10-07; exact dictionary patch unpinned", "source_type": "schema", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:12:00Z", "relevance": "Distinct molecular entities, polymers, sources, experimental methods, coordinate representations and assemblies." }, { "id": "SRC-006", "title": "Stand-alone wwPDB Validation Service", "organization": "Worldwide Protein Data Bank", "url": "https://www.wwpdb.org/validation/validation-servers", "version_or_date": "Living documentation accessed 2026-10-07", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 2, "accessed_at": "2026-10-06T21:12:00Z", "relevance": "Method-specific structure validation and its stated limitations; validation reports do not certify all molecular claims." }, { "id": "SRC-007", "title": "ModelCIF dictionary documentation", "organization": "ModelCIF Working Group", "url": "https://github.com/ihmwg/ModelCIF/blob/master/dictionary_documentation/documentation.md", "version_or_date": "Moving master documentation accessed 2026-10-07; commit pin pending", "source_type": "schema", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:12:00Z", "relevance": "Predicted structures and local or global model quality estimates, with metric definitions and software provenance." }, { "id": "SRC-008", "title": "Introduction to GO annotations", "organization": "Gene Ontology Consortium", "url": "https://geneontology.org/docs/go-annotations/", "version_or_date": "Living documentation accessed 2026-10-07; ontology release unpinned", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:12:00Z", "relevance": "Function, process and location assertions with evidence, references, relations and explicit negation; missing annotation is not absence." }, { "id": "SRC-009", "title": "PSI-MI TAB 2.8 Format", "organization": "HUPO Proteomics Standards Initiative", "url": "https://psicquic.github.io/MITAB28Format.html", "version_or_date": "MITAB 2.8 documentation accessed 2026-10-07", "source_type": "schema", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:12:00Z", "relevance": "Qualified interaction endpoints, detection evidence, participant roles, negative interactions and expansion of complexes." }, { "id": "SRC-010", "title": "PROV-O: The PROV Ontology", "organization": "World Wide Web Consortium", "url": "https://www.w3.org/TR/prov-o/", "version_or_date": "W3C Recommendation 2013-04-30", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-10-06T21:12:00Z", "relevance": "Attribution, derivation and revisions of scientific assertions; does not itself establish truth, rights or retention policy." }, { "id": "SRC-011", "title": "ProForma version and implementation status", "organization": "HUPO Proteomics Standards Initiative", "url": "https://www.psidev.info/proforma", "version_or_date": "Lists 2.0 final 2022-02-03 and 2.1 final 2026-06-09; accessed 2026-10-07", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 2, "accessed_at": "2026-10-06T21:12:00Z", "relevance": "Version selection must be explicit; the 2.0 paper is not evidence that 2.0 is the latest specification. Full 2.1 syntax audit deferred." } ], "structure": { "bundles": [ { "id": "bundle-identity", "name": "Identity and biological scope", "description": "Fix the subject resolution before admitting annotations.", "rationale": "These distinctions are needed to prevent identity, evidence or authority loss in a local molecular knowledge record; the hierarchy is a research proposal, not an external normative schema.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-009" ], "layers": [ { "id": "layer-identity-scope", "name": "Subject and repository identity", "description": "Proposed context group for subject and repository identity. External references retain their own masters.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004" ], "findings": [ { "id": "finding-identity", "name": "Molecular kind and identity granularity", "description": "Proposed root: one scoped molecular kind at an explicit resolution. A broad protein entry, isoform, fully specified form and chemical class are not automatically equivalent. Physical specimens and archive entries are separate objects.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ], "questions": [ { "id": "question-identity-1", "text": "What molecular kind and level of identity resolution does this record denote?", "kind": "identity", "answer_data": [ "subject identifier", "molecule category", "resolution: entry-level, sequence-form, chemical-form or unresolved", "boundary rationale" ] }, { "id": "question-identity-2", "text": "Which external classifications describe the subject without replacing its identity?", "kind": "classification", "answer_data": [ "classification IRI", "term release", "class versus individual status", "applicability" ] }, { "id": "question-identity-3", "text": "Which unresolved distinctions prevent treating this record as a single exact molecular form?", "kind": "exception", "answer_data": [ "ambiguity set", "unknown stereochemistry or form", "resolution limits", "split criteria" ] } ], "data_elements": [ { "id": "data-identity-scope", "name": "Subject scope", "description": "Required local scope distinguishes molecular kind from class, physical sample and data record.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] }, { "id": "data-identity-class", "name": "Classification references", "description": "Typed class links; broad classes cannot silently become fully specified molecular subjects.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] } ], "artifacts": [ { "id": "artifact-identity", "name": "Molecular boundary record", "description": "Versioned evidence view for molecular kind and identity granularity. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] } ], "inline_only_rationale": null }, { "id": "finding-accessions", "name": "Repository identities and crosswalks", "description": "Preserve repository namespace and release context. A cross-reference is a mapping assertion with a relation and evidence, not an unconditional equality assertion.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "questions": [ { "id": "question-accessions-1", "text": "Which primary accessions and version contexts anchor this molecular record?", "kind": "identity", "answer_data": [ "namespace", "primary accession", "sequence or entry version", "release", "retrieval time" ] }, { "id": "question-accessions-2", "text": "What evidence supports each exact, broader, narrower or related identifier mapping?", "kind": "interoperability", "answer_data": [ "source and target identifiers", "mapping relation", "evidence", "curator", "unresolved conflicts" ] }, { "id": "question-accessions-3", "text": "How are merged, split, deleted or secondary accessions resolved without losing prior citations?", "kind": "lifecycle", "answer_data": [ "accession history", "successor set", "mapping date", "ambiguity", "historical citation" ] } ], "data_elements": [ { "id": "data-accessions-keys", "name": "Master references", "description": "Qualified accessions for the declared subject; a local provisional identity is allowed with unresolved master status.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] }, { "id": "data-accessions-maps", "name": "Mapping assertions", "description": "Version-aware typed crosswalks with no inferred one-to-one guarantee.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "artifacts": [ { "id": "artifact-accessions", "name": "Identifier mapping ledger", "description": "Versioned evidence view for repository identities and crosswalks. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "inline_only_rationale": null } ] }, { "id": "layer-identity-origin", "name": "Origin and encoding context", "description": "Proposed context group for origin and encoding context. External references retain their own masters.", "source_refs": [ "SRC-002", "SRC-005", "SRC-009" ], "findings": [ { "id": "finding-origin", "name": "Biological origin and encoding context", "description": "Taxon, gene and source-system links are contextual evidence. An expression host is distinct from the source of the encoded sequence. A universal one-gene or one-organism requirement is rejected.", "source_refs": [ "SRC-002", "SRC-005", "SRC-009" ], "questions": [ { "id": "question-origin-1", "text": "Which taxon and encoding references are supported for this molecular form?", "kind": "relationship", "answer_data": [ "taxon reference", "gene or transcript reference", "relation type", "version", "evidence" ] }, { "id": "question-origin-2", "text": "How are native source, expression host and synthetic origin distinguished?", "kind": "provenance", "answer_data": [ "source role", "source reference", "origin category", "unknown reason", "evidence" ] }, { "id": "question-origin-3", "text": "When is an organism or gene link inapplicable or non-unique?", "kind": "constraint", "answer_data": [ "noncoding or nonencoded form", "multiple contexts", "applicability reason", "review decision" ] } ], "data_elements": [ { "id": "data-origin-origins", "name": "Origin assertions", "description": "Optional source-role references; no organism individual containment or ownership is implied.