{ "model": { "rank": 5348, "code": "thing-q719725", "model_id": "vr.tr.saccharomyces-cerevisiae", "name": "Saccharomyces cerevisiae", "purpose": "Enable an agent to identify Saccharomyces cerevisiae, assess a particular strain or culture, and decide whether it is suitable for a specified research or fermentation use.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q719725/", "tier": 2, "score": 68, "payload": { "layer": "wikidata", "aliases": [], "aliasCount": 0, "merged": 0, "knownIn": 68, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q719725", "url": "https://www.wikidata.org/wiki/Q719725", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-09T22:11:01Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 22.3, "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: 01a08838-80f0-7b43-b7a4-8546e02a89e0\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: Saccharomyces cerevisiae\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch ", "usd": 0, "recall": true }, "codex": { "seconds": 62.3, "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: 01a08838-8101-7dc2-8042-69dd4a35c9b9\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: Saccharomyces cerevisiae\nRegistry id: vr.tr.saccharomyces-cerevisiae\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded " } } }, "metaModel": { "id": "THING-Q719725", "registryId": "vr.tr.saccharomyces-cerevisiae", "name": "Saccharomyces cerevisiae", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q719725/", "model": { "registry_id": "vr.tr.saccharomyces-cerevisiae", "name": "Saccharomyces cerevisiae", "purpose": "Enable an agent to identify Saccharomyces cerevisiae, assess a particular strain or culture, and decide whether it is suitable for a specified research or fermentation use.", "definition": "Saccharomyces cerevisiae is a species of unicellular ascomycete fungus that commonly reproduces by budding, ferments sugars to ethanol and carbon dioxide, and is widely used in food production, biotechnology and research.", "scope_statement": "This model owns the species identity of Saccharomyces cerevisiae and the strain, cellular, physiological and culture-state distinctions needed to act on instances of it, separating species-level expectations from evidence about a particular isolate.", "in_scope": [ "Species identification and differentiation from related Saccharomyces species and hybrids", "Strain identity, provenance, genotype and modification history", "Ploidy, mating type, reproduction and population heterogeneity", "Fermentation, respiration, nutrient requirements and stress responses", "Culture viability, purity, stability and suitability for an intended use" ], "out_of_scope": [ "Yeasts or fungi as broader biological groups", "Other Saccharomyces species and interspecies hybrids as independent organisms", "Bread, beer, wine, yeast extracts and other products containing or derived from the organism", "Fermenters, cultivation equipment and complete manufacturing processes", "Host diseases, clinical diagnosis and treatment", "Purified metabolites and their chemical specifications" ], "distinguishing_features": [ "Require a documented species-identification method that distinguishes S. cerevisiae from close relatives; budding morphology alone does not establish species identity.", "Check whether identification evidence supports S. cerevisiae or a hybrid involving it, particularly when the material is described only as brewing yeast.", "Treat baker's yeast, brewer's yeast and similar use labels as insufficient identifiers without a strain or species record.", "Distinguish a viable S. cerevisiae culture from inactivated biomass or yeast extract before assigning growth or fermentation capabilities.", "Separate species membership from strain performance: a laboratory strain and a production strain need independent evidence of suitability." ], "characteristics": [ { "name": "Species assignment", "kind": "category", "unit_or_values": "Supported S. cerevisiae assignment | unresolved Saccharomyces | suspected hybrid | conflicting identification", "why_it_matters": "Determines whether this model applies and whether further identification is necessary." }, { "name": "Strain and lineage", "kind": "relation", "unit_or_values": "Culture-collection accession, supplier identifier, isolate identifier and parent-strain links", "why_it_matters": "Connects observations to the correct biological material rather than to the species in general." }, { "name": "Ploidy and chromosome state", "kind": "category", "unit_or_values": "Haploid | diploid | polyploid | aneuploid | mixed | unknown, with supporting assay", "why_it_matters": "Affects genetic interpretation, reproductive options and strain stability." }, { "name": "Mating-type configuration", "kind": "category", "unit_or_values": "MAT locus configuration, switching capability and assay evidence, or unknown", "why_it_matters": "Supports decisions about mating, crossing and maintenance of a defined lineage." }, { "name": "Genetic dependencies and modifications", "kind": "relation", "unit_or_values": "Documented alleles, auxotrophies, constructs, selectable