{ "model": { "rank": 5140, "code": "thing-bacteria", "model_id": "vr.tr.bacteria", "name": "bacteria", "purpose": "(microbiology) single-celled or noncellular spherical or spiral or rod-shaped organisms lacking chlorophyll that reproduce by fission; important as pathogens and for biochemical properties; taxonomy is difficult; often considered to be plants", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.LIV", "industry": "", "version": "", "url": "/models/thing/bacteria/", "tier": 2, "score": 69, "payload": { "layer": "wordnet", "aliases": [ "bacterium", "acidophil", "acidophile", "probiotic", "probiotic bacterium", "probiotic microflora", "probiotic flora", "bacteroid", "bacillus", "B", "coccus", "cocci", "coccobacillus", "spirillum", "spirilla", "eubacteria", "eubacterium", "true bacteria", "clostridium", "clostridia", "botulinus", "botulinum", "Clostridium botulinum", "clostridium perfringens", "cyanobacteria", "blue-green algae", "nostoc", "trichodesmium", "phototrophic bacteria", "phototropic bacteria", "purple bacteria", "ring rot bacteria", "Pseudomonas solanacearum", "pseudomonad", "xanthomonad", "nitric bacteria", "nitrobacteria", "nitrosobacteria", "nitrous bacteria", "thiobacillus" ], "aliasCount": 116, "merged": 69, "knownIn": 0, "facets": { "substance": "living", "origin": "natural", "agency": "inert", "mobility": "not-applicable", "scale": "not-applicable", "affordances": [ "observable" ] }, "markers": [], "lexicalClass": "noun.animal", "senseRank": 0, "alsoRegisteredAs": null, "source": { "dataset": "oewn:2024", "synset": "oewn-01351171-n", "ili": "i42419", "license": "CC BY 4.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-09T21:45:07Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 25.8, "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: 01a08820-bb18-79e2-860a-7d941394e5e9\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: bacteria\nSense to describe: (microbiology) single-celled or noncellular spherical or spiral or rod-shaped organisms lacking chlorophyll that reproduce b", "usd": 0, "recall": true }, "codex": { "seconds": 66.4, "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: 01a08820-bb1a-7f63-81c7-da9943588bbb\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: bacteria\nRegistry id: vr.tr.bacteria\nPlane / domain: PHY / PHY.LIV\nRegistry definition: (microbiology) single-celled or noncellular spherical or spir" } } }, "metaModel": { "id": "THING-BACTERIA", "registryId": "vr.tr.bacteria", "name": "bacteria", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.LIV" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/bacteria/", "model": { "registry_id": "vr.tr.bacteria", "name": "bacteria", "purpose": "Enable an AI agent to recognise bacterial entities, assess their identity and biological state, and determine appropriate observation, handling or use within the evidence and authorization available.", "definition": "Bacteria are cellular prokaryotic organisms belonging to the domain Bacteria, distinct from Archaea and Eukarya, that lack a membrane-bound nucleus, usually reproduce by binary fission, and exhibit extensive morphological, metabolic and ecological diversity.", "scope_statement": "This model owns bacteria as members of the domain Bacteria and the distinctions needed to describe a bacterial taxon, strain, individual cell, population or bacterial component of a community; it does not treat bacteria as a single species or adopt the registry definition's historical classification as plants.", "in_scope": [ "Bacterial identity, taxonomic placement and identification uncertainty", "Distinctions among taxa, strains, isolates, cells, populations and communities", "Cell structure, morphology, physiological activity and reproductive state", "Genetic variation, metabolic capabilities and environmental relationships", "Evidence governing bacterial handling, monitoring and intended use" ], "out_of_scope": [ "Archaea, viruses and microbial eukaryotes as independently modelled entities", "Host diseases, clinical diagnoses and treatment decisions", "Mixed microbiomes as whole ecological communities", "Culture vessels, laboratory instruments and experimental protocols", "Purified bacterial products, toxins and manufactured preparations" ], "distinguishing_features": [ "Establish affiliation with Bacteria using documented identification evidence; small size and absence of a membrane-bound nucleus alone do not distinguish bacteria from archaea.", "Distinguish bacterial cells from viruses through evidence of cellular organization and bacterial identity; dependence on a host alone does not resolve the boundary.", "Treat spherical, rod-shaped and spiral forms as descriptive observations, not sufficient identification tests.", "Do not require absence of chlorophyll: photosynthetic bacterial groups fall within scope.", "Separate a taxon name from a particular strain, isolate or observed cell; evidence about one does not automatically establish the properties of the others." ], "characteristics": [ { "name": "Entity level", "kind": "category", "unit_or_values": "taxon | strain | isolate | cell | population | bacterial community component", "why_it_matters": "Determines which observations and claims can legitimately describe the entity." }, { "name": "Taxonomic placement", "kind": "relation", "unit_or_values": "Taxon, rank, nomenclatural authority, reference taxonomy identifier and version or access date", "why_it_matters": "Makes identification traceable without treating Bacteria as a species with one binomial." }, { "name": "Identification confidence", "kind": "state", "unit_or_values": "unresolved | provisional | supported at a stated rank, with method and limitations", "why_it_matters": "Prevents action based on greater taxonomic precision than the evidence supports." }, { "name": "Cell morphology and dimensions", "kind": "measurement", "unit_or_values": "Shape and arrangement; length, width or diameter in µm; observation conditions", "why_it_matters": "Supports recognition and comparison while retaining growth-dependent variation." }, { "name": "Cell envelope phenotype", "kind": "category", "unit_or_values": "Observed staining response and envelope evidence; atypical, variable or unknown permitted", "why_it_matters": "Supports identification and interpretation without equating a stain result with complete envelope structure." }, { "name": "Physiological state", "kind": "state", "unit_or_values": "Evidence for activity, growth, dormancy, sporulation, injury or death; unknown permitted", "why_it_matters": "Separates detected material from evidence about living and active cells." }, { "name": "Population abundance", "kind": "measurement", "unit_or_values": "cells/mL, cells/g, CFU/mL, CFU/g or assay-specific quantity, with method and uncertainty", "why_it_matters": "Prevents cell counts, colony counts and molecular signals from being treated as interchangeable." }, { "name": "Metabolic and growth profile", "kind": "category", "unit_or_values": "Observed substrate use, energy sources and oxygen relationships under stated temperature, pH and medium conditions", "why_it_matters": "Connects physiological claims to the conditions under which they were demonstrated." }, { "name": "Genetic identity and functional evidence", "kind": "relation", "unit_or_values": "Sequence accession, strain or isolate linkage, detected features and associated phenotype evidence", "why_it_matters": "Separates genetic potential from demonstrated function." }, { "name": "Ecological occurrence", "kind": "relation", "unit_or_values": "Habitat, host or substrate; location, sampling date and evidence of association", "why_it_matters": "Distinguishes detection at a site from persistent residence or an established ecological role." }, { "name": "Handling and use status", "kind": "state", "unit_or_values": "Intended activity, applicable assessment, authorization, restrictions and unresolved evidence", "why_it_matters": "Makes permissible action specific to the organism, material and context." } ], "affordances": [ "Reconcile a bacterial identification with a named taxonomy while retaining synonyms and unresolved assignments.", "Compare cell, culture and molecular observations without conflating their measurement targets.", "Assess whether evidence supports active growth, survival, dormancy or only detection of bacterial material.", "Connect observed bacterial traits to a particular strain, environment and measurement method.", "Determine whether proposed observation, storage, transfer or use is supported by the applicable assessment and authorization.", "Flag when evidence supports only a broader bacterial group or mixed population rather than a single identified organism." ] }, "sources": [], "structure": { "bundles": [ { "id": "bacterial-identity-and-resolution", "name": "Bacterial identity and resolution", "description": "Establish bacterial affiliation and the biological entity to which each claim applies.", "rationale": "The registry term spans an entire domain, while most actionable observations concern narrower taxa, strains or samples.", "layers": [ { "id": "domain-and-taxonomic-placement", "name": "Domain and taxonomic placement", "description": "Record the evidence and authority used to place an entity within Bacteria.", "findings": [ { "id": "supported-bacterial-assignment", "name": "Supported bacterial assignment", "description": "An identification should specify its supported rank, reference taxonomy and remaining ambiguity.", "questions": [ { "text": "What evidence supports assignment to Bacteria and distinguishes the entity from archaea or microbial eukaryotes?", "kind": "definition", "id": "supported-bacterial-assignment-q01" }, { "text": "Which taxonomy, identifier, authority and version or access date support the reported name and rank?", "kind": "provenance", "id": "supported-bacterial-assignment-q02" } ] } ] }, { "id": "taxon-strain-and-sample-boundaries", "name": "Taxon, strain and sample boundaries", "description": "Separate named biological groups from particular lineages, collected material and observed cells.", "findings": [ { "id": "claim-bearing-entity", "name": "Claim-bearing entity", "description": "Properties should remain