{ "model": { "rank": 4710, "code": "thing-q30869", "model_id": "vr.tr.nucleolus", "name": "nucleolus", "purpose": "Enable an AI agent to recognise a nucleolus, assess its ribosome-biogenesis activity and structural state, and select context-appropriate observations or perturbations.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.LIV", "industry": "", "version": "", "url": "/models/thing/q30869/", "tier": 2, "score": 73, "payload": { "layer": "wikidata", "aliases": [], "aliasCount": 0, "merged": 0, "knownIn": 73, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q30869", "url": "https://www.wikidata.org/wiki/Q30869", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-09T20:50:04Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 18.3, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a087ee-6189-7d50-9198-22818040e1e1\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: nucleolus\nSense to describe: (none recorded)\nDomain code: PHY.LIV\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 005: 1001 regis", "usd": 0, "recall": true }, "codex": { "seconds": 63.4, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a087ee-6195-76e2-978b-e0ab6e37af2d\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: nucleolus\nRegistry id: vr.tr.nucleolus\nPlane / domain: PHY / PHY.LIV\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nCont" } } }, "metaModel": { "id": "THING-Q30869", "registryId": "vr.tr.nucleolus", "name": "nucleolus", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.LIV" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q30869/", "model": { "registry_id": "vr.tr.nucleolus", "name": "nucleolus", "purpose": "Enable an AI agent to recognise a nucleolus, assess its ribosome-biogenesis activity and structural state, and select context-appropriate observations or perturbations.", "definition": "The nucleolus is a non-membrane-bound compartment of the eukaryotic nucleus that forms around active ribosomal DNA regions and is the principal site of ribosomal RNA transcription, processing, and assembly with proteins into precursors of ribosomal subunits.", "scope_statement": "This model owns the nucleolus as a dynamic, non-membrane-bound compartment within a eukaryotic nucleus, including its organisation around ribosomal DNA, ribosomal RNA production and processing, ribosomal subunit assembly, and responses to cellular conditions.", "in_scope": [ "Identification and boundaries of individual nucleoli within a specified cell nucleus", "Association with nucleolar organiser regions and transcriptionally active ribosomal DNA", "Internal organisation and localisation of nucleolar RNA and proteins", "Ribosomal RNA transcription, processing and early ribosomal subunit assembly", "Nucleolar assembly, disassembly and responses to cellular stress" ], "out_of_scope": [ "Organism taxonomy, population biology and conservation assessment", "The entire nucleus, nuclear envelope and general chromatin organisation", "Complete ribosome structure and cytoplasmic protein translation", "Other nuclear bodies, including Cajal bodies and nuclear speckles", "Whole-cell disease classification and clinical treatment decisions" ], "distinguishing_features": [ "It is an intranuclear compartment without its own enclosing lipid membrane; it is neither the nucleus itself nor a membrane-bound organelle.", "Identification combines spatial organisation with evidence of ribosomal RNA production or processing; a dense nuclear spot alone is insufficient.", "It organises in relation to ribosomal DNA loci, whereas nuclear speckles and Cajal bodies have different defining molecular compositions and activities.", "It contains ribosome-biogenesis intermediates and associated machinery rather than representing an individual mature ribosome.", "It is a cellular compartment, not an organism or taxonomic unit; organism-level identifiers describe its host context." ], "characteristics": [ { "name": "Host cell and nuclear context", "kind": "relation", "unit_or_values": "Host organism, cell type, nucleus identifier and experimental condition", "why_it_matters": "Expected architecture and activity depend on the biological context." }, { "name": "Nucleolar count", "kind": "measurement", "unit_or_values": "Nucleoli per nucleus, with segmentation criteria", "why_it_matters": "Count supports comparisons only when cell state and rules for separating adjacent nucleoli are recorded." }, { "name": "Nucleolar size", "kind": "measurement", "unit_or_values": "Area in µm² or volume in µm³, with imaging and segmentation method", "why_it_matters": "Size describes morphology but requires independent evidence before being interpreted as biosynthetic activity." }, { "name": "Internal compartment organisation", "kind": "category", "unit_or_values": "Observed fibrillar and granular regions; unresolved, atypical or context-specific organisation", "why_it_matters": "Internal organisation helps locate functional stages without assuming all organisms display the same architecture." }, { "name": "Ribosomal DNA association", "kind": "relation", "unit_or_values": "Associated ribosomal DNA loci or nucleolar organiser regions, with evidence and activity status", "why_it_matters": "Distinguishes genomic association from