{ "model": { "rank": 6273, "code": "thing-q189998", "model_id": "vr.tr.flagellum", "name": "flagellum", "purpose": "Enable an agent to recognise a flagellum, assess its attachment, integrity and activity, and judge which observations or interventions are appropriate in its cellular context.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.LIV", "industry": "", "version": "", "url": "/models/thing/q189998/", "tier": 2, "score": 61, "payload": { "layer": "wikidata", "aliases": [ "bacterial-type flagellum", "eukaryotic flagellum", "archaeal-type flagellum", "periplasmic flagellum" ], "aliasCount": 4, "merged": 4, "knownIn": 61, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": "vr.tr.flagellum", "source": { "dataset": "wikidata", "item": "Q189998", "url": "https://www.wikidata.org/wiki/Q189998", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-07T13:35:41Z", "providers": [ "Codex", "Grok" ], "missingProviders": [], "pass": 2, "cost": { "grok": { "usd": 0.01307062, "turns": 1, "seconds": 208.1, "error": null }, "codex": { "seconds": 77.5, "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: 01a07c0f-ee9f-72b3-8c82-02a3e3f46c87\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: flagellum\nRegistry id: vr.tr.flagellum\nPlane / domain: PHY / PHY.LIV\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\nA Ver" } } }, "metaModel": { "id": "THING-Q189998", "registryId": "vr.tr.flagellum", "name": "flagellum", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.LIV" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q189998/", "model": { "registry_id": "vr.tr.flagellum", "name": "flagellum", "purpose": "Enable an agent to recognise a flagellum, assess its attachment, integrity and activity, and judge which observations or interventions are appropriate in its cellular context.", "definition": "A flagellum is a long, thin motility organelle that propels a cell either by rotation of an extracellular protein filament (Bacteria and Archaea) or by ATP-driven bending of a membrane-bounded 9+2 microtubule axoneme (Eukarya); the three domain-level machines are functionally analogous but not homologous.", "scope_statement": "This model owns an individual cell-associated appendage identified as a flagellum, including its lineage-dependent architecture, attachment apparatus, motion, functional state and response to intervention; it records identification uncertainty where terminology or evidence is insufficient.", "in_scope": [ "Evidence identifying the appendage as a flagellum and distinguishing its architectural type", "Flagellar structure, dimensions, continuity and attachment to the cell", "Motion generation, observed movement and coupling to cellular behaviour", "Assembly, maintenance, damage, detachment and recovery", "Conditions and interventions affecting flagellar observation or function" ], "out_of_scope": [ "Whole-cell identity, viability and metabolism except as context for flagellar state", "Complete models of cilia, pili, fimbriae and other neighbouring appendages", "Whole-organism locomotion, development or disease", "Environmental fluid dynamics beyond local conditions affecting the appendage", "Complete gene-regulatory and protein-interaction networks", "Laboratory instrument operation and general experimental protocols" ], "distinguishing_features": [ "Establish that the observed structure is a discrete appendage with evidence of cellular attachment or origin, rather than debris, a secreted fibre or a cell-body projection.", "Test whether structural or molecular evidence supports a bacterial flagellum, a eukaryotic flagellum, or an archaeal appendage requiring an explicit flagellum-versus-archaellum naming decision.", "Where motion is observable, distinguish rotation of a filament from bending waves along an appendage; do not infer architectural type from the word 'flagellum' alone.", "Distinguish bacterial flagella from pili or fimbriae using attachment machinery, filament composition or validated markers; length and apparent motility alone are insufficient identification criteria.", "For eukaryotic structures, record the organism-specific basis for calling an appendage a flagellum rather than a cilium; do not assume a universal distinction based on length or number." ], "characteristics": [ { "name": "Architectural identity", "kind": "category", "unit_or_values": "bacterial flagellum | eukaryotic flagellum | archaeal naming boundary unresolved | other unresolved identification", "why_it_matters": "Determines which structural expectations, activity measurements and interventions are applicable." }, { "name": "Host and attachment site", "kind": "relation", "unit_or_values": "host cell reference; attachment apparatus reference; position in a stated cellular coordinate frame", "why_it_matters": "Connects the appendage to its cellular context and distinguishes its movement from cell-body movement." }, { "name": "Length and diameter", "kind": "measurement", "unit_or_values": "µm or nm, with measurement method, uncertainty and contour-versus-projected