markers and mitochondrial alterations", "why_it_matters": "Determines medium requirements and limits which phenotypes can be attributed to the unmodified organism." }, { "name": "Viability", "kind": "measurement", "unit_or_values": "Percent viable cells or CFU/mL, with method, sampling time and culture conditions", "why_it_matters": "Distinguishes measured living material from total biomass and supports inoculum assessment." }, { "name": "Carbon-use phenotype", "kind": "state", "unit_or_values": "Growth, substrate consumption and product formation for each tested carbon source under stated oxygen conditions", "why_it_matters": "Prevents assumptions that all strains use the same substrates or produce equivalent fermentation outcomes." }, { "name": "Growth and fermentation performance", "kind": "measurement", "unit_or_values": "Specific growth rate in h^-1, substrate consumption in g/L/h and ethanol yield in g/g, with assay conditions", "why_it_matters": "Makes strain suitability testable without treating context-dependent performance as a species constant." }, { "name": "Culture purity", "kind": "state", "unit_or_values": "No contaminants detected by stated tests | mixed culture | contamination detected | untested", "why_it_matters": "Determines whether observed behavior can be assigned to the intended strain." }, { "name": "Stress-response profile", "kind": "measurement", "unit_or_values": "Growth or survival across tested temperature, pH, ethanol concentration and osmotic conditions", "why_it_matters": "Defines an evidence-based operating range for the particular strain and application." } ], "affordances": [ "Resolve a culture's species and strain identity against reference material and identification evidence.", "Compare strains for a specified fermentation or experimental objective using measurements made under comparable conditions.", "Determine whether documented nutrient dependencies and carbon-use phenotypes match a proposed cultivation environment.", "Assess whether mating, sporulation or genetic manipulation is compatible with the recorded strain state.", "Accept, quarantine, re-identify or replace a culture based on identity, purity, viability and stability evidence.", "Select a preservation and recovery approach supported for the strain and verify its condition after recovery." ] }, "sources": [], "structure": { "bundles": [ { "id": "species-and-strain-identity", "name": "Species and strain identity", "description": "Establish what biological material is present and which lineage-specific records apply.", "rationale": "Common yeast names and intended uses do not reliably establish S. cerevisiae identity or strain equivalence.", "layers": [ { "id": "species-boundary", "name": "Species boundary", "description": "Separate S. cerevisiae from related species, ambiguous isolates and hybrids.", "findings": [ { "id": "species-assignment-evidence", "name": "Evidence for species assignment", "description": "Record the identification method, reference comparison and its ability to resolve close relatives or mixed ancestry.", "questions": [ { "text": "Which identification results support assigning this isolate to S. cerevisiae?", "kind": "provenance", "id": "species-assignment-evidence-q01" }, { "text": "Can the method distinguish close Saccharomyces relatives and detect hybrid ancestry, or does that remain unresolved?", "kind": "boundary", "id": "species-assignment-evidence-q02" } ] } ] }, { "id": "strain-provenance", "name": "Strain provenance", "description": "Connect the working culture to a traceable isolate, accession or parent lineage.", "findings": [ { "id": "lineage-and-aliases", "name": "Lineage and aliases", "description": "Record strain identifiers, aliases, source material and derivation history without equating similar commercial names.", "questions": [ { "text": "Which accession or isolate identifier anchors this strain, and where did the current culture originate?", "kind": "provenance", "id": "lineage-and-aliases-q01" }, { "text": "Which names denote the same documented lineage, and which merely describe a baking, brewing or other use?", "kind": "boundary", "id": "lineage-and-aliases-q02" } ] } ] } ] }, { "id": "genome-and-reproductive-state", "name": "Genome and reproductive state", "description": "Represent the genetic configuration and reproductive capabilities of the particular strain.", "rationale": "Ploidy, mating configuration and engineered dependencies materially change what an agent can infer or do.", "layers": [ { "id": "genetic-configuration", "name": "Genetic configuration", "description": "Capture nuclear and mitochondrial features relevant to interpretation and maintenance.", "findings": [ { "id": "strain-genotype", "name": "Strain genotype and dependencies", "description": "Record measured ploidy, chromosome variation, relevant alleles, constructs and nutrient dependencies.", "questions": [ { "text": "What evidence establishes ploidy, aneuploidy or genetic heterogeneity in this culture?", "kind": "measurement", "id": "strain-genotype-q01" }, { "text": "Which auxotrophies, introduced