demonstrated transcriptional activity." }, { "name": "Ribosomal RNA synthesis", "kind": "measurement", "unit_or_values": "Assay-specific nascent RNA signal or calibrated synthesis rate, with time window and normalisation", "why_it_matters": "Measures production more directly than nucleolar size or marker abundance." }, { "name": "Pre-ribosomal RNA processing state", "kind": "state", "unit_or_values": "Expected precursor profile, intermediate accumulation, delayed processing or unresolved", "why_it_matters": "Separates successful RNA maturation from precursor accumulation." }, { "name": "Ribosomal assembly progression", "kind": "state", "unit_or_values": "Supported progression, suspected bottleneck, demonstrated arrest or unresolved", "why_it_matters": "RNA synthesis alone does not demonstrate productive ribosomal subunit assembly." }, { "name": "Cell-cycle-associated organisation", "kind": "state", "unit_or_values": "Assembling, maintained, reorganising or disassembling, with host cell-cycle stage", "why_it_matters": "Distinguishes expected cell-cycle changes from abnormal disruption." }, { "name": "Molecular exchange dynamics", "kind": "measurement", "unit_or_values": "Recovery half-time in seconds and mobile fraction for a specified probe and assay", "why_it_matters": "Characterises exchange while avoiding unsupported claims about the material state of the entire nucleolus." } ], "affordances": [ "Identify and segment nucleoli using validated imaging criteria and context-appropriate molecular markers.", "Map ribosomal DNA, nascent ribosomal RNA and processing factors relative to nucleolar regions.", "Compare morphology and ribosome-biogenesis measurements across matched cells or experimental conditions.", "Track assembly, disassembly, fusion and recovery through time-resolved observations.", "Design controlled perturbations of nucleolar processes and distinguish direct effects from broader cellular responses." ] }, "sources": [], "structure": { "bundles": [ { "id": "nucleolar-identity-and-boundaries", "name": "Nucleolar identity and boundaries", "description": "Establish what counts as a nucleolus in the observed biological and imaging context.", "rationale": "Nuclear density, marker enrichment and proximity to another nuclear body can otherwise be mistaken for nucleolar identity.", "layers": [ { "id": "host-and-compartment-identity", "name": "Host and compartment identity", "description": "Anchor each nucleolus to its host nucleus and establish evidence for its identity.", "findings": [ { "id": "supported-nucleolar-identification", "name": "Supported nucleolar identification", "description": "Record the combination of location, morphology and molecular evidence used to identify the compartment.", "questions": [ { "text": "Which host organism, cell type and nucleus contain the candidate nucleolus?", "kind": "provenance", "id": "supported-nucleolar-identification-q01" }, { "text": "Which observations distinguish it from a Cajal body, nuclear speckle, chromatin focus or imaging artefact?", "kind": "boundary", "id": "supported-nucleolar-identification-q02" } ] } ] }, { "id": "spatial-extent-and-count", "name": "Spatial extent and count", "description": "Define reproducible boundaries for counting and measuring nucleoli.", "findings": [ { "id": "nucleolar-segmentation", "name": "Nucleolar segmentation", "description": "Make explicit how nucleolar edges, touching compartments and internal cavities are handled.", "questions": [ { "text": "Which signal and segmentation rule define the nucleolar boundary, including internal cavities?", "kind": "definition", "id": "nucleolar-segmentation-q01" }, { "text": "What are the nucleolar count and area or volume per nucleus, and how are touching nucleoli distinguished?", "kind": "measurement", "id": "nucleolar-segmentation-q02" } ] } ] } ] }, { "id": "ribosomal-dna-and-rna-production", "name": "Ribosomal DNA and RNA production", "description": "Connect nucleolar organisation with ribosomal DNA and newly synthesised ribosomal RNA.", "rationale": "A nucleolus must be evaluated through its relationship to ribosomal gene activity, not through appearance alone.", "layers": [ { "id": "organiser-region-association", "name": "Organiser region association", "description": "Identify the genomic loci associated with the nucleolus.", "findings": [ { "id": "associated-ribosomal-dna-loci", "name": "Associated ribosomal DNA loci", "description": "Separate physical association with ribosomal DNA from evidence that particular loci are active.", "questions": [ { "text": "Which ribosomal DNA loci or nucleolar organiser regions are associated with this nucleolus?", "kind": "provenance", "id": "associated-ribosomal-dna-loci-q01" }, { "text": "What evidence distinguishes active loci from inactive repeats or nearby chromatin?", "kind": "measurement", "id": "associated-ribosomal-dna-loci-q02" } ] } ] }, { "id": "nascent-ribosomal-rna", "name": "Nascent ribosomal RNA", "description": "Assess RNA production using assays whose specificity and timing are known.", "findings": [ { "id": "ribosomal-transcription-readout", "name": "Ribosomal transcription readout", "description": "Distinguish newly produced ribosomal RNA from accumulated RNA and indirect