{ "model": { "rank": 5809, "code": "thing-q178355", "model_id": "vr.tr.centriole", "name": "centriole", "purpose": "Enable an AI agent to recognise an individual centriole, assess its assembly, integrity and functional readiness in cellular context, and choose justified observations or experimental interventions.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.LIV", "industry": "", "version": "", "url": "/models/thing/q178355/", "tier": 2, "score": 64, "payload": { "layer": "wikidata", "aliases": [ "Proximal Centriole-Like" ], "aliasCount": 1, "merged": 1, "knownIn": 64, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q178355", "url": "https://www.wikidata.org/wiki/Q178355", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-07T09:24:40Z", "providers": [ "Codex", "Grok" ], "missingProviders": [], "pass": 2, "cost": { "grok": { "usd": 0.00740792, "turns": 1, "seconds": 48.3, "error": null }, "codex": { "seconds": 117.2, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.3\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: 01a07b2d-5489-76f1-97cd-a8c7d04d9c8c\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: centriole\nRegistry id: vr.tr.centriole\nPlane / domain: PHY / PHY.LIV\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\nA Ver" } } }, "metaModel": { "id": "THING-Q178355", "registryId": "vr.tr.centriole", "name": "centriole", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.LIV" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q178355/", "model": { "registry_id": "vr.tr.centriole", "name": "centriole", "purpose": "Enable an AI agent to recognise an individual centriole, assess its assembly, integrity and functional readiness in cellular context, and choose justified observations or experimental interventions.", "definition": "A centriole is a barrel-shaped, nine-fold microtubule organelle that templates cilia and flagella and, in animal cells, pairs to form the centrosome that organizes the mitotic spindle.", "scope_statement": "This model owns the identity, architecture, developmental history, condition and immediate functional interfaces of a centriole under vr.tr.centriole, including continuity of identity when it serves as a basal body.", "in_scope": [ "Individual centriole identification and tracking within a specified organism, cell type and developmental context", "Microtubule barrel architecture, polarity, cartwheel, internal scaffold and appendages", "Procentriole assembly, elongation, maturation and duplication relationships", "Centriole integrity, abnormal architecture and context-dependent competence", "Interfaces with pericentriolar material, partner centrioles and the ciliary base", "Evidence needed to select and interpret centriole-directed observations and perturbations" ], "out_of_scope": [ "Whole-centrosome organisation and pericentriolar material dynamics beyond the centriole interface", "Ciliary axoneme structure, beating and signalling beyond the basal attachment", "Whole-cell cycle regulation, spindle mechanics and chromosome segregation", "Standalone molecular models of tubulin, assembly factors and signalling pathways", "Organism-level disease diagnosis, prognosis and treatment", "Microscope operation and laboratory protocol management" ], "distinguishing_features": [ "Resolve a discrete centriolar microtubule architecture with identifiable axial organisation; a fluorescent punctum alone is insufficient for confirmed identity.", "Separate the individual centriole from the surrounding centrosomal material: record the barrel boundary independently of the broader microtubule-organising region.", "Locate the boundary between the centriole barrel and a continuing ciliary axoneme; record basal-body service as a role of the tracked structure rather than automatically creating another physical object.", "Assess a candidate procentriole through its assembly architecture and developmental relationship, rather than confusing it with a fragment or requiring mature appendages.", "Evaluate symmetry, microtubule organisation and cartwheel features against organism-specific evidence rather than a single universal template; comparative tomography documents architectural diversity. [Primary research](https://pmc.ncbi.nlm.nih.gov/articles/PMC7667884/)" ], "characteristics": [ { "name": "Biological context", "kind": "relation", "unit_or_values": "Organism, cell type, specimen, host cell and developmental stage", "why_it_matters": "Determines which architectural and developmental comparisons are appropriate." }, { "name": "Identity confidence", "kind": "state", "unit_or_values": "Candidate, supported, confirmed, unresolved; evidence and criterion recorded", "why_it_matters": "Prevents marker-positive spots or fragments from becoming unquestioned centriole counts." }, { "name": "Barrel dimensions", "kind": "measurement", "unit_or_values": "Length and external diameter in nm, with uncertainty and preparation method", "why_it_matters": "Supports assessment of elongation, deformation and context-specific size abnormalities." }, { "name": "Microtubule architecture", "kind": "category", "unit_or_values": "Observed radial count; singlet, doublet, triplet, mixed or unresolved organisation by axial region", "why_it_matters": "Distinguishes structural variants from incomplete assembly or damage." }, { "name": "Axial polarity", "kind": "state", "unit_or_values": "Proximal and distal ends assigned, tentative or unresolved", "why_it_matters": "Makes appendage localisation, assembly position and ciliary attachment interpretable." }, { "name": "Assembly and maturation state", "kind": "state", "unit_or_values": "Initiating, elongating, structurally