length specified", "why_it_matters": "Supports identification and detection of growth, shortening or structural damage." }, { "name": "Structural integrity", "kind": "state", "unit_or_values": "apparently intact | incomplete | deformed | broken | detached | unresolved", "why_it_matters": "Separates visible structural defects from functional inactivity without a visible defect." }, { "name": "Motion mode", "kind": "category", "unit_or_values": "filament rotation | bending or beating | mixed apparent motion | no motion detected | unresolved", "why_it_matters": "Selects appropriate activity measurements and prevents conflating distinct mechanisms." }, { "name": "Motion rate", "kind": "measurement", "unit_or_values": "rotation frequency or beat frequency in Hz, with mode, observation interval and conditions", "why_it_matters": "Quantifies activity while preserving the distinction between rotation and beating." }, { "name": "Shape during movement", "kind": "measurement", "unit_or_values": "time-resolved centreline; curvature in µm⁻¹; applicable waveform amplitude and wavelength in µm", "why_it_matters": "Reveals changes in movement that a single frequency value would miss." }, { "name": "Relationship to other flagella", "kind": "relation", "unit_or_values": "other appendage references; observed physical grouping or movement coordination; unresolved", "why_it_matters": "Allows an individual flagellum's behaviour to be interpreted within a multi-appendage system." }, { "name": "Functional assessment", "kind": "state", "unit_or_values": "activity demonstrated | activity reduced against stated reference | no activity detected | not assessed", "why_it_matters": "Prevents absence of observed motion from being treated automatically as irreversible failure." } ], "affordances": [ "Identify and localise an appendage using imaging and type-appropriate structural or molecular evidence.", "Measure its dimensions, attachment continuity and movement under recorded conditions.", "Track assembly, shortening, damage, detachment or recovery across observations.", "Relate appendage movement to cell displacement or local fluid movement without assuming that correlation proves causation.", "Assess a proposed mechanical, chemical or genetic perturbation against architectural identity, host context and available evidence.", "Compare pre-intervention and post-intervention states with controls that distinguish flagellar effects from whole-cell effects." ] }, "sources": [ { "id": "berg-2003-arb", "title": "The Rotary Motor of Bacterial Flagella (Annual Reviews, Annual Review of Biochemistry, 2003)", "url": "https://doi.org/10.1146/annurev.biochem.72.121801.161737", "what_it_supports": "Bacterial flagellum structure, rotary motor mechanism, filament dimensions, rotation rates, and torque.", "url_status": "blocked" }, { "id": "jarrell-albers-2012-tim", "title": "The archaellum: an old motility structure with a new name (Elsevier, Trends in Microbiology, 2012)", "url": "https://doi.org/10.1016/j.tim.2012.04.007", "what_it_supports": "That archaeal flagella are not homologous to bacterial flagella, the name archaellum, and the type-IV-pilus relationship.", "url_status": "live" }, { "id": "alberts-mboc", "title": "Molecular Biology of the Cell, 6th edition (Garland Science, 2014)", "url": "", "what_it_supports": "Eukaryotic axoneme (9+2) architecture, dynein-driven bending, and the conventional cilium/flagellum identity." }, { "id": "grimont-weill-2007", "title": "Antigenic Formulae of the Salmonella Serovars, 9th edition (WHO Collaborating Centre for Reference and Research on Salmonella, Institut Pasteur, 2007)", "url": "", "what_it_supports": "Flagellar (H) antigens as a formal identifier in Salmonella serotyping (Kauffmann-White-Le Minor)." }, { "id": "who-semen-2021", "title": "WHO laboratory manual for the examination and processing of human semen, 6th edition (World Health Organization, 2021)", "url": "", "what_it_supports": "Clinical measurement of sperm motility as a real-world assay of eukaryotic flagellar function." } ], "structure": { "bundles": [ { "id": "flagellar-identity", "name": "Flagellar identity", "description": "Evidence that the structure belongs to the registered thing and identification of its architectural type.", "rationale": "The name flagellum spans contexts in which structural expectations and movement mechanisms cannot be treated as interchangeable.", "layers": [ { "id": "appendage-identification", "name": "Appendage identification", "description": "Establishes the observed object's identity and cellular origin.", "findings": [ { "id": "identification-evidence", "name": "Identification evidence", "description": "Records observations supporting flagellar identity and plausible competing identifications.", "questions": [ { "text": "What imaging, structural or molecular evidence identifies this appendage as a flagellum?", "kind": "definition", "id": "identification-evidence-q01" }, { "text": "What evidence excludes a pilus, fimbria, cell-body projection or detached