attached to the taxon, strain, isolate, cell or population actually examined.", "questions": [ { "text": "Does this record describe a taxon, strain, isolate, individual cell, population or bacterial fraction of a mixed sample?", "kind": "boundary", "id": "claim-bearing-entity-q01" }, { "text": "What collection accession, isolation history or sample lineage connects the observations to that entity?", "kind": "provenance", "id": "claim-bearing-entity-q02" } ] } ] } ] }, { "id": "cell-organization-and-state", "name": "Cell organization and state", "description": "Describe bacterial cellular features and the evidence for present biological activity.", "rationale": "Bacterial appearance, envelope traits and survival states affect recognition and interpretation but vary among lineages and conditions.", "layers": [ { "id": "morphology-and-envelope", "name": "Morphology and envelope", "description": "Capture observed cell dimensions, arrangements and envelope-related traits.", "findings": [ { "id": "observed-cell-phenotype", "name": "Observed cell phenotype", "description": "Morphology and staining are conditional observations rather than complete taxonomic diagnoses.", "questions": [ { "text": "What cell shapes, dimensions, arrangements and envelope-related observations were recorded, using which methods and growth conditions?", "kind": "measurement", "id": "observed-cell-phenotype-q01" }, { "text": "Which observations distinguish these cells from debris or other microbes, and which remain insufficient for identification?", "kind": "boundary", "id": "observed-cell-phenotype-q02" } ] } ] }, { "id": "growth-survival-and-dormancy", "name": "Growth, survival and dormancy", "description": "Separate replication, activity, viability and lineage-specific resting states.", "findings": [ { "id": "evidence-of-living-state", "name": "Evidence of living state", "description": "Record what each assay demonstrates about living cells without interpreting every positive signal as growth or every failed culture as death.", "questions": [ { "text": "What evidence distinguishes active division, metabolic activity, dormancy, injury and death in the observed population?", "kind": "measurement", "id": "evidence-of-living-state-q01" }, { "text": "If endospores or other differentiated states are reported, what supports that assignment for this lineage and sample?", "kind": "provenance", "id": "evidence-of-living-state-q02" } ] } ] } ] }, { "id": "metabolism-and-genetic-variation", "name": "Metabolism and genetic variation", "description": "Connect bacterial capabilities to measured physiology and appropriately attributed genetic evidence.", "rationale": "Related bacteria can differ in functional traits, and sequence evidence alone does not establish expression or performance.", "layers": [ { "id": "energy-and-growth-conditions", "name": "Energy and growth conditions", "description": "Describe resource use and environmental conditions associated with observed growth or activity.", "findings": [ { "id": "conditional-metabolic-profile", "name": "Conditional metabolic profile", "description": "Metabolic claims should state the tested resources, environmental conditions and response.", "questions": [ { "text": "Which carbon sources, energy sources and oxygen relationships are demonstrated rather than inferred for this entity?", "kind": "measurement", "id": "conditional-metabolic-profile-q01" }, { "text": "Under what temperature, pH, salinity and medium conditions were growth or metabolic activity observed?", "kind": "measurement", "id": "conditional-metabolic-profile-q02" } ] } ] }, { "id": "genome-and-trait-attribution", "name": "Genome and trait attribution", "description": "Relate sequence features and mobile genetic elements to their supported bacterial carriers and phenotypes.", "findings": [ { "id": "genetic-potential-versus-function", "name": "Genetic potential versus function", "description": "Keep detected genes, predicted functions and experimentally demonstrated traits distinct.", "questions": [ { "text": "Which sequence records and attribution evidence connect a detected feature to this strain or population rather than another member of a mixed sample?", "kind": "provenance", "id": "genetic-potential-versus-function-q01" }, { "text": "Is the reported capability supported by gene detection, expression evidence or a measured phenotype, and where do these disagree?", "kind": "boundary", "id": "genetic-potential-versus-function-q02" } ] } ] } ] }, { "id": "population-and-ecological-context", "name": "Population and ecological context", "description": "Locate bacterial observations in measurable populations, habitats and biological associations.", "rationale": "A bacterial detection does not by itself establish abundance, persistence, ecological function or host harm.", "layers": [ { "id": "abundance-and-organization", "name": "Abundance and organization", "description": "Describe population quantity and organization as dispersed cells, aggregates or surface-associated communities.", "findings": [ { "id": "interpretable-population-observation", "name": "Interpretable