assembled, maturing, mature or unresolved; context-specific criteria", "why_it_matters": "Separates completion of the barrel from acquisition of particular functions." }, { "name": "Cartwheel and scaffold condition", "kind": "state", "unit_or_values": "Present, partial, absent or unresolved for each structure, with axial extent", "why_it_matters": "Supports interpretation of assembly and barrel integrity without treating an undetected structure as absent." }, { "name": "Appendage complement", "kind": "category", "unit_or_values": "Distal and subdistal appendages separately recorded as present, partial, absent, unresolved or not applicable", "why_it_matters": "Provides context-dependent evidence for maturation and attachment capabilities." }, { "name": "Parentage and partner configuration", "kind": "relation", "unit_or_values": "Parent, offspring and neighbouring centriole identities; engagement state; separation in nm and axis angle in degrees", "why_it_matters": "Distinguishes developmental lineage from mere proximity." }, { "name": "Functional interface state", "kind": "state", "unit_or_values": "Pericentriolar-material association, membrane docking and axoneme continuity each observed, absent or unresolved", "why_it_matters": "Separates available structural interfaces from demonstrated functional activity." }, { "name": "Structural integrity", "kind": "state", "unit_or_values": "Intact, incomplete, fractured, distorted, disassembling or unresolved", "why_it_matters": "Guides follow-up while distinguishing biological defects from specimen damage." } ], "affordances": [ "Identify, count and track individual centrioles while retaining uncertainty about unresolved candidates.", "Measure barrel geometry, microtubule organisation and appendage localisation using suitable imaging evidence.", "Reconstruct centriole assembly history and parent-offspring relationships across observations.", "Assess evidence for duplication, centrosomal participation or basal-body readiness in the specified cellular context.", "Select a follow-up observation that distinguishes incomplete maturation, structural damage and detection failure.", "Plan and evaluate context-appropriate experimental perturbations of centriole assembly or interfaces with controls and explicit readouts." ] }, "sources": [ { "id": "src-nih-ncbi-books", "title": "The Cell: A Molecular Approach - Centrioles and Basal Bodies", "url": "https://www.ncbi.nlm.nih.gov/books/NBK9938/", "what_it_supports": "Organelle definition: nine-triplet microtubule barrel; basal-body role in cilia/flagella; centrosome pairing in animal cells.", "url_status": "live" }, { "id": "src-nature-edu", "title": "Centrosomes and centrioles - Nature Education / Scitable", "url": "", "what_it_supports": "Mother/daughter distinction, procentriole assembly, MTOC function, and typical dimensions.", "url_status": "dead" }, { "id": "src-wikidata-q190358", "title": "centriole (Q190358)", "url": "https://www.wikidata.org/wiki/Q190358", "what_it_supports": "Stable identifiers (Wikidata Q190358; GO:0005814; MeSH D002510; FMA 63835) and English preferred name.", "url_status": "live" }, { "id": "src-azimzadeh-bornens-2007", "title": "Structure and duplication of the centrosome - Journal of Cell Science", "url": "https://journals.biologists.com/jcs/article/120/13/2139/29624/Structure-and-duplication-of-the-centrosome", "what_it_supports": "Nine-fold cartwheel architecture, mother distal/subdistal appendages, duplication cycle, and size ranges.", "url_status": "blocked" } ], "structure": { "bundles": [ { "id": "centriole-recognition", "name": "Centriole recognition", "description": "Establish which observed structure is the centriole and maintain its identity across observations.", "rationale": "Misidentifying a spot, fragment or whole centrosome invalidates later counts and state assessments.", "layers": [ { "id": "structural-identification", "name": "Structural identification", "description": "Connect candidate identity to resolved architecture and localisation evidence.", "findings": [ { "id": "centriole-identity-evidence", "name": "Centriole identity evidence", "description": "Record the evidence supporting identification and the alternatives it excludes.", "questions": [ { "text": "Which resolved structural features and contextual markers support calling this object a centriole?", "kind": "definition", "id": "centriole-identity-evidence-q01" }, { "text": "Can the observation distinguish an individual barrel from a centrosome, protein aggregate or centriole fragment?", "kind": "boundary", "id": "centriole-identity-evidence-q02" }, { "text": "Which specimen, images and identification criteria support the assignment?", "kind": "provenance", "id": "centriole-identity-evidence-q03" } ] } ] }, { "id": "context-and-continuity", "name": "Context and continuity", "description": "Anchor the individual structure to its biological setting and observation history.", "findings": [ { "id": "individual-centriole-continuity", "name": "Individual centriole continuity", "description": "Keep host-cell context and tracking evidence separate from assumed identity.", "questions": [ { "text": "Which organism, cell type and developmental or cell-cycle stage contain this centriole?", "kind": "provenance", "id": "individual-centriole-continuity-q01" }, { "text": "What evidence shows that structures seen at successive times are the same centriole?", "kind": "provenance", "id": "individual-centriole-continuity-q02" }, { "text": "If it becomes membrane-docked, how is its identity preserved across a linked basal-body