extracellular fibre?", "kind": "boundary", "id": "identification-evidence-q02" } ] } ] }, { "id": "architecture-and-naming", "name": "Architecture and naming", "description": "Resolves which biological meaning of flagellum applies.", "findings": [ { "id": "architectural-assignment", "name": "Architectural assignment", "description": "Records the supported architectural class and any unresolved terminology boundary.", "questions": [ { "text": "Which structural features or validated markers support the proposed architectural type?", "kind": "definition", "id": "architectural-assignment-q01" }, { "text": "Does the source terminology require clarification against cilium or archaellum, and what convention is being followed?", "kind": "boundary", "id": "architectural-assignment-q02" } ] } ] } ] }, { "id": "structure-and-cellular-attachment", "name": "Structure and cellular attachment", "description": "The appendage's geometry, structural continuity and connection to its host cell.", "rationale": "Flagellar activity depends on a physical structure whose attachment and damage must be distinguishable from movement alone.", "layers": [ { "id": "filament-geometry", "name": "Filament geometry", "description": "Describes the observable appendage and type-appropriate internal organisation.", "findings": [ { "id": "dimensions-and-organisation", "name": "Dimensions and organisation", "description": "Records measured geometry and which structural components are resolved.", "questions": [ { "text": "What are the contour length, diameter and resting shape, with measurement uncertainty?", "kind": "measurement", "id": "dimensions-and-organisation-q01" }, { "text": "Which type-appropriate components, such as a filament, hook, membrane or axoneme, are directly resolved rather than inferred?", "kind": "provenance", "id": "dimensions-and-organisation-q02" } ] } ] }, { "id": "attachment-and-neighbours", "name": "Attachment and neighbours", "description": "Locates the flagellum on its cell and records interactions with other appendages.", "findings": [ { "id": "attachment-continuity", "name": "Attachment continuity", "description": "Records the connection to the cell and the individual appendage's place within any flagellar arrangement.", "questions": [ { "text": "Where does the flagellum attach, and what evidence shows continuity with its attachment apparatus?", "kind": "measurement", "id": "attachment-continuity-q01" }, { "text": "Can this flagellum be distinguished from neighbouring flagella throughout the observation, including when they form a moving group?", "kind": "boundary", "id": "attachment-continuity-q02" } ] } ] } ] }, { "id": "movement-and-functional-coupling", "name": "Movement and functional coupling", "description": "Observed flagellar movement and its relationship to cellular or local fluid behaviour.", "rationale": "A flagellum's presence, motion and functional contribution are separate assessments requiring different evidence.", "layers": [ { "id": "motion-pattern", "name": "Motion pattern", "description": "Characterises rotation, bending or apparent inactivity in an appropriate reference frame.", "findings": [ { "id": "resolved-flagellar-motion", "name": "Resolved flagellar motion", "description": "Records the movement mode, rate and shape changes supported by the observation.", "questions": [ { "text": "Does the appendage rotate, propagate bending waves or show another apparent pattern after accounting for cell-body movement?", "kind": "measurement", "id": "resolved-flagellar-motion-q01" }, { "text": "What rates, direction changes and waveform features are resolved at the recording's spatial and temporal resolution?", "kind": "measurement", "id": "resolved-flagellar-motion-q02" } ] } ] }, { "id": "functional-contribution", "name": "Functional contribution", "description": "Connects appendage activity to an observed outcome and separates evidence from assumed function.", "findings": [ { "id": "activity-outcome-coupling", "name": "Activity-outcome coupling", "description": "Records evidence relating flagellar activity to displacement, fluid movement or another demonstrated role.", "questions": [ { "text": "What cell displacement, local fluid movement or other outcome accompanies this flagellum's activity?", "kind": "measurement", "id": "activity-outcome-coupling-q01" }, { "text": "What comparison or intervention supports attributing that outcome to this flagellum rather than other appendages or external forces?", "kind": "provenance", "id": "activity-outcome-coupling-q02" } ] } ] } ] }, { "id": "state-transitions-and-intervention", "name": "State transitions and intervention", "description": "Changes in flagellar structure or activity and the evidence needed to choose and interpret interventions.", "rationale": "An agent must distinguish assembly, reversible inactivity and damage before deciding how to observe or alter the appendage.", "layers": [ { "id": "assembly-damage-and-recovery", "name": "Assembly, damage and recovery", "description": "Tracks structural and functional