{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T09:41:57Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 22.4, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a094fd-dfe1-7070-b454-bc9e3b2c381c\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: fibril\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001 register", "usd": 0.0, "recall": true }, "codex": { "seconds": 56.7, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a094fd-dfef-7993-9702-586b64ec5cb7\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: fibril\nRegistry id: vr.tr.fibril\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext fo" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:51:02+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "revisions": [ { "at": "2026-10-07T11:11:27+00:00", "engine": "codex", "fields": [ "agent_conduct", "definition", "distinguishing_features", "ethics", "failure_modes_and_hazards", "in_scope", "out_of_scope", "owners", "purpose", "scope_statement", "visual_identification" ], "answering_review": "b0771891d0fa67c2c9c8d8a589b8e40c4e1d5b991a972ab156ee8ede3f45ed7d" } ], "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T12:16:28+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q14860849", "registryId": "vr.tr.fibril", "name": "fibril", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q14860849/", "model": { "registry_id": "vr.tr.fibril", "name": "fibril", "purpose": "Enable an agent to recognise this extracellular matrix material, assess evidence of its composition and organisation, and report observations with their limits.", "definition": "A fibril, in this sense, is a fine, threadlike extracellular matrix material consisting of polysaccharides and protein.", "scope_statement": "This model covers fibrils as extracellular matrix material consisting of polysaccharides and protein, including their identity, morphology, composition, matrix relationships and condition.", "in_scope": [ "Evidence of extracellular matrix context and polysaccharide and protein composition is included.", "Fibril length, transverse dimensions, shape and continuity are included.", "Constituent material and internal organisation are included.", "Relationships to neighbouring fibrils and the surrounding extracellular matrix are included.", "Aggregation, damage and changes under specified conditions are included." ], "out_of_scope": [ "Synthetic fibrils and other threadlike structures outside the specified extracellular matrix sense are excluded.", "The complete biological organism or tissue containing the fibrils is excluded.", "The chemical identity and intrinsic hazards of each constituent substance are excluded.", "The full biological assembly process is excluded.", "Clinical diagnosis associated with particular fibrillar deposits is excluded.", "Bulk material properties not related to this extracellular matrix structure are excluded." ], "distinguishing_features": [ "Identity requires evidence of extracellular matrix context and both polysaccharide and protein constituents.", "A threadlike appearance alone does not establish this material identity.", "The term fibril in synthetic materials or other biological contexts does not establish equivalence to this sense.", "Distinguishing an individual fibril from unresolved strands depends on imaging resolution and evidence of constituent boundaries.", "Size alone is insufficient to distinguish this material from other fine structures." ], "characteristics": [ { "name": "Material-specific fibril class", "kind": "category", "unit_or_values": "Reported class and its operational definition; unresolved", "why_it_matters": "Determines which structural evidence and terminology justify identification." }, { "name": "Constituent material", "kind": "relation", "unit_or_values": "Links to constituent substances or macromolecular species, with evidence and uncertainty", "why_it_matters": "Separates fibrillar form from chemical identity and supports material-specific interpretation." }, { "name": "Contour length", "kind": "measurement", "unit_or_values": "nm or µm, with tracing method, uncertainty and whether both ends are visible", "why_it_matters": "Distinguishes measured length from a lower bound imposed by the field of view." }, { "name": "Transverse dimensions", "kind": "measurement", "unit_or_values": "Width, height or diameter in nm or µm, with method and cross-section assumptions", "why_it_matters": "Supports morphological identification without assuming every fibril is cylindrical." }, { "name": "Aspect ratio", "kind": "measurement", "unit_or_values": "Dimensionless length-to-transverse-size ratio, with the dimensions used identified", "why_it_matters": "Quantifies elongation while exposing uncertainty from incomplete length or width measurements." }, { "name": "Axial and internal organisation", "kind": "category", "unit_or_values": "Observed twist, repeat pattern, constituent arrangement or unresolved organisation", "why_it_matters": "Helps distinguish material-specific