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-005", "SRC-009" ] }, { "id": "data-origin-encoding", "name": "Encoding references", "description": "Optional versioned relations to externally mastered genes and transcripts.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-002", "SRC-005", "SRC-009" ] } ], "artifacts": [ { "id": "artifact-origin", "name": "Origin and encoding crosswalk", "description": "Versioned evidence view for biological origin and encoding context. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-002", "SRC-005", "SRC-009" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "bundle-constitution", "name": "Molecular constitution", "description": "Describe what defines a form without forcing every biomolecule into a protein sequence.", "rationale": "These distinctions are needed to prevent identity, evidence or authority loss in a local molecular knowledge record; the hierarchy is a research proposal, not an external normative schema.", "source_refs": [ "SRC-002", "SRC-003", "SRC-004", "SRC-005", "SRC-011" ], "layers": [ { "id": "layer-constitution-polymer", "name": "Sequence and modified forms", "description": "Proposed context group for sequence and modified forms. External references retain their own masters.", "source_refs": [ "SRC-002", "SRC-004", "SRC-005", "SRC-011" ], "findings": [ { "id": "finding-sequence", "name": "Sequence definition and coordinate frame", "description": "Sequences need alphabet, orientation, completeness and a stable coordinate frame. Reference, mature, fragment and observed sequence extents must not be substituted silently.", "source_refs": [ "SRC-002", "SRC-004", "SRC-005" ], "questions": [ { "id": "question-sequence-1", "text": "Which sequence, alphabet and orientation define the selected polymer form?", "kind": "definition", "answer_data": [ "sequence reference or literal", "alphabet", "orientation", "version", "digest" ] }, { "id": "question-sequence-2", "text": "What region and processing context distinguish the represented sequence from its precursor or reference?", "kind": "composition", "answer_data": [ "reference sequence", "start and end", "coordinate convention", "fragment or processing annotation", "evidence" ] }, { "id": "question-sequence-3", "text": "Which residues or intervals are ambiguous, missing or not represented?", "kind": "quality", "answer_data": [ "uncertain positions", "ambiguity notation", "missing versus unknown", "evidence limitations" ] } ], "data_elements": [ { "id": "data-sequence-sequence", "name": "Sequence representation", "description": "Required only for an applicable polymer profile; preserve unknown residues without filling them from a homolog.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-002", "SRC-004", "SRC-005" ] }, { "id": "data-sequence-frame", "name": "Coordinate frame", "description": "Reference version and numbering convention for all local features.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-002", "SRC-004", "SRC-005" ] } ], "artifacts": [ { "id": "artifact-sequence", "name": "Sequence definition snapshot", "description": "Versioned evidence view for sequence definition and coordinate frame. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-002", "SRC-004", "SRC-005" ] } ], "inline_only_rationale": null }, { "id": "finding-modifications", "name": "Modified forms and localization uncertainty", "description": "Specific form claims retain sequence differences, modifications and localization uncertainty. A valid notation does not establish that a form exists in a sample.", "source_refs": [ "SRC-004", "SRC-011" ], "questions": [ { "id": "question-modifications-1", "text": "Which sequence changes and modifications distinguish the form being asserted?", "kind": "state", "answer_data": [ "parent sequence reference", "change or modification term", "position", "form assertion", "evidence" ] }, { "id": "question-modifications-2", "text": "How certain is the localization or composition of each modification?", "kind": "measurement", "answer_data": [ "candidate sites", "localization evidence", "uncertainty type", "unknown composition", "source" ] }, { "id": "question-modifications-3", "text": "Which notation version and supported feature set encode the form without losing ambiguity?", "kind": "validation", "answer_data": [ "notation version", "vocabulary releases", "parser profile", "loss report", "validation status" ] } ], "data_elements": [ { "id": "data-modifications-forms", "name": "Form assertions", "description": "Candidate modification and sequence-form statements with localization and observation status.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-004", "SRC-011" ] }, { "id": "data-modifications-notation", "name": "Notation binding", "description": "Optional ProForma binding with explicit version; 2.1 conformance is not claimed.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-004", "SRC-011" ] } ], "artifacts": [ { "id": "artifact-modifications", "name": "Form qualification record", "description": "Versioned evidence view for modified forms and localization uncertainty. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-004", "SRC-011" ] } ], "inline_only_rationale": null } ] }, { "id": "layer-constitution-chemical", "name": "Chemical representation", "description": "Proposed context group for chemical representation. External references retain their own masters.", "source_refs": [ "SRC-003" ], "findings": [ { "id": "finding-chemical", "name": "Nonprotein chemical definition", "description": "A nonprotein biomolecule profile may require a chemical graph instead of a peptide sequence. Preserve charge, stereochemical and isotopic scope; broad ontology terms can denote unresolved classes.", "source_refs": [ "SRC-003" ], "questions": [ { "id": "question-chemical-1", "text": "Which chemical representation and identity precision describe this nonprotein subject?", "kind": "definition", "answer_data": [ "structure identifier", "representation type", "chemical class or exact form", "version", "unknown features" ] }, { "id": "question-chemical-2", "text": "What charge, stereochemical and isotopic distinctions are included in the stated identity?", "kind": "composition", "answer_data": [ "formal charge", "stereochemical scope", "isotope scope", "protonation assumption", "evidence" ] }, { "id": "question-chemical-3", "text": "Which polymer or branched molecule details require a specialist profile beyond this draft?", "kind": "exception", "answer_data": [ "molecule type", "unrepresented connectivity or branching", "external profile", "coverage gap" ] } ], "data_elements": [ { "id": "data-chemical-chemistry", "name": "Chemical definition", "description": "Optional graph-oriented definition; names and formula alone are not an exact-equivalence test.", "value_kind": "object", "cardinality": "0..1", "required": false, "source_refs": [ "SRC-003" ] }, { "id": "data-chemical-gaps", "name": "Specialist profile gaps", "description": "Explicit unresolved detail for glycans, lipids and nucleic acids; no universal sequence-only encoding.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-003" ] } ], "artifacts": [ { "id": "artifact-chemical", "name": "Chemical identity qualification", "description": "Versioned evidence view for nonprotein chemical definition. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-003" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "bundle-observation", "name": "Properties and recognition", "description": "Separate direct descriptors from observations and contextual applicability.", "rationale": "These distinctions are needed to prevent identity, evidence or authority loss in a local molecular knowledge record; the hierarchy is a research proposal, not an external normative schema.", "source_refs": [ "SRC-003", "SRC-004", "SRC-005", "SRC-006", "SRC-008", "SRC-009", "SRC-010" ], "layers": [ { "id": "layer-observation-properties", "name": "Property assertions", "description": "Proposed context group for property assertions. External references retain their own masters.", "source_refs": [ "SRC-003", "SRC-005", "SRC-010" ], "findings": [ { "id": "finding-properties", "name": "Physical and chemical property assertions", "description": "Values attach to a defined molecular form and evidence context. Computed descriptors and measured results remain distinct; sample-specific concentration or purity is delegated.", "source_refs": [ "SRC-003", "SRC-005", "SRC-010" ], "questions": [ { "id": "question-properties-1", "text": "Which mass, charge, length or other property values apply to the selected molecular form?", "kind": "measurement", "answer_data": [ "property kind", "value", "unit or dimensionless basis", "form reference", "applicability" ] }, { "id": "question-properties-2", "text": "Was each property measured, calculated or imported, and under which assumptions?", "kind": "provenance", "answer_data": [ "method or software version", "input form", "conditions", "source", "observation time" ] }, { "id": "question-properties-3", "text": "What uncertainty, tolerance or convention limits comparison of these values?", "kind": "quality", "answer_data": [ "uncertainty", "mass convention", "conditions", "comparability decision", "missing metadata" ] } ], "data_elements": [ { "id": "data-properties-values", "name": "Property assertions", "description": "Typed quantities with form, method, conditions, units and uncertainty when known; missing metadata remains explicit.