morphological proxies.", "questions": [ { "text": "Which assay measures nascent ribosomal RNA, over what interval and with what normalisation?", "kind": "measurement", "id": "ribosomal-transcription-readout-q01" }, { "text": "How does the assay distinguish ribosomal transcription from other RNA synthesis and retained precursor RNA?", "kind": "boundary", "id": "ribosomal-transcription-readout-q02" } ] } ] } ] }, { "id": "rna-maturation-and-ribosomal-assembly", "name": "RNA maturation and ribosomal assembly", "description": "Assess the progression from precursor ribosomal RNA to assembling ribosomal subunits.", "rationale": "High transcription can coexist with defective processing or assembly, so productive progression needs separate evidence.", "layers": [ { "id": "precursor-processing", "name": "Precursor processing", "description": "Evaluate cleavage and modification of ribosomal RNA using the host-specific maturation pathway.", "findings": [ { "id": "processing-intermediate-profile", "name": "Processing intermediate profile", "description": "Record precursor identities and evidence for normal progression or a processing bottleneck.", "questions": [ { "text": "Which precursor and intermediate ribosomal RNA species are expected in this host, and which are detected?", "kind": "definition", "id": "processing-intermediate-profile-q01" }, { "text": "What measurements distinguish increased precursor production from delayed cleavage or modification?", "kind": "measurement", "id": "processing-intermediate-profile-q02" } ] } ] }, { "id": "pre-ribosomal-particle-progression", "name": "Pre-ribosomal particle progression", "description": "Track recruitment and progression of assembly components within the nucleolus.", "findings": [ { "id": "assembly-and-nucleolar-exit", "name": "Assembly and nucleolar exit", "description": "Establish evidence that assembling particles progress beyond nucleolar stages.", "questions": [ { "text": "Which ribosomal proteins and assembly factors support assignment of the observed particles to particular assembly stages?", "kind": "measurement", "id": "assembly-and-nucleolar-exit-q01" }, { "text": "What evidence distinguishes nucleolar retention from progression into the nucleoplasm, and where does the neighbouring export model take over?", "kind": "boundary", "id": "assembly-and-nucleolar-exit-q02" } ] } ] } ] }, { "id": "internal-architecture-and-dynamics", "name": "Internal architecture and dynamics", "description": "Describe spatial organisation, molecular exchange and changes over the cell cycle.", "rationale": "Nucleolar function depends on dynamic internal organisation that cannot be reduced to a single size or marker measurement.", "layers": [ { "id": "functional-subcompartments", "name": "Functional subcompartments", "description": "Resolve internal regions without imposing an unsupported universal compartment pattern.", "findings": [ { "id": "region-specific-localisation", "name": "Region-specific localisation", "description": "Associate observed regions with validated markers and appropriately qualified functional interpretations.", "questions": [ { "text": "Which fibrillar or granular regions are resolved, and which markers support their identification in this host?", "kind": "measurement", "id": "region-specific-localisation-q01" }, { "text": "Which apparent absences reflect biological organisation, and which may result from limited resolution or preparation?", "kind": "boundary", "id": "region-specific-localisation-q02" } ] } ] }, { "id": "exchange-and-cell-cycle-remodelling", "name": "Exchange and cell-cycle remodelling", "description": "Track molecular movement and compartment reorganisation through time.", "findings": [ { "id": "contextualised-nucleolar-dynamics", "name": "Contextualised nucleolar dynamics", "description": "Interpret exchange, fusion and disassembly relative to probe behaviour and the host cell cycle.", "questions": [ { "text": "What exchange or recovery behaviour is measured for each labelled component, and how might the label alter that behaviour?", "kind": "measurement", "id": "contextualised-nucleolar-dynamics-q01" }, { "text": "How does nucleolar organisation change across the observed cell-cycle stages in this host?", "kind": "measurement", "id": "contextualised-nucleolar-dynamics-q02" } ] } ] } ] }, { "id": "stress-and-experimental-intervention", "name": "Stress and experimental intervention", "description": "Evaluate nucleolar disruption and select experiments that clarify its cause and reversibility.", "rationale": "Nucleolar changes can arise from direct interference with ribosome biogenesis or broader cellular changes that require different interpretations.", "layers": [ { "id": "stress-associated-reorganisation", "name": "Stress-associated reorganisation", "description": "Connect structural and functional changes with documented exposures and cellular responses.", "findings": [ { "id": "nucleolar-disruption-evidence", "name": "Nucleolar disruption evidence", "description": "Record the temporal relationship between exposure, nucleolar changes and independently measured cellular effects.", "questions": [ { "text": "Which exposure or cellular condition preceded changes in nucleolar morphology, RNA production