fibril architectures without assuming a shared molecular structure." }, { "name": "Structural level", "kind": "relation", "unit_or_values": "Constituents, peer fibrils, enclosing bundle or fibre, and host material", "why_it_matters": "Prevents counting a parent bundle and its constituent fibrils as the same structural unit." }, { "name": "Association state", "kind": "state", "unit_or_values": "Isolated, laterally associated, bundled, entangled, embedded or unresolved", "why_it_matters": "Affects accessibility, apparent dimensions and interpretation of individual-fibril measurements." }, { "name": "Structural integrity", "kind": "state", "unit_or_values": "Observed continuity, fractures, fraying or other alterations, with observation conditions", "why_it_matters": "Supports decisions about whether the fibril remains suitable for the intended examination or use." }, { "name": "Condition during observation", "kind": "state", "unit_or_values": "Temperature, surrounding medium, hydration, substrate contact and applied loading where relevant", "why_it_matters": "Makes dimensional and condition assessments interpretable and comparable." } ], "affordances": [ "Classify an observed strand using material-specific fibril criteria and record unresolved alternatives.", "Measure dimensions and organisation with methods capable of resolving the relevant structural level.", "Trace how individual fibrils contribute to a bundle, fibre or host material.", "Compare fibril morphology before and after a specified treatment or environmental change.", "Select an isolation, dispersion or manipulation procedure using constituent identity and evidence of structural sensitivity." ], "agent_conduct": { "may": [ "Describe fibrils in the specified extracellular matrix context.", "Report fibril measurements with method and source." ], "must_not": [ "Treat all biological or synthetic fibrils as this extracellular matrix material.", "Misreport fibril size or composition in safety or quality data.", "Declare biological material safe to handle without supporting evidence." ], "requires_human": [ "Decisions about biological sample use and handling require responsible human oversight." ] }, "ethics": { "considerations": [ "Accurate reporting of biological origin and composition matters for research integrity.", "Biological sample use must respect applicable consent and stewardship requirements." ], "affected_parties": [ "Sample donors are affected where human material is involved.", "Researchers and sample handlers are affected." ] }, "owners": { "steward": "The responsible sample custodian stewards material and records; the structural category itself has no owner.", "master_systems": [] }, "visual_identification": [ "Microscopic images may show fine, elongated extracellular structures.", "Images alone do not establish polysaccharide and protein composition." ], "failure_modes_and_hazards": [ "Morphology alone can lead to confusion with unrelated fibrillar materials.", "Unsupported assumptions about composition or biological origin can mislead interpretation.", "Sample handling risks depend on the biological source and associated material." ], "what_it_is_for": [ "Extracellular matrix fibrils are encountered when examining the fine structural organization of biological tissues and matrix materials.", "Their composition, alignment and assembly are studied to understand tissue support, interactions with cells and changes associated with damage or repair.", "Microscopy and material characterization help distinguish individual fibrils from larger fibres and surrounding matrix components." ], "facets_not_applicable": { "interfaces": "No universal standard, law or official classification applies specifically to extracellular matrix fibrils across all compositions and uses." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q14860849: fibril", "url": "https://www.wikidata.org/wiki/Q14860849", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Fibril", "url": "https://en.wikipedia.org/wiki/Fibril", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "fibril-identity-and-boundaries", "name": "Fibril identity and boundaries", "description": "Establishes what the term fibril denotes for the observed material and which structural unit is being modelled.", "rationale": "Fibril terminology depends on material context, and the registry supplies no definition that resolves its intended breadth.", "layers": [ { "id": "material-specific-recognition", "name": "Material-specific recognition", "description": "Connects the fibril label to explicit morphological and contextual evidence.", "findings": [ { "id": "operational-fibril-definition", "name": "Operational fibril definition", "description": "Record the criteria used to call this structure a fibril without imposing an unsupported universal size cutoff.", "questions": [ { "text": "What definition of fibril applies to this material, and which observable criteria does it require?", "kind": "definition", "id": "operational-fibril-definition-q01" }, { "text": "Which