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-003", "SRC-005", "SRC-010" ] }, { "id": "data-properties-delegation", "name": "Sample property references", "description": "Concentration, purity and batch stability stay with the specimen or assay record.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-003", "SRC-005", "SRC-010" ] } ], "artifacts": [ { "id": "artifact-properties", "name": "Property assertion table", "description": "Versioned evidence view for physical and chemical property assertions. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-003", "SRC-005", "SRC-010" ] } ], "inline_only_rationale": null } ] }, { "id": "layer-observation-recognition", "name": "Recognition and biological context", "description": "Proposed context group for recognition and biological context. External references retain their own masters.", "source_refs": [ "SRC-004", "SRC-006", "SRC-008", "SRC-009", "SRC-010" ], "findings": [ { "id": "finding-recognition", "name": "Recognition and identification evidence", "description": "Recognition records describe why a candidate molecular identity is supported. Similarity, a shared feature or a predicted structure alone does not resolve all competing identities.", "source_refs": [ "SRC-004", "SRC-006", "SRC-009", "SRC-010" ], "questions": [ { "id": "question-recognition-1", "text": "Which observations or external analyses support recognizing the asserted molecular form?", "kind": "evidence", "answer_data": [ "observation reference", "analysis method", "sample reference", "candidate identity", "evidence status" ] }, { "id": "question-recognition-2", "text": "Which alternative forms remain compatible with the available recognition evidence?", "kind": "quality", "answer_data": [ "candidate set", "discriminating coverage", "shared evidence", "uncertainty", "reviewer conclusion" ] }, { "id": "question-recognition-3", "text": "What evidence would be needed to resolve a mismatch between the recognized form and reference?", "kind": "validation", "answer_data": [ "mismatch", "required independent evidence", "review state", "responsible role", "refusal reason" ] } ], "data_elements": [ { "id": "data-recognition-recognition", "name": "Recognition assertions", "description": "Evidence-linked candidate matches, including rejected or unresolved alternatives.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-004", "SRC-006", "SRC-009", "SRC-010" ] }, { "id": "data-recognition-observations", "name": "Observation references", "description": "Links only; acquisition procedure, instrument operation and raw-data management are external.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-004", "SRC-006", "SRC-009", "SRC-010" ] } ], "artifacts": [ { "id": "artifact-recognition", "name": "Recognition evidence assessment", "description": "Versioned evidence view for recognition and identification evidence. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-004", "SRC-006", "SRC-009", "SRC-010" ] } ], "inline_only_rationale": null }, { "id": "finding-context", "name": "Biological location and contextual applicability", "description": "A location or process association is a qualified assertion. Cellular localization is not storage location, and contextual annotation is not a universal property of every specimen.", "source_refs": [ "SRC-008", "SRC-009" ], "questions": [ { "id": "question-context-1", "text": "Which biological location or compartment is supported for the molecular activity?", "kind": "spatial", "answer_data": [ "location term", "relation", "biological context", "form reference", "evidence" ] }, { "id": "question-context-2", "text": "What observation period, developmental context or annotation date bounds the context claim?", "kind": "temporal", "answer_data": [ "biological timing reference", "annotation date", "observation time", "unknown precision" ] }, { "id": "question-context-3", "text": "Which taxon, tissue or condition restrictions prevent transferring the annotation to another context?", "kind": "constraint", "answer_data": [ "context qualifiers", "source restriction", "transfer decision", "unresolved applicability" ] } ], "data_elements": [ { "id": "data-context-contexts", "name": "Context assertions", "description": "Optional qualified cellular and biological context claims; absence remains unknown.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-008", "SRC-009" ] }, { "id": "data-context-times", "name": "Context time qualifiers", "description": "Keep biological timing and record timestamps distinct; date-only source values retain precision.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-008", "SRC-009" ] } ], "artifacts": [ { "id": "artifact-context", "name": "Context applicability record", "description": "Versioned evidence view for biological location and contextual applicability. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-008", "SRC-009" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "bundle-structures", "name": "Structure and assembly evidence", "description": "Keep structural representations and their quality distinct from molecular identity.", "rationale": "These distinctions are needed to prevent identity, evidence or authority loss in a local molecular knowledge record; the hierarchy is a research proposal, not an external normative schema.", "source_refs": [ "SRC-005", "SRC-006", "SRC-007", "SRC-009" ], "layers": [ { "id": "layer-structures-models", "name": "Representations and quality", "description": "Proposed context group for representations and quality. External references retain their own masters.", "source_refs": [ "SRC-005", "SRC-006", "SRC-007" ], "findings": [ { "id": "finding-structure", "name": "Structure representation and residue mapping", "description": "A coordinate model is evidence about a molecule, not the molecule identity itself. Preserve experimental, computational or mixed origin and explicit sequence coverage.", "source_refs": [ "SRC-005", "SRC-007" ], "questions": [ { "id": "question-structure-1", "text": "Which structure entry, model, entity and chain identify the representation being linked?", "kind": "identity", "answer_data": [ "archive namespace", "entry version", "model identifier", "entity and chain", "artifact reference" ] }, { "id": "question-structure-2", "text": "What experimental, predicted or combined evidence produced this structure representation?", "kind": "provenance", "answer_data": [ "origin category", "method", "software and version", "data references", "limitations" ] }, { "id": "question-structure-3", "text": "How do modeled residues map to the molecular reference and its unmodeled regions?", "kind": "interoperability", "answer_data": [ "reference version", "chain mapping", "numbering scheme", "coverage", "missing or engineered differences" ] } ], "data_elements": [ { "id": "data-structure-representations", "name": "Structure references", "description": "Multiple conformers and models may be linked without overwriting the subject definition.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-005", "SRC-007" ] }, { "id": "data-structure-residue-map", "name": "Residue mapping", "description": "Versioned relation between model coordinates and molecular sequence; no forced full coverage.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-005", "SRC-007" ] } ], "artifacts": [ { "id": "artifact-structure", "name": "Structure mapping dossier", "description": "Versioned evidence view for structure representation and residue mapping. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-005", "SRC-007" ] } ], "inline_only_rationale": null }, { "id": "finding-structure-quality", "name": "Method-specific structure quality", "description": "Record metric meaning and scope. Experimental resolution, model-data agreement and prediction confidence answer different questions and cannot share a universal quality threshold.", "source_refs": [ "SRC-006", "SRC-007" ], "questions": [ { "id": "question-structure-quality-1", "text": "Which quality metric, scale and spatial scope apply to this structure?", "kind": "measurement", "answer_data": [ "metric definition", "value", "unit or scale", "local or global scope", "method" ] }, { "id": "question-structure-quality-2", "text": "Which validation report and experimental support were actually available?", "kind": "validation", "answer_data": [ "report identifier and revision", "validated inputs", "method applicability", "warnings", "unchecked aspects" ] }, { "id": "question-structure-quality-3", "text": "Which regions or uses remain unsupported despite favorable aggregate scores?", "kind": "exception", "answer_data": [ "regional limitations", "unsupported inference", "intended use", "review decision" ] } ], "data_elements": [ { "id": "data-structure-quality-metrics", "name": "Quality metrics", "description": "Method-specific estimates with definitions; prediction confidence is not measured resolution.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-006", "SRC-007" ] }, { "id": "data-structure-quality-reports", "name": "Validation references", "description": "External reports and limitations; this model does not run a structure validation service.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-006", "SRC-007" ] } ], "artifacts": [ { "id": "artifact-structure-quality", "name": "Structure quality assessment", "description": "Versioned evidence view for method-specific structure quality. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-006", "SRC-007" ] } ], "inline_only_rationale": null } ] }, { "id": "layer-structures-assembly", "name": "Assembly context", "description": "Proposed context group for assembly context. External references retain their own masters.", "source_refs": [ "SRC-005", "SRC-009" ], "findings": [ { "id": "finding-assembly", "name": "Assembly, component and partner context", "description": "Reference a complex or assembly without confusing a coordinate chain with a biological subunit. Interaction expansion is not proof that every participant pair binds directly.", "source_refs": [ "SRC-005", "SRC-009" ], "questions": [ { "id": "question-assembly-1", "text": "Which assembly or complex is asserted, and which component roles and stoichiometry are supported?", "kind": "composition", "answer_data": [ "assembly reference", "component molecular references", "role", "stoichiometry or unknown", "evidence" ] }, { "id": "question-assembly-2", "text": "How is a biological assembly distinguished from other groupings in the structure record?", "kind": "relationship", "answer_data": [ "grouping type", "representation reference", "assembly interpretation", "support", "uncertainty" ] }, { "id": "question-assembly-3", "text": "Were pairwise links derived from a larger complex rather than directly demonstrated?", "kind": "quality", "answer_data": [ "original interaction identifier", "expansion method", "directness claim", "evidence limitations" ] } ], "data_elements": [ { "id": "data-assembly-assemblies", "name": "Assembly membership references", "description": "Optional membership assertions; complex lifecycle and experimental construction remain external.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-005", "SRC-009" ] }, { "id": "data-assembly-components", "name": "Component qualifications", "description": "Roles and supported stoichiometry, without treating unknown values as one.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-005", "SRC-009" ] } ], "artifacts": [ { "id": "artifact-assembly", "name": "Assembly context record", "description": "Versioned evidence view for assembly, component and partner context. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-005", "SRC-009" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "bundle-behavior", "name": "Capabilities, interactions and limits", "description": "Express supported biological roles without implying authority to act.", "rationale": "These distinctions are needed to prevent identity, evidence or authority loss in a local molecular knowledge record; the hierarchy is a research proposal, not an external normative schema.", "source_refs": [ "SRC-006", "SRC-008", "SRC-009", "SRC-010" ], "layers": [ { "id": "layer-behavior-claims", "name": "Function and interaction claims", "description": "Proposed context group for function and interaction claims. External references retain their own masters.", "source_refs": [ "SRC-008", "SRC-009" ], "findings": [ { "id": "finding-function", "name": "Molecular capability and function claims", "description": "Keep function, biological process involvement and actual observation distinct. Annotation evidence and explicit negation are retained; missing annotation is not a negative result.", "source_refs": [ "SRC-008" ], "questions": [ { "id": "question-function-1", "text": "Which molecular activity or process relation is asserted for the selected form?", "kind": "classification", "answer_data": [ "subject form", "term", "relation", "ontology release", "qualifier" ] }, { "id": "question-function-2", "text": "Which reference and evidence category support each function annotation?", "kind": "evidence", "answer_data": [ "reference", "evidence code", "annotation source", "curation state", "context" ] }, { "id": "question-function-3", "text": "How are explicit negative claims, unresolved disagreement and absent annotations distinguished?", "kind": "exception", "answer_data": [ "negation qualifier", "conflicting claim references", "unknown status", "scope of disagreement" ] } ], "data_elements": [ { "id": "data-function-annotations", "name": "Function annotations", "description": "Evidence-linked relations; no automatic inference of clinical effect or observed activity.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-008" ] }, { "id": "data-function-negation", "name": "Claim polarity", "description": "Explicit positive, qualified negative, unknown or disputed status with source semantics.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-008" ] } ], "artifacts": [ { "id": "artifact-function", "name": "Function evidence ledger", "description": "Versioned evidence view for molecular capability and function claims. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-008" ] } ], "inline_only_rationale": null }, { "id": "finding-interactions", "name": "Interaction and behavior assertions", "description": "Interaction type, partner roles and detection context qualify behavior. Association, direct binding and a causal assertion require their own evidence rather than inference from proximity.", "source_refs": [ "SRC-009" ], "questions": [ { "id": "question-interactions-1", "text": "Which exact participant forms and relation types define each interaction claim?", "kind": "relationship", "answer_data": [ "participant identifiers", "form qualifiers", "interaction type", "direction if supported", "source identifier" ] }, { "id": "question-interactions-2", "text": "Which detection evidence, publication and confidence definition support that interaction?", "kind": "evidence", "answer_data": [ "method reference", "publication", "score type and value", "biological and experimental roles" ] }, { "id": "question-interactions-3", "text": "Is the interaction positive, explicitly negative, inferred or unresolved in the stated context?", "kind": "state", "answer_data": [ "claim polarity", "context", "inference method", "evidence conflict", "review state" ] } ], "data_elements": [ { "id": "data-interactions-interactions", "name": "Interaction assertions", "description": "Typed evidence links preserve original n-ary provenance and do not imply execution.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-009" ] }, { "id": "data-interactions-roles", "name": "Participant roles", "description": "Separate biological and experimental roles with form and context references.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-009" ] } ], "artifacts": [ { "id": "artifact-interactions", "name": "Interaction evidence view", "description": "Versioned evidence view for interaction and behavior assertions. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-009" ] } ], "inline_only_rationale": null } ] }, { "id": "layer-behavior-limits", "name": "Use boundaries", "description": "Proposed context group for use boundaries. External references retain their own masters.", "source_refs": [ "SRC-006", "SRC-008", "SRC-010" ], "findings": [ { "id": "finding-limits", "name": "Use constraints and safety review routing", "description": "Proposed local policy: biological capability does not authorize a scientific, clinical or material action. Retain intended-use limits and route sensitive requests to qualified review; this is not a hazard classifier.", "source_refs": [ "SRC-006", "SRC-008", "SRC-010" ], "questions": [ { "id": "question-limits-1", "text": "What evidence and qualified review are required for the intended use of this molecular record?", "kind": "requirement", "answer_data": [ "intended use", "evidence requirements", "review role", "acceptance criteria", "pending restrictions" ] }, { "id": "question-limits-2", "text": "Which policy review prevents a sensitive molecular request from becoming unauthorized operational guidance?", "kind": "security", "answer_data": [ "policy reference", "sensitivity classification", "authorized reviewer", "allowed output scope", "decision reference" ] }, { "id": "question-limits-3", "text": "Who may approve reuse or a local curation decision without claiming authority over an external master?", "kind": "authority", "answer_data": [ "responsible role", "delegated authority", "scope", "approval record", "external correction route" ] } ], "data_elements": [ { "id": "data-limits-limits", "name": "Use limitations", "description": "Adopting-Dimension policy overlay, not a legal or biological safety certification.", "value_kind": "collection", "cardinality": "1..n", "required": true, "source_refs": [ "SRC-006", "SRC-008", "SRC-010" ] }, { "id": "data-limits-review", "name": "Review routing", "description": "Role-based human review references for clinical, regulatory, rights or biosecurity questions.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-006", "SRC-008", "SRC-010" ] } ], "artifacts": [ { "id": "artifact-limits", "name": "Use and review decision record", "description": "Versioned evidence view for use constraints and safety review routing. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-006", "SRC-008", "SRC-010" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "bundle-continuity", "name": "Evidence and record continuity", "description": "Preserve provenance, changes and governed exchange.", "rationale": "These distinctions are needed to prevent identity, evidence or authority loss in a local molecular knowledge record; the hierarchy is a research proposal, not an external normative schema.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-008", "SRC-010", "SRC-011" ], "layers": [ { "id": "layer-continuity-lineage", "name": "Provenance and revisions", "description": "Proposed context group for provenance and revisions. External references retain their own masters.", "source_refs": [ "SRC-001", "SRC-004", "SRC-008", "SRC-010" ], "findings": [ { "id": "finding-provenance", "name": "Assertion provenance and disagreement", "description": "Every scientific assertion can retain its source, attribution and derivation. A citation establishes traceability, not truth; contradictory evidence stays visible.", "source_refs": [ "SRC-010", "SRC-008" ], "questions": [ { "id": "question-provenance-1", "text": "Which source version, activity and responsible role produced this assertion?", "kind": "provenance", "answer_data": [ "assertion identifier", "source version", "derivation activity", "role", "record time" ] }, { "id": "question-provenance-2", "text": "What conflicting, retracted or superseded evidence affects acceptance of the assertion?", "kind": "quality", "answer_data": [ "evidence references", "conflict relation", "review status", "impact on current view" ] }, { "id": "question-provenance-3", "text": "Who stewards the local record and which external authority controls each master reference?", "kind": "ownership", "answer_data": [ "local steward role", "master authority role", "record scope", "correction responsibility" ] } ], "data_elements": [ { "id": "data-provenance-lineage", "name": "Assertion lineage", "description": "Source and derivation references for local assertions; origin is distinct from ownership.", "value_kind": "collection", "cardinality": "1..n", "required": true, "source_refs": [ "SRC-010", "SRC-008" ] }, { "id": "data-provenance-disputes", "name": "Evidence disputes", "description": "Parallel sourced claims and resolution history; do not erase dissent by choosing a preferred source.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-010", "SRC-008" ] } ], "artifacts": [ { "id": "artifact-provenance", "name": "Assertion lineage dossier", "description": "Versioned evidence view for assertion provenance and disagreement. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-010", "SRC-008" ] } ], "inline_only_rationale": null }, { "id": "finding-continuity", "name": "Record revisions and molecular state changes", "description": "A revised annotation does not change a molecule. A transformation or different form is represented by a qualified relation or new identity when the adopted identity profile requires it.", "source_refs": [ "SRC-001", "SRC-004", "SRC-010" ], "questions": [ { "id": "question-continuity-1", "text": "Which local record state and supersession relations preserve historical molecular references?", "kind": "lifecycle", "answer_data": [ "draft or reviewed or retired state", "revision", "successor references", "reason", "authority" ] }, { "id": "question-continuity-2", "text": "Does the reported change describe a biological transformation, a different form or a record correction?", "kind": "event", "answer_data": [ "change category", "before and after references", "event evidence", "identity decision" ] }, { "id": "question-continuity-3", "text": "How are evidence occurrence, source release and local ingestion times preserved separately?", "kind": "temporal", "answer_data": [ "event time", "source release", "ingestion time", "precision", "unknown reason" ] } ], "data_elements": [ { "id": "data-continuity-revisions", "name": "Revision lineage", "description": "Record-state transitions with immutable revision identifiers and reversible local view selection.", "value_kind": "collection", "cardinality": "1..n", "required": true, "source_refs": [ "SRC-001", "SRC-004", "SRC-010" ] }, { "id": "data-continuity-changes", "name": "Change classifications", "description": "No biochemical event is inferred from a metadata revision or deprecation.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-004", "SRC-010" ] } ], "artifacts": [ { "id": "artifact-continuity", "name": "Continuity and supersession ledger", "description": "Versioned evidence view for record revisions and molecular state changes. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-001", "SRC-004", "SRC-010" ] } ], "inline_only_rationale": null } ] }, { "id": "layer-continuity-exchange", "name": "Exchange governance", "description": "Proposed context group for exchange governance. External references retain their own masters.", "source_refs": [ "SRC-003", "SRC-010", "SRC-011" ], "findings": [ { "id": "finding-exchange", "name": "Exchange, access and retention envelope", "description": "Proposed local governance surrounds evidence exchange. Public molecular metadata does not authorize release of linked restricted observations or personal data.", "source_refs": [ "SRC-003", "SRC-010", "SRC-011" ], "questions": [ { "id": "question-exchange-1", "text": "Which binding versions and loss reports accompany an exported molecular view?", "kind": "interoperability", "answer_data": [ "binding identifier", "schema version", "source revisions", "unsupported fields", "loss report" ] }, { "id": "question-exchange-2", "text": "What access and reuse conditions apply to each linked artifact and derived view?", "kind": "access", "answer_data": [ "artifact policy", "license reference", "purpose", "recipient scope", "redaction decision" ] }, { "id": "question-exchange-3", "text": "Which approved retention decision permits payload disposal while preserving necessary reference continuity?", "kind": "retention", "answer_data": [ "policy version", "retention trigger", "hold status", "authorized action", "minimal tombstone", "execution authority" ] } ], "data_elements": [ { "id": "data-exchange-bindings", "name": "Exchange bindings", "description": "Versioned candidate mappings; no executable conformance until fixtures and parsers are checked.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-003", "SRC-010", "SRC-011" ] }, { "id": "data-exchange-governance", "name": "Access and retention envelope", "description": "Required local policy references; external systems own their own deletion and access enforcement.