changes through time.", "findings": [ { "id": "flagellar-state-trajectory", "name": "Flagellar state trajectory", "description": "Records whether a flagellum is forming, maintained, changing, damaged or recovering.", "questions": [ { "text": "What observations distinguish assembly or normal remodelling from breakage, loss or preparation artefacts?", "kind": "boundary", "id": "flagellar-state-trajectory-q01" }, { "text": "How do length, attachment integrity and movement change over time, and is recovery observed?", "kind": "measurement", "id": "flagellar-state-trajectory-q02" } ] } ] }, { "id": "perturbation-and-interpretation", "name": "Perturbation and interpretation", "description": "Assesses proposed actions and the conditions needed to interpret their effects.", "findings": [ { "id": "type-appropriate-intervention", "name": "Type-appropriate intervention", "description": "Records an intervention's intended flagellar target, evidential basis and distinguishable outcomes.", "questions": [ { "text": "Which observation or perturbation is supported for this architectural type, host cell and intended outcome?", "kind": "action", "id": "type-appropriate-intervention-q01" }, { "text": "Which controls and local conditions are needed to distinguish a flagellar effect from altered host viability, energy availability, fluid resistance or surface attachment?", "kind": "action", "id": "type-appropriate-intervention-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-kinds", "name": "Kinds and varieties", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Bacterial flagellum (helical flagellin filament driven by a rotary basal motor, typically assembled by distal-tip growth)", "Sheathed bacterial flagellum (filament wrapped by an outer-membrane extension; typical of Vibrio and Helicobacter)", "Periplasmic flagellum / endoflagellum of spirochetes (filaments in the periplasm that produce corkscrew motility of the cell body)", "Archaellum (archaeal rotary filament homologous to type IV pili and assembled from the base, not to the bacterial flagellum)", "Eukaryotic motile flagellum (9+2 axoneme with dynein arms; the same organelle class as a motile cilium)", "Mammalian sperm flagellum (9+2 axoneme plus outer dense fibers and, in the principal piece, a fibrous sheath)", "Polar versus lateral bacterial flagellar systems (distinct motors/filaments used for swimming versus surface swarming in some Vibrionaceae)", "Protist flagella with extra-axonemal specializations (e.g. the paraflagellar rod of trypanosomes)" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of flagellum 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": "MeSH", "value_or_pattern": "D005407", "note": "Heading Flagella; covers prokaryotic and eukaryotic cellular flagella, not the insect antennal homonym." }, { "scheme": "Gene Ontology", "value_or_pattern": "GO:0009288", "note": "Cellular-component term bacterial-type flagellum." }, { "scheme": "Gene Ontology", "value_or_pattern": "GO:0005929", "note": "Cellular-component term cilium; eukaryotic flagella are annotated in this hierarchy rather than as a separate GO organelle." }, { "scheme": "UniProt keyword", "value_or_pattern": "KW-0282", "note": "Keyword Flagellum on proteins that are structural or functional components of a flagellum." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of flagellum this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-standards-and-regulation", "name": "Standards and regulation", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Kauffmann-White-Le Minor antigenic formulae, including H (flagellar) antigens - WHO Collaborating Centre for Reference and Research on Salmonella, Institut Pasteur", "ISO/TR 6579-3:2014 Microbiology of the food chain - Horizontal method for the detection, enumeration and serotyping of Salmonella - Part 3: Guidelines for serotyping of Salmonella spp. - International Organization for Standardization", "WHO laboratory manual for the examination and processing of human semen, 6th edition (2021) - World Health Organization (sperm motility as a clinical readout of flagellar function)", "European Respiratory Society guidelines for the diagnosis of primary ciliary dyskinesia - European Respiratory Society (axonemal/flagellar ultrastructure and beat in PCD)" ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of flagellum 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": [ "Soft-agar swarm/swim plates and hanging-drop microscopy to score bacterial motility in clinical and food microbiology", "Salmonella serotyping by H (flagellar) antigens in public-health reference laboratories", "Sperm-motility assessment in fertility clinics as a direct readout of flagellar beating", "Pathogenesis and innate immunity: flagellin is a TLR5 ligand, and flagella aid colonization or invasion in Salmonella, Pseudomonas, Helicobacter and others", "Structural biology and nanomotor engineering of the bacterial rotary motor", "Diagnostic electron microscopy of sperm tails and respiratory cilia for ultrastructural