observation or reference supports applying that definition to this structure?", "kind": "provenance", "id": "operational-fibril-definition-q02" } ] } ] }, { "id": "strand-and-bundle-boundaries", "name": "Strand and bundle boundaries", "description": "Distinguishes the selected fibril from constituent strands and enclosing assemblies.", "findings": [ { "id": "resolved-structural-unit", "name": "Resolved structural unit", "description": "Record whether the selected object is a single fibril, an unresolved assembly or a larger structure described using overlapping terminology.", "questions": [ { "text": "What evidence distinguishes this fibril from a bundle of smaller strands?", "kind": "boundary", "id": "resolved-structural-unit-q01" }, { "text": "How does the applicable terminology distinguish fibril from fibre, filament and microfibril?", "kind": "definition", "id": "resolved-structural-unit-q02" } ] } ] } ] }, { "id": "fibril-morphology-and-resolution", "name": "Fibril morphology and resolution", "description": "Describes elongated geometry together with the observation limits that affect it.", "rationale": "Apparent fibril dimensions can reflect incomplete visibility, preparation and instrument resolution.", "layers": [ { "id": "longitudinal-geometry", "name": "Longitudinal geometry", "description": "Captures contour length, curvature and visible endpoints.", "findings": [ { "id": "traceable-length-and-continuity", "name": "Traceable length and continuity", "description": "Distinguish contour length from endpoint separation and identify truncated or obscured traces.", "questions": [ { "text": "What are the contour length and endpoint separation, and are both physical ends visible?", "kind": "measurement", "id": "traceable-length-and-continuity-q01" }, { "text": "Where do overlaps, apparent junctions or image boundaries prevent reliable tracing of one fibril?", "kind": "boundary", "id": "traceable-length-and-continuity-q02" } ] } ] }, { "id": "transverse-geometry", "name": "Transverse geometry", "description": "Captures transverse size and variation without assuming a circular cross-section.", "findings": [ { "id": "resolved-cross-section", "name": "Resolved cross-section", "description": "Record measured width or height, variation along the axis and evidence supporting any inferred diameter.", "questions": [ { "text": "Which transverse dimensions were measured, in what units, and how do they vary along the fibril?", "kind": "measurement", "id": "resolved-cross-section-q01" }, { "text": "How do resolution, substrate contact and specimen preparation affect the reported dimensions?", "kind": "provenance", "id": "resolved-cross-section-q02" } ] } ] } ] }, { "id": "constituents-and-fibrillar-organisation", "name": "Constituents and fibrillar organisation", "description": "Links material identity to organisation within and between fibrils.", "rationale": "Similar strand-like appearances do not establish equivalent composition, internal architecture or assembly behaviour.", "layers": [ { "id": "constituents-and-internal-order", "name": "Constituents and internal order", "description": "Separates evidence about chemical constituents from evidence about their arrangement.", "findings": [ { "id": "supported-internal-architecture", "name": "Supported internal architecture", "description": "Record constituent identification and observed internal organisation independently, preserving unresolved assignments.", "questions": [ { "text": "Which constituents have been identified in this fibril, and by what evidence?", "kind": "provenance", "id": "supported-internal-architecture-q01" }, { "text": "What measurements support any assigned axial repeat, twist or internal arrangement?", "kind": "measurement", "id": "supported-internal-architecture-q02" } ] } ] }, { "id": "interfibril-and-host-relations", "name": "Interfibril and host relations", "description": "Describes association with other fibrils and placement within a surrounding material.", "findings": [ { "id": "fibrillar-assembly-membership", "name": "Fibrillar assembly membership", "description": "Identify the fibril's parent assembly and distinguish observed contact from demonstrated connection.", "questions": [ { "text": "Is this fibril isolated, bundled, entangled or embedded, and which larger structure contains it?", "kind": "boundary", "id": "fibrillar-assembly-membership-q01" }, { "text": "What evidence distinguishes physical connection between fibrils from overlap in an image?", "kind": "provenance", "id": "fibrillar-assembly-membership-q02" } ] } ] } ] }, { "id": "fibril-condition-and-intervention", "name": "Fibril condition and intervention", "description": "Tracks structural changes and supports actions that depend on preserving or deliberately altering fibrillar form.", "rationale": "An agent needs to know whether observation, isolation or treatment changes the structure it intends to assess.", "layers": [ { "id": "integrity-and-condition-history", "name": "Integrity