population observation", "description": "Abundance and organization require methods that identify what was counted and how bacterial cells were arranged.", "questions": [ { "text": "Does the reported quantity measure cells, colony-forming units, sequence abundance or another signal, and what are its units and detection limits?", "kind": "measurement", "id": "interpretable-population-observation-q01" }, { "text": "What evidence distinguishes dispersed cells, aggregates and a biofilm, and can the observation be attributed to the bacterial entity in this record?", "kind": "boundary", "id": "interpretable-population-observation-q02" } ] } ] }, { "id": "habitat-and-host-association", "name": "Habitat and host association", "description": "Record where bacteria occur and what is established about their relationships with hosts and surroundings.", "findings": [ { "id": "occurrence-versus-established-role", "name": "Occurrence versus established role", "description": "Separate sampling occurrence from persistence, ecological contribution, colonization and disease causation.", "questions": [ { "text": "Where, when and from which host, substrate or environmental compartment was this bacterial entity detected?", "kind": "provenance", "id": "occurrence-versus-established-role-q01" }, { "text": "What evidence supports persistent residence, a beneficial interaction or a harmful role beyond simple co-occurrence?", "kind": "boundary", "id": "occurrence-versus-established-role-q02" } ] } ] } ] }, { "id": "bacterial-handling-and-use", "name": "Bacterial handling and use", "description": "Connect proposed actions to bacterial identity, material state and context-specific evidence.", "rationale": "Handling and use decisions cannot be inferred from the word bacteria or from a taxon name alone.", "layers": [ { "id": "hazard-and-susceptibility-evidence", "name": "Hazard and susceptibility evidence", "description": "Track relevant hazard assessments and measured susceptibility without converting them into clinical decisions.", "findings": [ { "id": "context-specific-biological-assessment", "name": "Context-specific biological assessment", "description": "Attribute hazard and susceptibility claims to the assessed strain, material, method and exposure context.", "questions": [ { "text": "Which assessment addresses this bacterial entity, material state and proposed activity, and what is its source and date?", "kind": "provenance", "id": "context-specific-biological-assessment-q01" }, { "text": "If antimicrobial susceptibility or resistance is reported, which method, conditions and interpretive standard support it?", "kind": "measurement", "id": "context-specific-biological-assessment-q02" } ] } ] }, { "id": "permitted-actions-and-material-fate", "name": "Permitted actions and material fate", "description": "Determine whether observation, storage, transfer, application or disposal is supported for the bacterial material.", "findings": [ { "id": "action-readiness", "name": "Action readiness", "description": "An action decision should reflect unresolved identification, viability, purity and authorization where these affect the proposed use.", "questions": [ { "text": "Which proposed actions are supported by the current identification, material assessment and applicable authorization?", "kind": "action", "id": "action-readiness-q01" }, { "text": "What additional evidence about identity, viability, contamination or material fate is needed before the proposed action can proceed?", "kind": "action", "id": "action-readiness-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": [ "The supplied sense is historically dated: bacteria are cellular, are not classified as plants, and some contain chlorophyll or bacteriochlorophyll.", "Morphological kinds are descriptive groupings, not mutually exclusive evolutionary taxa; bacterial species boundaries and classifications require framework-specific interpretation.", "This is recall without source consultation. Verify current standards editions and taxonomic details before operational use; no single binomial, native range or conservation assessment applies to Bacteria as a whole." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of bacteria this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Cocci: approximately spherical cells", "Bacilli: rod-shaped cells", "Vibrios: curved rod-shaped cells", "Spirilla: relatively rigid spiral-shaped cells", "Spirochetes: flexible, helically shaped cells with periplasmic flagella", "Filamentous bacteria: cells forming elongated filaments, sometimes branching" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of bacteria 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": "NCBI Taxonomy", "value_or_pattern": "taxid:2", "note": "Identifies Bacteria as a broad taxonomic group, not a species, strain or individual cell." }, { "scheme": "Prokaryotic scientific nomenclature", "value_or_pattern": "Genus species, with author and publication year where appropriate", "note": "Binomials name bacterial species; Bacteria itself is a domain-level name." }, { "scheme": "Culture collection accession", "value_or_pattern": "Collection acronym followed by an accession identifier", "note": "Collections such as ATCC and DSMZ identify deposited strains; equivalent deposits can have different collection identifiers." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of bacteria this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-standards-and-regulation", "name": "Standards and regulation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "International Code of Nomenclature of Prokaryotes, maintained through the International Committee on Systematics of Prokaryotes, governs prokaryotic nomenclature.", "WHO Laboratory Biosafety Manual provides guidance for risk-based handling of biological agents.", "ISO 7218, issued by the International Organization for Standardization, sets general requirements and guidance for microbiological examinations in the food chain.", "CLSI M100, issued by the Clinical and Laboratory Standards Institute, provides performance standards for antimicrobial susceptibility testing." ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of bacteria 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": [ "Food fermentation, including yogurt production and vegetable fermentation.", "Production of enzymes, recombinant proteins and other industrial biochemicals.", "Wastewater treatment and biodegradation of pollutants.", "Agricultural nutrient cycling, including nitrogen fixation by particular bacterial groups.", "Research on genetics, metabolism, evolution and host-microbe interactions." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of bacteria 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": "Cell length or diameter", "typical_range": "Approximately 0.2-10 for many familiar bacteria; substantial exceptions exist", "unit": "µm" }, { "quantity": "Population doubling time", "typical_range": "Tens of minutes to days under growth-supporting conditions, depending on organism and environment", "unit": "time" }, { "quantity": "Culturable concentration", "typical_range": "Sample- and method-dependent; a colony may originate from one cell or a cell aggregate", "unit": "CFU/mL or CFU/g" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of bacteria 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": [ "Some bacteria cause infections or produce toxins; pathogenicity cannot be inferred from membership in Bacteria alone.", "Antimicrobial resistance can compromise treatment and spread through bacterial populations.", "Contamination can spoil food or compromise water, medicines and industrial processes.", "Biofilms can promote persistence on equipment, infrastructure and medical devices.", "Culture-based detection can miss organisms that do not grow under the selected conditions." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of bacteria 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": [ "Community composition varies with climate, salinity, soil chemistry, host distribution and other environmental conditions.", "Pathogen prevalence and antimicrobial resistance patterns differ geographically and over time.", "Biosafety, environmental release and food or water microbiological requirements vary by jurisdiction." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of bacteria 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": "Archaea", "difference": "Also prokaryotic, but distinguished by evolutionary relationships and characteristic differences in membrane chemistry and molecular machinery." }, { "name": "Viruses", "difference": "Viruses are acellular infectious entities that depend on host cells for replication; bacteria are cells with their own ribosomes." }, { "name": "Eukaryotic microorganisms", "difference": "Their cells possess a membrane-bound nucleus; bacterial cells do not." }, { "name": "Cyanobacteria", "difference": "A subgroup within Bacteria characterized by oxygenic photosynthesis, rather than a separate peer category." }, { "name": "Bacterial species", "difference": "A species is a narrower taxonomic grouping within Bacteria; the domain encompasses many such groups." }, { "name": "Bacterial strain", "difference": "A strain denotes a particular isolate or lineage; it is neither the whole domain nor an individual cell." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of bacteria this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which taxonomy and nomenclatural authorities should govern this registry entry, and how should conflicting or revised bacterial names be represented?", "Does an existing Vercy world model already own bacteria or any of these responsibilities, requiring a link or reuse instead of a duplicate publication?", "What evidence thresholds should distinguish supported strain identification, provisional taxon assignment and unresolved mixed-sample detection?", "Which lineage-specific developmental states and ecological traits require extensions beyond this domain-level model?", "For which narrower bacterial taxa are native range or conservation assessment meaningful and available, rather than inappropriate inherited fields?