or processing?", "kind": "provenance", "id": "nucleolar-disruption-evidence-q01" }, { "text": "What evidence distinguishes nucleolar disruption from expected cell-cycle remodelling or general loss of cell viability?", "kind": "boundary", "id": "nucleolar-disruption-evidence-q02" } ] } ] }, { "id": "perturbation-and-recovery", "name": "Perturbation and recovery", "description": "Choose interpretable interventions and assess recovery using both structural and functional readouts.", "findings": [ { "id": "controlled-nucleolar-intervention", "name": "Controlled nucleolar intervention", "description": "Specify the targeted process, relevant controls and evidence needed to assess the outcome.", "questions": [ { "text": "Which perturbation can test the suspected transcription, processing or assembly defect, and which controls address broader cellular effects?", "kind": "action", "id": "controlled-nucleolar-intervention-q01" }, { "text": "Which time-resolved structural and functional measurements would establish recovery after reversal or rescue?", "kind": "action", "id": "controlled-nucleolar-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-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "This describes a subcellular compartment, not an organism; taxonomic authorities and conservation status do not apply.", "The size range is approximate and should be checked for the organism, cell type, and measurement method.", "Recall only: no sources were consulted. Nucleolar organization and stress responses should not be generalized across all eukaryotes." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of nucleolus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "scheme": "Gene Ontology cellular component", "value_or_pattern": "GO:0005730", "note": "Identifies the nucleolus as a cellular component, not an organism or taxon." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of nucleolus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Nucleolar size, number, and appearance are examined in histology and cytology, including tumour assessment.", "Nucleoli are studied to investigate ribosome production, cellular growth, and stress responses.", "Nucleolar proteins such as fibrillarin and nucleophosmin serve as experimental localization markers." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of nucleolus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Diameter", "typical_range": "Approximately 0.5-5 in many mammalian cells; strongly dependent on cell type and physiological state", "unit": "µm" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of nucleolus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Disruption of ribosomal RNA synthesis, processing, or subunit assembly can impair ribosome production and trigger nucleolar stress.", "Nucleolar stress can activate p53-dependent responses in mammalian cells, although responses depend on cellular context.", "Defects in ribosome biogenesis contribute to some ribosomopathies.", "Enlarged or irregular nucleoli can accompany malignancy but are not independently diagnostic." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of nucleolus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-regional-variation", "name": "Regional variation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Variation is primarily biological rather than geographic: nucleolar organization differs among eukaryotic groups and cell types.", "Many mammalian nucleoli show fibrillar centres, a dense fibrillar component, and a granular component; this tripartite organization is not universal." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of nucleolus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "nucleus", "difference": "The nucleus is the membrane-enclosed compartment containing most cellular DNA; the nucleolus is a compartment within it without its own enclosing membrane." }, { "name": "nucleolus organizer region", "difference": "A nucleolus organizer region is a chromosomal region containing repeated ribosomal RNA genes; the nucleolus is the molecular compartment organized around active regions." }, { "name": "ribosome", "difference": "A ribosome translates messenger RNA into protein; the nucleolus produces and assembles precursors of its subunits." }, { "name": "Cajal body", "difference": "A Cajal body is a distinct nuclear body involved in the maturation of several ribonucleoprotein complexes, rather than the principal site of ribosome biogenesis." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of nucleolus this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which host organisms and cell types must the model cover, and what differences in internal architecture and cell-cycle behaviour require explicit variants?", "Which marker combinations and imaging methods reliably distinguish nucleoli and their subcompartments in the intended experimental systems?", "Which host-specific ribosomal RNA intermediates and assembly readouts are needed to identify processing and assembly bottlenecks?", "What matched reference conditions support interpretation of nucleolar size, count and activity without treating morphology as a direct measure of function?", "Which additional nucleolar roles, such as sequestration of regulatory proteins or stress signalling, have sufficient evidence in the target context to warrant dedicated extensions?