flagellar/ciliary defects" ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of flagellum 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": "Bacterial filament length", "typical_range": "5-20", "unit": "µm" }, { "quantity": "Bacterial filament diameter", "typical_range": "~20", "unit": "nm" }, { "quantity": "Eukaryotic flagellum diameter", "typical_range": "0.20-0.30", "unit": "µm" }, { "quantity": "Human sperm flagellum length", "typical_range": "45-55", "unit": "µm" }, { "quantity": "Bacterial motor rotation rate", "typical_range": "100-300 (some species >1000)", "unit": "Hz" }, { "quantity": "Escherichia coli free-swimming speed", "typical_range": "20-40", "unit": "µm/s" }, { "quantity": "Human sperm beat frequency", "typical_range": "10-25", "unit": "Hz" }, { "quantity": "Bacterial flagellar-motor torque", "typical_range": "1000-4000", "unit": "pN·nm" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of flagellum 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": [ "Loss-of-function mutations in motor, hook or filament genes abolish swimming and can reduce colonization or virulence where motility is required", "Phase variation of flagellin (e.g. Salmonella FliC/FljB) switches H antigen and evades antibody", "Shed flagellin activates TLR5 and can drive mucosal inflammation", "Primary ciliary dyskinesia (including Kartagener syndrome): defective dynein arms yield immotile axonemes, with bronchiectasis, laterality defects and male infertility", "Asthenozoospermia from ultrastructural defects of the sperm flagellum", "Mechanical shearing in high-shear culture strips bacterial filaments and yields false motility-negative phenotypes", "Motility-agar false negatives from wrong agar concentration, temperature or phase-off Salmonella" ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of flagellum 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": [ "Cell-biology usage treats the eukaryotic cilium and flagellum as one organelle; zoological usage still splits them by number and relative length", "Archaellum (name proposed 2012) is standard in archaeal microbiology, while many general textbooks still say archaeal flagellum", "CDC and WHO/Pasteur Salmonella serovar aliases have differed historically for some H-antigen formulae", "Clinic language for the sperm organelle varies (flagellum, sperm tail, flagellum spermatozoi) by medical tradition and language", "East Asian technical literature uses 鞭毛 for the cellular organelle; the insect antennal sense is usually separated as flagellomeres/鞭节" ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of flagellum 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": "Cilium (motile)", "difference": "Same 9+2 axoneme as a eukaryotic flagellum; no ultrastructural test separates them - the split is conventional (few and long versus many and short)." }, { "name": "Primary (non-motile) cilium", "difference": "Usually 9+0, lacks motile dynein arms, and functions in sensing rather than propulsion." }, { "name": "Type IV pilus", "difference": "Thinner filament used for twitching, attachment or DNA uptake by extension/retraction, not rotary helical propulsion; related to the archaellum, not to the bacterial flagellum." }, { "name": "Type III secretion injectisome", "difference": "Homologous to the bacterial flagellar basal body but translocates effectors and has no motility filament." }, { "name": "Fimbria / common pilus", "difference": "Short, numerous adhesin filaments with no rotary motor and no flagellin." }, { "name": "Stereocilium", "difference": "Actin-core projection on sensory hair cells, not a tubulin axoneme." }, { "name": "Axoneme", "difference": "The 9+2 microtubule core of a eukaryotic flagellum, not the whole organelle (membrane plus accessory structures)." }, { "name": "Insect antennal flagellum", "difference": "Homonym: the distal cuticular region of an arthropod antenna made of flagellomeres, not a cellular motility filament." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of flagellum this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does this registry entry include archaeal archaella under historical flagellum terminology, or should it relate to a separate registered concept?", "How should this registry divide or connect eukaryotic flagella and cilia when terminology does not establish a universal structural boundary?", "Which architectural components and identification markers should be required for each supported lineage, and which remain optional or unresolved?", "What reference conditions and measurement limits are needed to distinguish reduced activity, reversible inactivity and structural failure in each supported context?", "Which non-propulsive roles and intervention responses have sufficient organism-specific evidence to include in a researched publication?