representation?", "kind": "boundary", "id": "individual-centriole-continuity-q03" } ] } ] } ] }, { "id": "barrel-architecture", "name": "Barrel architecture", "description": "Describe the centriole's axial geometry, microtubule wall and supporting structures.", "rationale": "Architectural observations are needed to distinguish a valid variant from incomplete assembly or structural failure.", "layers": [ { "id": "geometry-and-wall", "name": "Geometry and wall", "description": "Resolve dimensions, polarity and microtubule organisation along the barrel.", "findings": [ { "id": "axial-wall-profile", "name": "Axial wall profile", "description": "Record observed geometry by axial region without imposing one reference morphology.", "questions": [ { "text": "What are the barrel length and diameter, and what uncertainty follows from resolution and sample preparation?", "kind": "measurement", "id": "axial-wall-profile-q01" }, { "text": "How do radial count and singlet, doublet or triplet organisation vary along its axis?", "kind": "measurement", "id": "axial-wall-profile-q02" }, { "text": "Which landmarks establish the proximal and distal ends?", "kind": "definition", "id": "axial-wall-profile-q03" } ] } ] }, { "id": "internal-support", "name": "Internal support", "description": "Assess cartwheel, wall connections and internal scaffold where resolvable.", "findings": [ { "id": "support-structure-condition", "name": "Support structure condition", "description": "Record support architecture and its condition; comparative cryotomography provides evidence linking an inner scaffold to centriole cohesion. [Primary research](https://pmc.ncbi.nlm.nih.gov/articles/PMC7021493/)", "questions": [ { "text": "Which cartwheel, inter-microtubule connections and inner-scaffold features are resolved, and over what axial extent?", "kind": "measurement", "id": "support-structure-condition-q01" }, { "text": "Is an apparently missing feature expected for this organism and maturation stage, or could preparation or limited resolution explain it?", "kind": "boundary", "id": "support-structure-condition-q02" }, { "text": "Which matched structural reference supports judging the observed arrangement as intact or abnormal?", "kind": "provenance", "id": "support-structure-condition-q03" } ] } ] } ] }, { "id": "assembly-and-inheritance", "name": "Assembly and inheritance", "description": "Track centriole formation, maturation and relationships through the host cell's history.", "rationale": "Chronological age, parentage and functional maturity must not be inferred from proximity or size alone.", "layers": [ { "id": "formation-and-elongation", "name": "Formation and elongation", "description": "Establish how a candidate centriole arose and how its structure develops.", "findings": [ { "id": "assembly-trajectory", "name": "Assembly trajectory", "description": "Record observed formation route and structural progression.", "questions": [ { "text": "Was formation observed beside a pre-existing centriole, through another assembly route, or only after the structure was already present?", "kind": "provenance", "id": "assembly-trajectory-q01" }, { "text": "Which changes in barrel length and assembly landmarks establish initiation, elongation or arrest?", "kind": "measurement", "id": "assembly-trajectory-q02" }, { "text": "What additional observation would distinguish an assembling procentriole from a damaged pre-existing centriole?", "kind": "action", "id": "assembly-trajectory-q03" } ] } ] }, { "id": "maturation-and-parentage", "name": "Maturation and parentage", "description": "Separate inherited relationships, engagement and acquisition of mature features.", "findings": [ { "id": "maturation-and-duplication-status", "name": "Maturation and duplication status", "description": "Maintain distinct assessments of centriole age, appendage acquisition and duplication competence.", "questions": [ { "text": "Which lineage observations support mother, daughter or unresolved age assignments?", "kind": "provenance", "id": "maturation-and-duplication-status-q01" }, { "text": "What evidence distinguishes parent-procentriole engagement from another close centriole association?", "kind": "boundary", "id": "maturation-and-duplication-status-q02" }, { "text": "Which context-specific observations establish maturity or duplication competence beyond apparent barrel completion?", "kind": "definition", "id": "maturation-and-duplication-status-q03" } ] } ] } ] }, { "id": "functional-interfaces", "name": "Functional interfaces", "description": "Assess the centriole's immediate connections to centrosomal material and the ciliary base.", "rationale": "A structurally recognisable centriole does not by itself demonstrate centrosomal or ciliary function.", "layers": [ { "id": "centrosomal-interface", "name": "Centrosomal interface", "description": "Describe local material association and positioning without attributing the entire centrosome's activity to the barrel.", "findings": [ { "id": "local-centrosomal-participation", "name": "Local centrosomal participation", "description": "Link the individual centriole to measured pericentriolar material and microtubule organisation.", "questions": [ { "text": "What pericentriolar material is associated with this centriole, and how was that association localised?", "kind": "measurement", "id": "local-centrosomal-participation-q01" }, { "text": "Which functional readout distinguishes centriole participation from activity of the surrounding centrosomal material?", "kind": "boundary", "id": "local-centrosomal-participation-q02" }, { "text": "How is the centriole positioned relative to its partner and the relevant cellular microtubule