constructs or mitochondrial changes affect cultivation and phenotype interpretation?", "kind": "definition", "id": "strain-genotype-q02" } ] } ] }, { "id": "reproductive-capability", "name": "Reproductive capability", "description": "Separate vegetative propagation from strain-specific mating and sporulation behavior.", "findings": [ { "id": "mating-and-sporulation", "name": "Mating and sporulation competence", "description": "Record mating-type configuration, switching behavior and evidence of successful mating or sporulation.", "questions": [ { "text": "What are the strain's MAT configuration and documented mating-type switching behavior?", "kind": "definition", "id": "mating-and-sporulation-q01" }, { "text": "Under which tested conditions does this strain mate or produce viable spores?", "kind": "measurement", "id": "mating-and-sporulation-q02" } ] } ] } ] }, { "id": "carbon-metabolism-and-growth", "name": "Carbon metabolism and growth", "description": "Describe how the strain grows and partitions carbon under specified environmental conditions.", "rationale": "S. cerevisiae performance depends on substrate, oxygen availability, nutrient supply and strain background.", "layers": [ { "id": "fermentation-and-respiration", "name": "Fermentation and respiration", "description": "Capture measured carbon-use behavior without inferring metabolism from oxygen presence alone.", "findings": [ { "id": "condition-dependent-carbon-flux", "name": "Condition-dependent carbon use", "description": "Associate growth, sugar consumption, ethanol production and respiratory evidence with the conditions of observation.", "questions": [ { "text": "Which carbon sources support growth or fermentation in this strain, and under what oxygen and concentration conditions?", "kind": "measurement", "id": "condition-dependent-carbon-flux-q01" }, { "text": "What measurements distinguish fermentative, respiratory or mixed activity in the observed culture?", "kind": "measurement", "id": "condition-dependent-carbon-flux-q02" } ] } ] }, { "id": "nutrients-and-stress", "name": "Nutrients and stress", "description": "Represent the strain's nutritional requirements and responses to fermentation-relevant stresses.", "findings": [ { "id": "supported-growth-envelope", "name": "Supported growth envelope", "description": "Record tested nutrient requirements and responses to temperature, acidity, ethanol and osmotic stress.", "questions": [ { "text": "Which nutrients or supplements are required under the intended oxygen regime and strain genotype?", "kind": "measurement", "id": "supported-growth-envelope-q01" }, { "text": "What growth and survival evidence defines acceptable temperature, pH, ethanol and osmotic conditions for this use?", "kind": "action", "id": "supported-growth-envelope-q02" } ] } ] } ] }, { "id": "culture-condition-and-continuity", "name": "Culture condition and continuity", "description": "Assess the present population and maintain a traceable connection to its reference stock.", "rationale": "A correctly named strain can still be nonviable, contaminated, heterogeneous or altered during propagation.", "layers": [ { "id": "population-condition", "name": "Population condition", "description": "Distinguish biomass, viable cells, aggregation and contamination.", "findings": [ { "id": "viability-purity-and-aggregation", "name": "Viability, purity and aggregation", "description": "Interpret culture measurements using assay limitations, including budding cells, flocculation and mixed populations.", "questions": [ { "text": "What are the measured viable fraction and viable concentration, and how did counting account for buds or cell aggregates?", "kind": "measurement", "id": "viability-purity-and-aggregation-q01" }, { "text": "Which tests assessed bacterial contamination, other yeasts and unintended S. cerevisiae strains?", "kind": "measurement", "id": "viability-purity-and-aggregation-q02" } ] } ] }, { "id": "stock-continuity", "name": "Stock continuity", "description": "Track preservation, recovery and passage history against a reference culture.", "findings": [ { "id": "preservation-and-drift", "name": "Preservation and drift", "description": "Record handling history and checks for loss of defining genetic or performance traits.", "questions": [ { "text": "Which reference stock, preservation conditions and propagation history link to the current culture?", "kind": "provenance", "id": "preservation-and-drift-q01" }, { "text": "Which identity, genotype or performance checks must pass after recovery or repeated propagation?", "kind": "action", "id": "preservation-and-drift-q02" } ] } ] } ] }, { "id": "use-fitness-and-handling", "name": "Use fitness and handling", "description": "Translate strain evidence into decisions for a defined application and handling context.", "rationale": "Species identity alone cannot establish production performance, experimental validity or permission for a particular use.", "layers": [ { "id": "application-performance", "name": "Application performance", "description": "Connect the intended role to strain-specific acceptance