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-003", "SRC-010", "SRC-011" ] } ], "artifacts": [ { "id": "artifact-exchange", "name": "Exchange assurance record", "description": "Versioned evidence view for exchange, access and retention envelope. Preserve assertion scope, source pointer and unresolved values; it is not a new authoritative scientific record.", "media_or_form": [ "structured record", "human-readable view" ], "serial": true, "identity_strategy": "Authoritative master-system artifact identifier and revision first; otherwise governed IRI, then Dimension UUID or ULID. Parent molecular identity and assertion revision are separate. Filenames and dates never establish identity.", "source_refs": [ "SRC-003", "SRC-010", "SRC-011" ] } ], "inline_only_rationale": null } ] } ] } ] }, "functions": [ { "id": "function-resolve", "name": "Resolve a molecular reference", "description": "Proposed, unimplemented local operation. Compare supplied master references and form scope; preserve ambiguity instead of automatically merging records.", "inputs": [ "master references and versions", "subject resolution", "mapping evidence" ], "outputs": [ "qualified crosswalk or unresolved-match report" ], "preconditions": [ "Authorized local curator or reader within the requested scope.", "Expected current revision and evidence permissions checked.", "Unsupported authority, missing mandatory context or conflicting identity causes refusal or review." ], "effects": [ "Propose a local mapping revision; external master identity is unchanged." ], "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] }, { "id": "function-qualify", "name": "Qualify a molecular form", "description": "Proposed, unimplemented local operation. Check whether a proposed sequence or chemical representation states its assumptions and uncertainty. This is metadata checking, not molecular design.", "inputs": [ "form definition", "coordinate frame", "notation and vocabulary versions" ], "outputs": [ "form qualification or refusal report" ], "preconditions": [ "Authorized local curator or reader within the requested scope.", "Expected current revision and evidence permissions checked.", "Unsupported authority, missing mandatory context or conflicting identity causes refusal or review." ], "effects": [ "Attach explicit ambiguity and unsupported-feature flags." ], "source_refs": [ "SRC-003", "SRC-004", "SRC-011" ] }, { "id": "function-attach", "name": "Attach structure evidence", "description": "Proposed, unimplemented local operation. Link a supplied model and quality report with coverage and origin qualifiers; do not run experiments or structure prediction.", "inputs": [ "structure artifact reference", "sequence mapping", "quality evidence" ], "outputs": [ "qualified representation link or mismatch report" ], "preconditions": [ "Authorized local curator or reader within the requested scope.", "Expected current revision and evidence permissions checked.", "Unsupported authority, missing mandatory context or conflicting identity causes refusal or review." ], "effects": [ "Append an evidence reference with distinct experimental or computational origin." ], "source_refs": [ "SRC-005", "SRC-006", "SRC-007" ] }, { "id": "function-annotate", "name": "Record an evidence-qualified claim", "description": "Proposed, unimplemented local operation. Attach supplied function or interaction evidence without inferring clinical efficacy or unobserved activity.", "inputs": [ "form reference", "typed claim and polarity", "source and evidence category" ], "outputs": [ "claim revision or incomplete-evidence report" ], "preconditions": [ "Authorized local curator or reader within the requested scope.", "Expected current revision and evidence permissions checked.", "Unsupported authority, missing mandatory context or conflicting identity causes refusal or review." ], "effects": [ "Preserve contradictory claims and unknowns in the local view." ], "source_refs": [ "SRC-008", "SRC-009", "SRC-010" ] }, { "id": "function-revise", "name": "Reconcile a record revision", "description": "Proposed, unimplemented local operation. Classify an external update and propose local successor or retirement links.", "inputs": [ "old and new source revisions", "affected assertions", "identity profile" ], "outputs": [ "reviewable patch or unresolved split report" ], "preconditions": [ "Authorized local curator or reader within the requested scope.", "Expected current revision and evidence permissions checked.", "Unsupported authority, missing mandatory context or conflicting identity causes refusal or review." ], "effects": [ "Mark affected derived assertions stale; preserve prior references subject to retention policy." ], "source_refs": [ "SRC-001", "SRC-010" ] }, { "id": "function-export", "name": "Prepare a governed molecular view", "description": "Proposed, unimplemented local operation. Project only permitted assertions into a selected binding and report information loss.", "inputs": [ "recipient scope and purpose", "selected binding version", "artifact rights and current policy" ], "outputs": [ "permitted local view and loss report or refusal" ], "preconditions": [ "Authorized local curator or reader within the requested scope.", "Expected current revision and evidence permissions checked.", "Unsupported authority, missing mandatory context or conflicting identity causes refusal or review." ], "effects": [ "Create a local export artifact; no external transmission or master submission." ], "source_refs": [ "SRC-003", "SRC-010", "SRC-011" ] } ], "composition": [ { "target": "WM-LIV-002", "relation": "REFERENCE", "purpose": "Candidate organism context only when an identified source individual is relevant. Reject registry parent_ids as biological inheritance or containment: a molecular kind is not an organism individual.", "required": false, "source_refs": [ "SRC-002", "SRC-005" ] }, { "target": "WM-LIV-013", "relation": "REFERENCE", "purpose": "Candidate gene context; gene identity, genomic coordinates and its lifecycle remain external. Binding version must be reviewed before implementation.", "required": false, "source_refs": [ "SRC-002" ] }, { "target": "WM-LIV-023", "relation": "REFERENCE", "purpose": "Candidate specimen context; custody, consent and specimen measurements remain externally mastered, not molecular-kind properties.", "required": false, "source_refs": [ "SRC-005", "SRC-010" ] }, { "target": "WM-LIV-016", "relation": "REFERENCE", "purpose": "Candidate pathway context; this root holds participation evidence, not pathway dynamics or process execution.", "required": false, "source_refs": [ "SRC-008", "SRC-009" ] }, { "target": "WM-MAT-001", "relation": "REFERENCE", "purpose": "Candidate chemical-substance boundary reconciliation for nonprotein forms. Preserve one external chemical master; avoid duplicate substance, batch or inventory lifecycles.", "required": false, "source_refs": [ "SRC-003" ] }, { "target": "PDBx/mmCIF Version 5 and ModelCIF", "relation": "ALIGN", "purpose": "Selected molecular entity and structure-evidence mapping only; entry, entity, chain and assembly identifiers are distinct. Exact dictionary pins and conformance deferred.", "required": false, "source_refs": [ "SRC-005", "SRC-007" ] }, { "target": "ProForma 2.0 and 2.1", "relation": "ALIGN", "purpose": "Explicit version selection for form notation. The 2.0 research paper supports concepts; 2.1 syntax and parser support require a separate conformance check.", "required": false, "source_refs": [ "SRC-004", "SRC-011" ] }, { "target": "Gene Ontology annotations and PSI-MITAB 2.8", "relation": "ALIGN", "purpose": "Preserve function evidence and interaction qualifiers using versioned vocabulary bindings; no automatic whole-schema equivalence.", "required": false, "source_refs": [ "SRC-008", "SRC-009" ] }, { "target": "PROV-O 2013-04-30", "relation": "ALIGN", "purpose": "Attribution and derivation of local assertions; rights, truth, audit enforcement and runtime policy are not supplied by this ontology.", "required": false, "source_refs": [ "SRC-010" ] } ], "serviceLayers": { "dimension": { "owner_package_requirements": [ "An adopting Dimension designates a scientific data steward role and curation authority for local records.", "Record molecular identity profile, external master references and version resolution rules.", "Declare access, reuse, sensitivity, retention and correction policies with responsible roles.", "Separate molecular kind stewardship from ownership of specimens, datasets and external repository records." ], "namespace_guidance": "Use a governed namespace with stable local subject, assertion and artifact IDs. Repository accessions retain their own namespaces and revisions. Never derive stable identity from a timestamp or a display name.", "registry_links": [ "vr.wm-liv-014", "Candidate neighbor model versions remain unpinned; no required runtime dependency is asserted." ] }, "canon_and_patch": { "canonicalization_rules": [ "Normalize display labels without collapsing molecular forms, taxon context, chemical precision or evidence polarity.", "Keep source-native values and versioned mapping provenance; unknown, absent and not applicable are distinct." ], "patch_rules": [ "Patches require expected revision, authorized role, rationale and affected