array?", "kind": "measurement", "id": "local-centrosomal-participation-q03" } ] } ] }, { "id": "basal-body-interface", "name": "Basal-body interface", "description": "Assess distal attachment features, docking and continuity with a cilium.", "findings": [ { "id": "ciliary-attachment-status", "name": "Ciliary attachment status", "description": "Distinguish attachment-related architecture, actual membrane docking and observed axoneme connection.", "questions": [ { "text": "Which distal appendage or attachment structures are observed in this biological context?", "kind": "measurement", "id": "ciliary-attachment-status-q01" }, { "text": "Is membrane docking directly demonstrated, and is an axoneme continuous with the distal end?", "kind": "measurement", "id": "ciliary-attachment-status-q02" }, { "text": "Where does this centriole record hand off ownership to the transition-zone and cilium models?", "kind": "boundary", "id": "ciliary-attachment-status-q03" } ] } ] } ] }, { "id": "condition-and-intervention", "name": "Condition and intervention", "description": "Judge centriole abnormalities and choose observations or perturbations that can resolve them.", "rationale": "Useful decisions require separating intrinsic defects, normal context-dependent variation and artefacts.", "layers": [ { "id": "abnormality-assessment", "name": "Abnormality assessment", "description": "Interpret structural condition and membership in an abnormal centriole population.", "findings": [ { "id": "defect-versus-context", "name": "Defect versus context", "description": "Record suspected defects with matched comparisons and alternative explanations.", "questions": [ { "text": "Does this centriole differ from an appropriate reference in length, wall continuity, symmetry or appendage complement?", "kind": "measurement", "id": "defect-versus-context-q01" }, { "text": "If the host cell has an unusual centriole count, how were individual barrels distinguished from fragments and unresolved pairs?", "kind": "measurement", "id": "defect-versus-context-q02" }, { "text": "What evidence separates a biological defect from normal developmental variation or preparation damage?", "kind": "boundary", "id": "defect-versus-context-q03" } ] } ] }, { "id": "experimental-decisions", "name": "Experimental decisions", "description": "Connect unresolved centriole states to discriminating measurements and interpretable interventions.", "findings": [ { "id": "centriole-directed-action", "name": "Centriole-directed action", "description": "Specify an experimental objective, target, controls and readouts without assuming selective effects.", "questions": [ { "text": "Which next observation would best resolve the disputed centriole identity, maturation state or structural defect?", "kind": "action", "id": "centriole-directed-action-q01" }, { "text": "For a proposed perturbation, which centriole feature is targeted and which effects on the host cell, centrosome or cilium could confound interpretation?", "kind": "action", "id": "centriole-directed-action-q02" }, { "text": "Which baseline, control and follow-up measurements would distinguish the intended centriole effect from general toxicity or detection loss?", "kind": "action", "id": "centriole-directed-action-q03" } ] } ] } ] }, { "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-kinds", "name": "Kinds and varieties", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "mother (mature) centriole", "daughter centriole", "procentriole", "primary cilium basal body", "motile cilium/flagellum basal body", "deuterosome-amplified centriole", "atypical/non-canonical centriole" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of centriole this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ { "scheme": "Wikidata", "value_or_pattern": "Q190358", "note": "item 'centriole'" }, { "scheme": "Gene Ontology", "value_or_pattern": "GO:0005814", "note": "cellular component 'centriole'" }, { "scheme": "MeSH", "value_or_pattern": "D002510", "note": "heading 'Centrioles'" }, { "scheme": "FMA", "value_or_pattern": "63835", "note": "Foundational Model of Anatomy 'Centriole'" }, { "scheme": "Uberon / CL", "value_or_pattern": "not a tissue/cell class; use GO:0005814 or FMA:63835", "note": "centriole is an organelle, not an anatomical region" } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of centriole this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Diagnostic and research marker of centrosome number and integrity in cancer cytology (supernumerary centrioles, multipolar mitoses).", "Model for ciliopathies: defects in centriole-to-basal-body conversion or distal appendages abolish primary cilia (e.g. OFD1, CEP164 pathway work).", "Experimental MTOC: isolated centrioles/basal bodies seed microtubule asters in vitro and in Xenopus egg extract.", "Cell-cycle and centriole-duplication screens (PLK4, SAS-6, STIL) in Drosophila, C. elegans, and cultured vertebrate cells.", "Veterinary/clinical andrology: sperm centriole (proximal centriole) inheritance and its role in zygotic centrosome assembly in most animals except rodents." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of centriole this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ { "quantity": "length (mature vertebrate centriole)", "typical_range": "400-500", "unit": "nm" }, { "quantity": "outer diameter", "typical_range": "200-250", "unit": "nm" }, { "quantity": "microtubule organization", "typical_range": "9 triplets (A, B, C tubules) in most animal centrioles; 9 doublets or singlets in some protists and in distal cilium transition", "unit": "fold / protofilament architecture" }, { "quantity": "centrioles per G1 animal cell", "typical_range": "2 (one mother, one daughter)", "unit": "count" }, { "quantity": "centrioles at mitotic centrosomes after duplication", "typical_range": "4 (two pairs)", "unit": "count" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of centriole this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Centriole amplification (PLK4 overexpression, failed licensing) yields extra centrosomes, multipolar spindles, chromosome missegregation, and is common in carcinomas.", "Failed duplication (loss of PLK4, SAS-6, STIL, CEP152) produces acentriolar or monopolar spindles and mitotic catastrophe in cells that require centrosomes.", "Defective mother-centriole appendages or distal-end maturation block primary-cilium assembly (ciliopathies: oral-facial-digital, some Joubert/Meckel spectrum genes that act at the centriole/basal body).", "Sperm centriole defects impair zygotic aster formation and can cause early embryonic arrest (species that inherit a paternal centriole).", "Over-long or structurally aberrant centrioles (CPAP/CENPJ, POC1) disrupt cilium and spindle geometry." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of centriole this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-regional-variation", "name": "Regional variation", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Most animals: sperm contributes a centriole that seeds the zygotic centrosome; mice and other rodents are an exception (early embryos assemble acentriolar centrosomes de novo).", "Land plants, most fungi, and many seed-free plant cells lack centrioles; they organize MTOCs without a 9-fold barrel. Moss/fern sperm and many algae still form centriole/basal-body flagella.", "Protist centrioles/basal bodies vary (e.g. Trichonympha, Chlamydomonas) in length, linkage, and whether triplets persist into the axoneme.", "Clinical literature may say 'centrosome' when only centriole number was scored; pathology reports from different labs are not interchangeable on that point." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of centriole this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ { "name": "centrosome", "difference": "The centrosome is the pericentriolar matrix plus (usually) a centriole pair; a centriole is the nine-fold microtubule barrel. PCM can nucleate microtubules with no centriole (plant cells, early mouse embryo)." }, { "name": "basal body", "difference": "A basal body is a centriole (or centriole-derived barrel) docked at the plasma membrane that templates a cilium/flagellum; the same organelle is called a centriole when it is the centrosomal cylinder in the cytoplasm." }, { "name": "axoneme", "difference": "The axoneme is the 9+2 or 9+0 microtubule core of the cilium/flagellum distal to the transition zone; it is templated by the basal body but is not the centriole." }, { "name": "microtubule-organizing center (MTOC) / spindle pole body", "difference": "MTOC is the functional class; yeast spindle pole bodies are laminar plaques, not nine-fold centrioles. Presence of a SAS-6 cartwheel and nine-fold symmetry distinguishes a centriole." }, { "name": "ciliary rootlet / striated rootlet", "difference": "Rootlets are filamentous, often rootletin-based, attachments at the basal-body proximal end; they lack the 9-triplet microtubule wall." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of centriole this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which organism- and cell-type-specific reference sets are sufficient to define acceptable barrel architecture, dimensions and appendage complements?", "What minimum combination of imaging and molecular evidence should qualify a candidate as a confirmed centriole when ultrastructure is unavailable?", "How should this registry link centriole and basal-body models while preserving the identity of a single physical structure?", "Which validated readouts distinguish structural maturity, duplication competence and ciliary competence in each supported biological context?", "Which observed abnormalities predict functional impairment, and which remain morphological differences without demonstrated consequences?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 17, "questions": 37 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "organism", "method": "Written from the archetype playbook - what this kind of thing needs beyond identity and provenance - and from the structure that recurred across 6,333 models already researched by two engines. Applied to this entry by rule. No source was read for this thing and no claim here is researched. This entry carries no facets of its own, so they were inferred from its domain - a guess about a whole domain applied to one thing.", "facetsInferred": true, "nextPass": "A researcher replaces this draft with a sourced specification. Treat every sentence below as a proposal to argue with.", "purpose": "Give an agent a durable, checkable way to recognise a centriole, record what state it is in, and decide what may be done with it.", "whatItIs": "Enable an AI agent to recognise an individual centriole, assess its assembly, integrity and functional readiness in cellular context, and choose justified observations or experimental interventions.", "characteristics": { "substance": "living", "origin": "natural", "agency": "autonomous", "mobility": "self-moving" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: Proximal Centriole-Like.", "1 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 64 Wikipedia languages, which is a measure of how widely the thing is known, not of how important it is." ], "openQuestionsForResearch": [ "Which of the bundles below does a real task actually need, and