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 16, "questions": 24 } }, "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 flagellum, record what state it is in, and decide what may be done with it.", "whatItIs": "Enable an agent to recognise a flagellum, assess its attachment, integrity and activity, and judge which observations or interventions are appropriate in its cellular context.", "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: bacterial-type flagellum, eukaryotic flagellum, archaeal-type flagellum, periplasmic flagellum.", "4 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 61 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 flagellum, 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": [ "bacterial-type flagellum", "eukaryotic flagellum", "archaeal-type flagellum", "periplasmic flagellum" ] } ], "standing": "Described in 61 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 4 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 flagellum from another, and a flagellum 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 flagellum, 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 flagellum, 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 flagellum 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 flagellum, 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 flagellum, 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 flagellum 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 flagellum 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 flagellum, 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 flagellum, 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 flagellum 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 flagellum from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a flagellum, 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 flagellum, 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 flagellum 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 flagellum 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 flagellum, 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 flagellum, 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 flagellum 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 flagellum and the stages it passes through.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a flagellum, 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 flagellum, 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 flagellum 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 flagellum is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a flagellum, 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 flagellum, 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 flagellum 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 flagellum 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 flagellum is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a flagellum, 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 flagellum, 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 flagellum 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 flagellum 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 flagellum, 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 flagellum, 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 flagellum 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 flagellum 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 flagellum between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a flagellum, 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 flagellum, 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 flagellum 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 flagellum, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a flagellum 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 flagellum, 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 flagellum, 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 flagellum 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 flagellum 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 flagellum, 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 flagellum 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 flagellum 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 flagellum 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 flagellum 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 flagellum 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 flagellum 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 flagellum, 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 flagellum 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 flagellum 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 flagellum and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a flagellum, 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 flagellum, 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 flagellum 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 flagellum is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a flagellum, 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 flagellum, 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 flagellum 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 } } } }