assertion IDs.", "A sequence or chemical identity change requires an explicit same-subject versus new-subject decision; local record correction is not a biochemical transformation." ], "compatibility_rules": [ "Version mappings and report lost uncertainty, qualifiers or coordinate information.", "Breaking identity or semantic changes require a profile revision and review; this draft is noncanonical." ] }, "artifact_rules": { "identity_priority": [ "Authoritative master-system identifier plus artifact revision", "Governed global identifier or IRI", "UUID or ULID assigned by the adopting Dimension" ], "timestamp_rule": "Use RFC 3339 with seconds and an explicit offset or Z for known instants. Separate evidence event time, source release and observation or ingestion time. Preserve date-only precision without inventing midnight.", "serial_naming_rule": "Serial artifacts use stable parent and artifact IDs plus a revision token; display filenames are labels and dates do not serve as IDs.", "integrity_rule": "Record cryptographic digest, media type, source revision and derivation for payloads when available. A digest shows byte integrity, not molecular identity, truth or access permission." }, "policies": [ "Reviewable draft under the owner-authorized single-provider waiver; independent external review is absent.", "Candidate structure and service rules are local design choices informed by cited sources; they are not a claim that those sources prescribe Vercy governance.", "Do not convert prediction confidence, sequence similarity or a database annotation into experimental proof, clinical effect or a universal biological capability.", "Sensitive biomolecule requests remain at policy and evidence-routing level. No design, production, enhancement, procurement or handling instructions for harmful biological agents are authorized by this model.", "Qualified scientific, clinical, regulatory and rights review belongs to the adopting context. No legal compliance, safety certification or diagnostic authority is implied.", "Public metadata and a citation do not grant permission to redistribute every linked artifact or restricted observation." ], "crud": { "read": [ "Resolve the subject profile, current view, source versions, recipient scope and visible holds before interpreting evidence." ], "create": [ "Require scoped identity, steward role and provenance; accept provisional subjects only with unresolved master status and explicit uncertainty." ], "update": [ "Use authorized revision patches; keep disagreements, source history and correction reasons without overwriting external masters." ], "delete": [ "Retire local records through authorized retention and disposal policy. Retain only permitted minimal tombstones and required provenance; lawful payload deletion can override full history retention.", "The adopting Dimension or referenced repository executes access changes and deletion under its own authority. Local retirement neither destroys a physical specimen nor deletes an external scientific accession." ] }, "roles": [ { "name": "Scientific data steward", "responsibilities": [ "Own the local identity profile and source-version decisions." ] }, { "name": "Scientific curator", "responsibilities": [ "Assess claim evidence, form ambiguity and context restrictions." ] }, { "name": "Evidence reviewer", "responsibilities": [ "Challenge mappings, contradictions and method applicability." ] }, { "name": "Access and retention custodian", "responsibilities": [ "Apply the adopting policy to linked artifacts and local payload disposal." ] }, { "name": "Model agent", "responsibilities": [ "Perform only authorized local read, validation and proposal operations; escalate unresolved scientific or policy decisions." ] } ], "access": { "default_rule": "Allow local use only under the adopting Dimension policy and the most restrictive applicable artifact conditions; do not infer public access from a public accession.", "scopes": [ "bundle", "layer", "finding", "artifact" ], "exceptions": [ "Restricted observations may be referenced through a minimal authorized pointer.", "An authorized disclosure exception needs a purpose, approver, scope and expiry; no silent widening of access." ], "audit_requirements": [ "Record actor role, purpose, policy version, before and after revision and decision result for local mutations.", "Keep audit evidence under the adopting retention and access policy; this model references the audit service rather than implementing it." ] }, "agents_bootstrap": { "filename": "AGENTS.md", "required_fields": [ "Name", "Type", "Specification URL", "Storage type URL", "Interface URL", "Processes URL" ], "read_order": [ "Nearest adopting Dimension policy and AGENTS.md", "This package AGENTS.md and spec.yaml", "Pinned molecular profile, external sources and artifact access rules" ] } }, "coverage": { "claim": "Source-grounded proposed structure for one molecular kind at declared identity resolution, with protein and peptide depth and bounded nonprotein chemical support. A separate frozen local no-tools self-audit found no critical conflict. Independent external review, source/version verification, specialist profiles and executable conformance remain open; this is a noncanonical reviewable draft.", "confidence": "medium", "checklist": [ { "dimension": "identity", "status": "covered", "notes": "Explicit molecular resolution, namespace and mapping qualifiers." }, { "dimension": "lifecycle", "status": "covered", "notes": "Local curation revisions are separate from molecular changes." }, { "dimension": "relationships", "status": "covered", "notes": "Genes, organisms, specimens, structures and pathways retain their own masters." }, { "dimension": "temporal", "status": "covered", "notes": "Evidence time, source release and ingestion remain distinct." }, { "dimension": "provenance", "status": "covered", "notes": "Assertion attribution, derivation, disagreement and retraction impact." }, { "dimension": "ownership", "status": "covered", "notes": "Local steward role is distinct from external scientific authority and specimen holder." }, { "dimension": "validation", "status": "gap", "notes": "Research schema validation is separate from executable instance and scientific validation." }, { "dimension": "access", "status": "covered", "notes": "Policy-scoped views preserve artifact restrictions." }, { "dimension": "retention and deletion", "status": "covered", "notes": "Authorized payload disposal with permitted minimal reference continuity." }, { "dimension": "interoperability", "status": "gap", "notes": "Conceptual mappings supplied; binding versions, parsers and loss fixtures remain open." }, { "dimension": "direct properties", "status": "covered", "notes": "Form-specific quantities with units, method, conditions and uncertainty where known." }, { "dimension": "recognition", "status": "covered", "notes": "Evidence-qualified identification with unresolved alternatives." }, { "dimension": "capabilities and behavior", "status": "covered", "notes": "Function and interaction assertions are separated from operations and authority." }, { "dimension": "nonprotein breadth", "status": "gap", "notes": "Chemical profile supports general identity; specialist branching and polymer details deferred." }, { "dimension": "source verification", "status": "gap", "notes": "Browser source review is recorded separately from unmeasured direct HTTP status." } ], "known_omissions": [ "Independent external provider review is absent; a separate local Codex self-audit cannot replace it.", "Direct HTTP checks are not run because the sandbox is blocked; current release pins and complete source text remain unverified for selected sources.", "Specialist nucleic-acid, glycan, lipid, heterogeneous polymer and complex identity profiles need further research.", "Nested instance schemas, precise neighbor bindings, parser support and adversarial conformance fixtures are not implemented.", "Clinical, regulatory, jurisdictional access and benefit-sharing requirements require qualified profile research; no universal rule is asserted." ], "conflicts": [], "regional_assumptions": [ "Scientific identity conventions are not jurisdictional permissions. Adopting profiles must assess local data, sample and intended-use requirements." ], "adversarial_checks": [ "Reject a secondary accession as proof of one-to-one identity after a split.", "Do not merge a gene, sequence form, physical sample or structure entry into the molecular kind.", "Keep missing annotation distinct from explicit negative evidence and preserve disagreement.", "Do not equate prediction confidence with experimental resolution or a measured biological effect.", "Prevent source host, sample owner or database name from becoming a universal molecule