which are ceremony?", "What does this thing have that the facets do not capture at all?", "Which neighbouring kind is most often confused with a centriole, and on what evidence are they told apart?" ], "whatItIsMadeOf": "a living thing", "physicalCharacter": [ "Moves under its own power or of its own accord.", "Acts on its own behalf.", "These come from the domain this entry sits in rather than from the entry itself, so treat them as a first guess about the whole domain applied to one thing." ], "whatCanBeDoneWithIt": [ "observe it, measure it, record its state" ], "howItIsRecognised": [ "Recognised by diagnostic characters, and those differ by life stage - the young of many kinds are mistaken for other kinds entirely. A sighting is settled by characters, a photograph and a place, not by a name alone." ], "relatedModels": [ { "relation": "covers", "note": "Finer kinds folded into this entry because telling them apart needs a task that asks for it. Each is a model waiting to be split out when one does.", "targets": [ "Proximal Centriole-Like" ] } ], "standing": "Described in 64 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 1 finer distinctions are held inside this entry as names rather than as separate models.", "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one centriole from another, and a centriole from things that resemble it.", "rationale": "Recognition comes before every other claim. Without stable identity nothing else in the model can be trusted to be about the same thing twice.", "layers": [ { "id": "naming-and-identifiers", "name": "Names and identifiers", "description": "The names this thing goes by and the identifiers that survive translation and time.", "findings": [ { "id": "preferred-name-and-aliases", "name": "Preferred name, aliases and local names", "description": "Which name to use, which names mean the same thing, and which merely sound similar.", "questions": [ { "id": "preferred-name-and-aliases-q01", "text": "What identifies and describes the name of a centriole, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "preferred-name-and-aliases-q02", "text": "Who or what asserted this about the name of a centriole, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "preferred-name-and-aliases-q03", "text": "What may an agent decide or do once the name of a centriole is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "stable-identifiers", "name": "Stable identifiers and external keys", "description": "Identifiers that keep pointing at this kind of thing across systems and languages.", "questions": [ { "id": "stable-identifiers-q01", "text": "What identifies and describes an identifier for a centriole, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stable-identifiers-q02", "text": "Who or what asserted this about an identifier for a centriole, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stable-identifiers-q03", "text": "What may an agent decide or do once an identifier for a centriole is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "classification-and-granularity", "name": "Classification and granularity", "description": "Where a centriole sits among kinds, and how finely a task needs to cut it.", "findings": [ { "id": "kind-and-parents", "name": "Kind, parents and neighbouring kinds", "description": "The classes this thing belongs to and the ones it is next to.", "questions": [ { "id": "kind-and-parents-q01", "text": "What identifies and describes the kind of a centriole, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "kind-and-parents-q02", "text": "Who or what asserted this about the kind of a centriole, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "kind-and-parents-q03", "text": "What may an agent decide or do once the kind of a centriole is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "distinguishing-features", "name": "Distinguishing features", "description": "What separates a centriole from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a centriole, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "distinguishing-features-q02", "text": "Who or what asserted this about what distinguishes a centriole, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "distinguishing-features-q03", "text": "What may an agent decide or do once what distinguishes a centriole is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "form-and-composition", "name": "Form, composition and condition", "description": "What a centriole is made of, what shape and size it takes, and what state it is in.", "rationale": "A physical thing can be measured, and a model that cannot record its measurements cannot support any decision that depends on them.", "layers": [ { "id": "form-and-dimensions", "name": "Form and dimensions", "description": "Shape, size, mass and the ranges these take across examples.", "findings": [ { "id": "measurable-dimensions", "name": "Measurable dimensions and their units", "description": "The quantities worth recording and the units they are recorded in.", "questions": [ { "id": "measurable-dimensions-q01", "text": "What identifies and describes the dimensions of a centriole, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "measurable-dimensions-q02", "text": "Who or what asserted this about the dimensions of a centriole, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "measurable-dimensions-q03", "text": "What may an agent decide or do once the dimensions of a centriole is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "material-and-composition", "name": "Material and composition", "description": "Anatomy, parts and life stage.", "findings": [ { "id": "parts-and-materials", "name": "Parts and life stages", "description": "The parts of a centriole and the stages it passes through.