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 19, "questions": 29 } }, "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.", "facetsInferred": false, "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 bacteria, record what state it is in, and decide what may be done with it.", "whatItIs": "(microbiology) single-celled or noncellular spherical or spiral or rod-shaped organisms lacking chlorophyll that reproduce by fission; important as pathogens and for biochemical properties; taxonomy is difficult; often considered to be plants", "characteristics": { "substance": "living", "origin": "natural", "agency": "inert" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: bacterium, acidophil, acidophile, probiotic, probiotic bacterium, probiotic microflora, probiotic flora, bacteroid, bacillus, B, coccus, cocci.", "69 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it." ], "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 bacteria, and on what evidence are they told apart?" ], "whatItIsMadeOf": "a living thing", "physicalCharacter": [ "Does nothing on its own; everything it does, something else did to it." ], "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": [ "bacterium", "acidophil", "acidophile", "probiotic", "probiotic bacterium", "probiotic microflora", "probiotic flora", "bacteroid", "bacillus", "B", "coccus", "cocci" ] } ], "standing": "69 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 bacteria from another, and a bacteria 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 bacteria, 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 bacteria, 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 bacteria 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 bacteria, 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 bacteria, 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 bacteria 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 bacteria 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 bacteria, 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 bacteria, 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 bacteria 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 bacteria from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a bacteria, 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 bacteria, 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 bacteria 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 bacteria 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 bacteria, 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 bacteria, 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 bacteria 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 bacteria and the stages it passes through.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a bacteria, 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 bacteria, 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 bacteria 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 bacteria is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a bacteria, 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 bacteria, 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 bacteria 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 bacteria 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 bacteria between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a bacteria, 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 bacteria, 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 bacteria 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 bacteria, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a bacteria 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 bacteria, 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 bacteria, 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 bacteria 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 bacteria 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 bacteria, 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 bacteria 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 bacteria 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 bacteria 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 bacteria 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 bacteria 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 bacteria 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 bacteria, 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 bacteria 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 bacteria 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 bacteria and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a bacteria, 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 bacteria, 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 bacteria 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 bacteria is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a bacteria, 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 bacteria, 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 bacteria is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 7, "layers": 15, "findings": 17, "questions": 45 } } } }