owner." ] }, "researchAdjudication": { "providerMode": "single-provider-waiver", "activeProviders": [ "codex" ], "waivedProviders": [ "claude", "grok" ], "providerPolicy": { "contract_version": "1.0.0", "mode": "single-provider-waiver", "effective_at": "2026-09-06T00:00:00Z", "scope": "Canonical single-stream subject-model research after the six-workstream consolidation", "active_providers": [ "codex" ], "waived_providers": [ { "provider": "claude", "authorized_by": "repository owner", "authorized_at": "2026-09-06T00:00:00Z", "reason": "Claude produced no result on prior 1800-second and 900-second attempts and again timed out on bounded 600-second Sonnet and 300-second Haiku passes. The owner prioritized completion over provider availability." }, { "provider": "grok", "authorized_by": "repository owner", "authorized_at": "2026-09-06T00:00:00Z", "reason": "The repository owner authorized completion without Grok when Grok is unavailable, slow or schema-invalid. Grok may still be attempted as a bounded supplemental reviewer, but its failure never blocks a valid Claude plus no-tools result." } ], "review_rule": "Codex may complete source-grounded fallback research after bounded Claude and Grok attempts fail. It requires a separate no-tools adversarial audit and remains reviewable-draft with a visible absence-of-external-review hold.", "supplemental_provider_attempts": [ { "provider": "claude", "required": false, "maximum_attempts": 1, "failure_policy": "record-and-continue", "admission_rule": "Use only a locally schema-valid result whose sources and boundaries survive adjudication." }, { "provider": "grok", "required": false, "maximum_attempts": 1, "failure_policy": "record-and-continue", "admission_rule": "Use only a locally schema-valid result whose sources and boundaries survive adjudication." } ] }, "boundaryDecision": { "entry_kind": "entity", "status": "accepted", "rationale": "The subject is one molecular kind described at explicit identity resolution through persistent local assertions. It is not an individual physical specimen, a gene, a structure entry or a taxonomy. Required scope and form ambiguity prevent an entry-level accession from silently becoming an exact chemical identity. The registry standalone-mm value is a separate classification plane." }, "decisions": [ { "concept": "Molecular kind versus exact form", "disposition": "accepted with resolution qualification", "rationale": "Identity questions require declared resolution and ambiguity; the entity root does not assert every repository entry denotes one fully specified form." }, { "concept": "Registry organism parent", "disposition": "inheritance rejected", "rationale": "A molecular kind is not an organism individual. The frozen registry parent is retained only as an optional contextual reference, with no inherited organism lifecycle." }, { "concept": "Gene, specimen and pathway neighbors", "disposition": "reference boundaries accepted", "rationale": "Gene context uses the checked WM-LIV-013 candidate. All links are optional and unpinned; genomic identity, sample custody and pathway execution remain external." }, { "concept": "Accession and mapping identity", "disposition": "qualified", "rationale": "Namespace, version, form scope and relation type survive mapping. Secondary accessions and split successors cannot authorize an automatic one-to-one merge." }, { "concept": "Sequence and modified forms", "disposition": "accepted", "rationale": "Coordinate frames, processing extents and modification uncertainty are retained. A syntactically representable form is not treated as evidence of existence in a specimen." }, { "concept": "Nonprotein scope", "disposition": "limited and held", "rationale": "The chemical-definition finding avoids protein-only fields for every subject. Specialist nucleic-acid, glycan, lipid and heterogeneous polymer identities remain explicit coverage gaps." }, { "concept": "Properties, recognition and context", "disposition": "accepted with evidence qualification", "rationale": "Values and identification claims preserve form, method, conditions and uncertainty. Sample-specific properties and unobserved biological context are not promoted to universal molecule properties." }, { "concept": "Structure identity and quality", "disposition": "separated", "rationale": "Entry, entity, chain and model references remain distinct. Method-specific quality measures cannot be interchanged with predicted confidence or a universal acceptance threshold." }, { "concept": "Assembly and interaction expansion", "disposition": "qualified", "rationale": "Membership and supported stoichiometry retain their evidence. Pairwise expansion of a complex cannot by itself establish direct binding between each pair." }, { "concept": "Function and negative evidence", "disposition": "accepted with source semantics", "rationale": "Function and interaction assertions retain evidence, polarity and context. Missing annotations, inconclusive evidence, explicit negation and disagreement are distinct states." }, { "concept": "Supplement and legacy material", "disposition": "lead only; no legacy applies", "rationale": "The unreviewed supplement is not a source or external provider result. Universal property and natural-only claims are narrowed. The frozen registry has no legacy alias or specification." }, { "concept": "Local operations and authority", "disposition": "proposed only", "rationale": "All six operations describe local metadata proposals with authority and revision checks. None conducts experiments, designs molecules, changes external masters or authorizes clinical or sensitive operational use." }, { "concept": "Provenance, ownership and retention", "disposition": "accepted as local governance", "rationale": "Source organizations are attributions, not assigned owners. Provenance is not truth or permission; payload disposal follows adopting policy and can limit retained history." }, { "concept": "Source and version assurance", "disposition": "held", "rationale": "Eight browser document readings and three indexed source readings support selected concepts only. Zero direct requests means no measured HTTP statuses. The 2.0 conceptual source is not a claim that ProForma 2.0 is latest." }, { "concept": "Research validation and independent review", "disposition": "reviewable draft only", "rationale": "Candidate data groups and conceptual alignments are not executable conformance. This frozen local self-audit adds no facts or waived-provider nodes and does not restore independent external review." } ], "publicationHolds": [ "Independent external review is absent under the owner-authorized single-provider waiver. Claude and Grok were skipped with zero attempts; the separate local Codex no-tools self-audit is not independent second-provider review.", "Direct HTTP source checks were not attempted because the sandbox is blocked. No response status or payload hash was measured; the coordinator must run check_sources.py outside the sandbox. Eight sources supplied browser document content and three supplied indexed excerpts with full retrieval limits. Current source releases and exact mutable-document pins remain incompletely verified.", "Specialist molecular identity and adoption profiles remain incomplete for nucleic acids, glycans, lipids, heterogeneous polymers and complexes. Protein coverage does not establish exhaustive coverage of every biomolecule implied by the model title.", "Intended-use, licensing, clinical, regulatory, jurisdictional access and benefit-sharing, and biosecurity policies require qualified context-specific review. The proposed local policy overlay is not a legal, clinical or safety certification.", "Nested instance schemas, pinned neighbor bindings, source-specific negation mappings, dictionary versions, ProForma parser feature support and executable conformance fixtures remain incomplete. Research validation does not validate molecular instances or scientific truth.", "Independent external review was explicitly waived by the repository owner; this codex-only result remains a reviewable draft." ], "deferredResearch": [ "Run the coordinator source checker, retrieve complete limited-access source text and pin source versions; separately assess claim support and applicable licenses.", "Develop specialist nonprotein identity profiles and reconcile chemical-substance overlap without duplicating scientific master identity.", "Implement and test nested schemas and bindings with accession splits, ambiguous forms, partial structures, complex expansion, negative annotations and permitted payload disposal.", "Restore independent scientific and external provider review before any canonical or publishable-draft promotion." ] }, "statistics": { "sources": 11, "bundles": 6, "layers": 12, "findings": 18, "questions": 54, "artifacts": 18, "functions": 6 } }