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a centriole, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "parts-and-materials-q02", "text": "Who or what asserted this about the composition of a centriole, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "parts-and-materials-q03", "text": "What may an agent decide or do once the composition of a centriole is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "condition-and-integrity", "name": "Condition and integrity", "description": "Wear, damage, health and the difference between working and broken.", "findings": [ { "id": "condition-assessment", "name": "Condition, damage and health", "description": "How the condition of a centriole is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a centriole, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "condition-assessment-q02", "text": "Who or what asserted this about the condition of a centriole, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "condition-assessment-q03", "text": "What may an agent decide or do once the condition of a centriole is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "place-and-movement", "name": "Place and movement", "description": "Where a centriole is, how it got there and where it may go (self-moving).", "rationale": "A thing that can move needs its position recorded with a time, or every later claim about it is about a place it has left.", "layers": [ { "id": "location-and-placement", "name": "Location and placement", "description": "Position, containment and the reference frame the position is given in.", "findings": [ { "id": "position-and-frame", "name": "Position, container and reference frame", "description": "Where a centriole is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a centriole, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "position-and-frame-q02", "text": "Who or what asserted this about the location of a centriole, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "position-and-frame-q03", "text": "What may an agent decide or do once the location of a centriole is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "movement-and-transfer", "name": "Movement and transfer", "description": "How a centriole moves on its own.", "findings": [ { "id": "movement-events", "name": "Movement events and constraints", "description": "What counts as a movement, what records it and what limits it.", "questions": [ { "id": "movement-events-q01", "text": "What identifies and describes the movement of a centriole, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "movement-events-q02", "text": "Who or what asserted this about the movement of a centriole, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "movement-events-q03", "text": "What may an agent decide or do once the movement of a centriole is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "state-and-lifecycle", "name": "State and lifecycle", "description": "The states a centriole passes through and the events that move it between them.", "rationale": "Most decisions about a thing depend on what state it is in now, which is a claim with a time on it, not a property.", "layers": [ { "id": "lifecycle-stages", "name": "Lifecycle stages", "description": "From coming into existence to ceasing to be one of these.", "findings": [ { "id": "stages-and-transitions", "name": "Stages and transitions", "description": "The stages worth naming and what moves a centriole between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a centriole, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stages-and-transitions-q02", "text": "Who or what asserted this about the lifecycle of a centriole, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stages-and-transitions-q03", "text": "What may an agent decide or do once the lifecycle of a centriole is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "observations-and-status", "name": "Observations and current status", "description": "What is observed about a centriole, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a centriole is recorded so that it can be superseded rather than overwritten.", "questions": [ { "id": "observation-record-q01", "text": "What identifies and describes an observation of a centriole, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "observation-record-q02", "text": "Who or what asserted this about an observation of a centriole, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "observation-record-q03", "text": "What may an agent decide or do once an observation of a centriole is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "taxonomic-placement", "name": "Taxonomic placement and identification", "description": "What centriole is called scientifically, by whose authority, and how a specimen is recognised.", "rationale": "Names change with revisions while the organism does not, so a name without its authority and date cannot be reconciled later.", "layers": [ { "id": "accepted-name", "name": "Accepted name and synonymy", "description": "The current binomial, its author and date, and the names it replaced.", "findings": [ { "id": "name-and-authority", "name": "Accepted name, authority and synonyms", "description": "What to record so a later revision can be applied without losing the old data.", "questions": [ { "id": "name-and-authority-q01", "text": "What is the accepted scientific name of centriole, with its author and year, and which synonyms does it absorb?", "kind": "definition" }, { "id": "name-and-authority-q02", "text": "Which taxonomic