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 17, "questions": 27 } }, "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 nucleolus, record what state it is in, and decide what may be done with it.", "whatItIs": "Enable an AI agent to recognise a nucleolus, assess its ribosome-biogenesis activity and structural state, and select context-appropriate observations or perturbations.", "characteristics": { "substance": "living", "origin": "natural", "agency": "autonomous", "mobility": "self-moving" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Described in 73 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 nucleolus, 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": [], "standing": "Described in 73 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is.", "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one nucleolus from another, and a nucleolus 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 nucleolus, 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 nucleolus, 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 nucleolus 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 nucleolus, 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 nucleolus, 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 nucleolus 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 nucleolus 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 nucleolus, 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 nucleolus, 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 nucleolus 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 nucleolus from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a nucleolus, 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 nucleolus, 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 nucleolus 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 nucleolus 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 nucleolus, 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 nucleolus, 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 nucleolus 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 nucleolus and the stages it passes through.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a nucleolus, 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 nucleolus, 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 nucleolus 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 nucleolus is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a nucleolus, 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 nucleolus, 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 nucleolus 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 nucleolus 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 nucleolus is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a nucleolus, 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 nucleolus, 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 nucleolus 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 nucleolus 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 nucleolus, 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 nucleolus, 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 nucleolus 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 nucleolus 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 nucleolus between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a nucleolus, 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 nucleolus, 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 nucleolus 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 nucleolus, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a nucleolus 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 nucleolus, 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 nucleolus, 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 nucleolus 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 nucleolus 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 nucleolus, 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 nucleolus 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 nucleolus 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 nucleolus 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 nucleolus 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 nucleolus 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 nucleolus 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 nucleolus, 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 nucleolus 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 nucleolus 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 nucleolus and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a nucleolus, 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 nucleolus, 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 nucleolus 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 nucleolus is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a nucleolus, 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 nucleolus, 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 nucleolus 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 } } } }