criteria.", "findings": [ { "id": "role-specific-acceptance", "name": "Role-specific acceptance", "description": "Evaluate traits such as gas production, fermentation completion, flocculation or experimental phenotype according to the actual task.", "questions": [ { "text": "Is the strain intended for baking, brewing, winemaking, another bioprocess or laboratory research, and which outcomes define success?", "kind": "definition", "id": "role-specific-acceptance-q01" }, { "text": "Which representative-condition results establish that this culture meets those acceptance criteria?", "kind": "measurement", "id": "role-specific-acceptance-q02" } ] } ] }, { "id": "handling-and-use-status", "name": "Handling and use status", "description": "Associate the exact strain and preparation with applicable handling assessments and use documentation.", "findings": [ { "id": "context-specific-use-decision", "name": "Context-specific use decision", "description": "Distinguish live cultures, inactivated preparations and modified strains when assessing an intended use.", "questions": [ { "text": "Which documented handling assessment and use status apply to this exact strain, preparation and jurisdiction?", "kind": "provenance", "id": "context-specific-use-decision-q01" }, { "text": "Do the intended exposure route, genetic modifications or culture condition require additional review before use?", "kind": "action", "id": "context-specific-use-decision-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 chemical-material context is inappropriate for this organism: strain identity, viability and culture conditions matter more than chemical purity or melting point.", "The kinds listed are overlapping functional strain groups, not formal taxonomic subdivisions; dimensions and performance vary with strain and conditions.", "This is recalled knowledge without source consultation; strain-specific safety claims and jurisdiction-specific regulatory status require verification." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of Saccharomyces cerevisiae 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": [ "Baking strains", "Ale-brewing strains", "Wine-fermentation strains", "Distilling and industrial ethanol strains", "Laboratory strains", "Probiotic strains commonly called Saccharomyces boulardii" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of Saccharomyces cerevisiae 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": "Scientific binomial", "value_or_pattern": "Saccharomyces cerevisiae", "note": "Identifies a fungal species, not a chemical substance or a particular commercial yeast preparation." }, { "scheme": "NCBI Taxonomy", "value_or_pattern": "4932", "note": "Species-level taxonomy identifier." }, { "scheme": "Laboratory strain designation", "value_or_pattern": "S288C", "note": "A widely used reference strain; findings about it do not necessarily describe every strain of the species." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of Saccharomyces cerevisiae 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": [ "Leavening bread through carbon dioxide production.", "Producing alcoholic beverages through fermentation.", "Producing fuel and industrial ethanol.", "Serving as a model organism for genetics, cell biology and molecular biology.", "Producing recombinant proteins and other biotechnology products." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of Saccharomyces cerevisiae 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": "Typical vegetative cell dimension", "typical_range": "Approximately 3-10, depending on strain, growth conditions and cell-cycle stage", "unit": "µm" }, { "quantity": "Reference haploid nuclear genome size", "typical_range": "Approximately 12", "unit": "megabase pairs" }, { "quantity": "Reference haploid nuclear chromosome count", "typical_range": "16", "unit": "chromosomes" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of Saccharomyces cerevisiae 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": [ "Fermentation can slow or stop because of nutrient limitation, unsuitable temperature, inhibitory compounds or ethanol stress.", "Contaminating microorganisms can alter fermentation performance and product quality.", "Uncontrolled fermentation in sealed containers can cause pressure buildup.", "Strain variation and genetic instability can reduce industrial consistency or experimental reproducibility.", "Rare opportunistic infections, including fungemia associated with probiotic strains, can occur in vulnerable patients." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of Saccharomyces cerevisiae 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": [ "Traditional baking, brewing and winemaking practices use different locally selected strains.", "Requirements for food, feed, probiotic and genetically modified yeast products vary by jurisdiction and intended use." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of Saccharomyces cerevisiae 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": "Yeast", "difference": "Yeast describes a growth form shared by many fungi; Saccharomyces cerevisiae is one particular species." }, { "name": "Saccharomyces pastorianus", "difference": "The principal lager-brewing yeast is a hybrid involving Saccharomyces cerevisiae and Saccharomyces eubayanus, rather than simply a cold-growing strain of Saccharomyces cerevisiae." }, { "name": "Saccharomyces boulardii", "difference": "This name commonly denotes probiotic lineages classified within Saccharomyces cerevisiae; probiotic properties require strain-level identification." }, { "name": "Baker's yeast", "difference": "Baker's yeast denotes strains or preparations selected for baking, whereas the species includes many other strains and uses." }, { "name": "Yeast extract", "difference": "Yeast extract is a processed mixture of cellular constituents, not a living organism or fungal species." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of Saccharomyces cerevisiae this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which authoritative taxonomic reference and identification criteria should anchor the registry entry and resolve ambiguous or hybrid isolates?", "How should strains marketed as Saccharomyces boulardii be represented under the chosen taxonomic authority without creating duplicate species models?", "Which physiological claims are sufficiently supported across S. cerevisiae strains to record at species level, and which must remain strain-specific?", "Which comparable assays and reference conditions should define growth, fermentation, viability and stress-response measurements?", "Which strain-specific handling and use-status sources are needed for the intended applications and jurisdictions?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 18, "questions": 28 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "chemical substance or material", "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 Saccharomyces cerevisiae, record what state it is in, and decide what may be done with it.", "whatItIs": "Enable an agent to identify Saccharomyces cerevisiae, assess a particular strain or culture, and decide whether it is suitable for a specified research or fermentation use.", "characteristics": { "substance": "material", "origin": "natural", "agency": "inert", "mobility": "varies" }, "whatYouCanDoWithIt": [ "observed and measured", "consumed or used up" ], "distinguishingFeatures": [ "Described in 68 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 Saccharomyces cerevisiae, and on what evidence are they told apart?" ], "whatItIsMadeOf": "matter you can touch", "physicalCharacter": [ "Mobility varies between examples.", "Does nothing on its own; everything it does, something else did to it.", "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", "use it up, and then need more of it" ], "howItIsRecognised": [ "Not recognisable by sight in any reliable way. Appearance varies with grade, form and additives; identification is by label, by documentation, or by assay." ], "relatedModels": [], "standing": "Described in 68 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 Saccharomyces cerevisiae from another, and a Saccharomyces cerevisiae 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae 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 Saccharomyces cerevisiae 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae 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 Saccharomyces cerevisiae from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae 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 Saccharomyces cerevisiae 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae 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": "Materials, parts and how they are put together.", "findings": [ { "id": "parts-and-materials", "name": "Parts and materials", "description": "What a Saccharomyces cerevisiae is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae 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 Saccharomyces cerevisiae is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae 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 Saccharomyces cerevisiae is, how it got there and where it may go (varies).", "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 Saccharomyces cerevisiae is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae 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 Saccharomyces cerevisiae is carried, installed or relocated.", "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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae 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 Saccharomyces cerevisiae 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 Saccharomyces cerevisiae between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae 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 Saccharomyces cerevisiae, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a Saccharomyces cerevisiae 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "use-and-operation", "name": "Use and operation", "description": "What can be done with a Saccharomyces cerevisiae and what it takes to do it.", "rationale": "An agent that can recognise a thing