authority is being followed, and what would a competing authority say?", "kind": "provenance" } ] } ] }, { "id": "field-identification", "name": "Field identification", "description": "The characters that separate centriole from what it is confused with.", "findings": [ { "id": "diagnostic-characters", "name": "Diagnostic characters and confusable kinds", "description": "Features that settle an identification, and those that only suggest it.", "questions": [ { "id": "diagnostic-characters-q01", "text": "Which observable characters distinguish centriole from its closest look-alikes, and at which life stage are they visible?", "kind": "boundary" }, { "id": "diagnostic-characters-q02", "text": "What evidence is enough to record an identification as confirmed rather than provisional?", "kind": "provenance" } ] } ] } ] }, { "id": "life-cycle-and-condition", "name": "Life stages, condition and behaviour", "description": "What centriole does over its life and how its state is judged.", "rationale": "Stage and condition change what may be done - handled, treated, harvested, left alone - and both are observations with a time.", "layers": [ { "id": "stages-and-reproduction", "name": "Stages and reproduction", "description": "Development from origin to death, including forms that look like different animals.", "findings": [ { "id": "life-stages", "name": "Life stages and their marks", "description": "The stages worth recording and what tells them apart.", "questions": [ { "id": "life-stages-q01", "text": "What stages does centriole pass through, and what observable change marks each transition?", "kind": "definition" }, { "id": "life-stages-q02", "text": "Which stages are so unlike the adult that they are mistaken for another kind?", "kind": "boundary" } ] } ] }, { "id": "health-and-condition", "name": "Health and condition", "description": "How condition is assessed and by whom.", "findings": [ { "id": "condition-assessment", "name": "Condition assessment", "description": "Signs of health, injury and stress, and who is competent to judge them.", "questions": [ { "id": "condition-assessment-q01", "text": "How is the condition of centriole judged, on what scale, and by whom?", "kind": "measurement" }, { "id": "condition-assessment-q02", "text": "What condition obliges an agent to act, and what act is permitted to whom?", "kind": "action" } ] } ] } ] }, { "id": "range-and-status", "name": "Habitat, range and conservation status", "description": "Where centriole lives and how threatened it is.", "rationale": "Range and status govern what is lawful, and both are assessments with an assessor and a year rather than facts of nature.", "layers": [ { "id": "habitat-and-range", "name": "Habitat and range", "description": "Native range, introductions and the habitat it needs.", "findings": [ { "id": "range-record", "name": "Range, introductions and habitat", "description": "What to record about where it is found and how it got there.", "questions": [ { "id": "range-record-q01", "text": "What is the native range of centriole, where has it been introduced, and what habitat does it require?", "kind": "definition" }, { "id": "range-record-q02", "text": "What distinguishes a native record from an introduced or vagrant one?", "kind": "boundary" } ] } ] }, { "id": "protection-status", "name": "Protection and legal status", "description": "Conservation assessments and the rules that follow from them.", "findings": [ { "id": "status-and-rules", "name": "Conservation status and legal consequence", "description": "The assessment, its date, and what it forbids or requires where.", "questions": [ { "id": "status-and-rules-q01", "text": "What conservation status does centriole hold, under which assessment and year?", "kind": "provenance" }, { "id": "status-and-rules-q02", "text": "What does that status forbid or require of an agent, and in which jurisdiction?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a centriole came from and when it held.", "rationale": "A claim without a source and a time cannot be superseded, only overwritten, and an agent that overwrites loses the ability to explain itself.", "layers": [ { "id": "source-and-authority", "name": "Source and authority", "description": "Who said it, on what evidence, and how strongly.", "findings": [ { "id": "claim-provenance", "name": "Claim provenance and confidence", "description": "The authority behind each claim about a centriole and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a centriole, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "claim-provenance-q02", "text": "Who or what asserted this about a claim about a centriole, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "claim-provenance-q03", "text": "What may an agent decide or do once a claim about a centriole is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "time-and-versions", "name": "Time, versions and supersession", "description": "When a claim was true, when it was learnt, and what replaced it.", "findings": [ { "id": "validity-and-supersession", "name": "Validity period and supersession", "description": "How an old claim about a centriole is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a centriole, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "validity-and-supersession-q02", "text": "Who or what asserted this about the validity of a claim about a centriole, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "validity-and-supersession-q03", "text": "What may an agent decide or do once the validity of a claim about a centriole is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 8, "layers": 17, "findings": 19, "questions": 51 } } } }