and condition history", "description": "Relates visible damage and morphological changes to the specimen's exposure and preparation history.", "findings": [ { "id": "interpretable-structural-change", "name": "Interpretable structural change", "description": "Record breaks, fraying and other changes relative to a stated baseline while distinguishing specimen history from inferred causes.", "questions": [ { "text": "Which changes in continuity, transverse size or organisation are observed relative to the baseline?", "kind": "measurement", "id": "interpretable-structural-change-q01" }, { "text": "What preparation, storage and exposure history is known before those changes were observed?", "kind": "provenance", "id": "interpretable-structural-change-q02" } ] } ] }, { "id": "structure-sensitive-actions", "name": "Structure-sensitive actions", "description": "Connects proposed manipulation to the fibrillar features that must be preserved or changed.", "findings": [ { "id": "action-and-structural-acceptance", "name": "Action and structural acceptance", "description": "Specify the intended outcome of isolation, dispersion or treatment and how the fibril's resulting condition will be assessed.", "questions": [ { "text": "Which fibrillar features must the proposed action preserve, and which may it deliberately alter?", "kind": "action", "id": "action-and-structural-acceptance-q01" }, { "text": "What before-and-after observations will establish whether the action achieved an acceptable result?", "kind": "measurement", "id": "action-and-structural-acceptance-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "No sense is recorded; this describes the general materials and biological-structure meaning.", "Fibril denotes morphology and organisation, not one chemical substance, so no universal CAS number, composition or hazard classification applies.", "Dimensions and terminology must be checked for the specific material; the collagen repeat spacing is not a property of fibrils generally." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of fibril this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Collagen fibrils", "Amyloid fibrils", "Cellulose fibrils", "Fibrin fibrils", "Synthetic polymer fibrils" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of fibril this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Cellulose fibrils reinforce paper, composites and films.", "Collagen fibrils provide structural organisation in tissue-engineering scaffolds.", "Polymer fibrils contribute to the structure of some porous membranes.", "Amyloid fibrils serve as research systems for studying protein assembly." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of fibril this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Axial repeat spacing in typical banded collagen fibrils", "typical_range": "Approximately 67; depends on preparation and hydration", "unit": "nm" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of fibril this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Fibril rupture or separation can weaken a fibrous material.", "Aggregation can impair dispersion and processing of fibril-containing materials.", "Some amyloid-forming proteins produce disease-associated assemblies; toxicity depends on the protein and assembly state.", "Airborne fibrillar particles require material-specific assessment of dimensions, persistence and exposure." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of fibril this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "Fibre", "difference": "A fibre is often a larger elongated structure containing fibrils, although the size boundary depends on the discipline." }, { "name": "Microfibril", "difference": "Microfibril names a particular fine structural unit in some material hierarchies; its relationship to fibril is discipline-dependent." }, { "name": "Filament", "difference": "Filament is a broader term for a threadlike structure and does not necessarily imply the molecular assembly or hierarchical role associated with a fibril." }, { "name": "Fibrin", "difference": "Fibrin is a specific protein material that forms clot networks; a fibril is a structural form that many materials can adopt." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of fibril this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry intend fibril as a general material morphology or a narrower biological or material-specific concept?", "Which authoritative definitions govern the boundaries among fibril, microfibril, filament and fibre for the intended coverage?", "Which related registry entries or existing world models already own overlapping structural concepts?", "Which measurement and specimen-preparation conventions are needed to compare fibril dimensions across material classes?", "Which material-specific evidence is required before recommending isolation, dispersion or other structure-altering actions?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 14, "questions": 22 } }