but not act on it has only half a model.", "layers": [ { "id": "intended-use", "name": "Intended use and function", "description": "What a Saccharomyces cerevisiae is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a Saccharomyces cerevisiae performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a Saccharomyces cerevisiae, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "function-and-purpose-q02", "text": "Who or what asserted this about the use of a Saccharomyces cerevisiae, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "function-and-purpose-q03", "text": "What may an agent decide or do once the use of a Saccharomyces cerevisiae is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "handling-and-procedure", "name": "Handling and procedure", "description": "The steps, skills and tools involved in using a Saccharomyces cerevisiae.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a Saccharomyces cerevisiae at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a Saccharomyces cerevisiae, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "procedures-and-skills-q02", "text": "Who or what asserted this about handling a Saccharomyces cerevisiae, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "procedures-and-skills-q03", "text": "What may an agent decide or do once handling a Saccharomyces cerevisiae is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "supply-and-consumption", "name": "Supply and consumption", "description": "Quantities, rates and what running out means.", "findings": [ { "id": "consumption-and-stock", "name": "Consumption, stock and replenishment", "description": "How much of a Saccharomyces cerevisiae there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a Saccharomyces cerevisiae, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "consumption-and-stock-q02", "text": "Who or what asserted this about the supply of a Saccharomyces cerevisiae, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "consumption-and-stock-q03", "text": "What may an agent decide or do once the supply of a Saccharomyces cerevisiae is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "composition-and-identity", "name": "Composition, grade and chemical identity", "description": "What Saccharomyces cerevisiae is made of and how pure the thing in hand is.", "rationale": "Grade decides what a substance may be used for, so a model that records only the name cannot support any decision about use.", "layers": [ { "id": "chemical-identity", "name": "Chemical identity", "description": "Formula, structure and the registry numbers that name it unambiguously.", "findings": [ { "id": "identity-record", "name": "Identity and registry numbers", "description": "What identifies this substance across suppliers and regulators.", "questions": [ { "id": "identity-record-q01", "text": "What formula, structure and registry identifiers name Saccharomyces cerevisiae unambiguously?", "kind": "definition" }, { "id": "identity-record-q02", "text": "Which related substances share a name in common use but not an identifier?", "kind": "boundary" } ] } ] }, { "id": "grade-and-impurities", "name": "Grade, purity and impurities", "description": "The specification a batch meets and what else is in it.", "findings": [ { "id": "specification", "name": "Specification and assay", "description": "How purity is stated and measured, and which impurities matter.", "questions": [ { "id": "specification-q01", "text": "What grades of Saccharomyces cerevisiae exist, how is purity assayed, and which impurities are limited?", "kind": "measurement" }, { "id": "specification-q02", "text": "Which use requires which grade, and what happens when a lower grade is substituted?", "kind": "action" } ] } ] } ] }, { "id": "properties-and-behaviour", "name": "Properties and behaviour", "description": "How Saccharomyces cerevisiae behaves under conditions an agent can measure or change.", "rationale": "Physical constants are the part of a substance model that transfers between contexts, and each needs its unit and its conditions.", "layers": [ { "id": "physical-constants", "name": "Physical constants", "description": "Values that hold for the pure substance, with their conditions.", "findings": [ { "id": "constants-record", "name": "Constants and conditions", "description": "The quantities worth recording and the state they apply in.", "questions": [ { "id": "constants-record-q01", "text": "What are the defining physical constants of Saccharomyces cerevisiae, in what units and under what conditions?", "kind": "measurement" }, { "id": "constants-record-q02", "text": "Which of these values change with grade or form rather than being fixed?", "kind": "boundary" } ] } ] }, { "id": "stability-and-reactivity", "name": "Stability and reactivity", "description": "What it reacts with, degrades into, and how it is stored.", "findings": [ { "id": "incompatibilities", "name": "Incompatibilities and degradation", "description": "What must not meet it, and what it becomes over time.", "questions": [ { "id": "incompatibilities-q01", "text": "What is Saccharomyces cerevisiae incompatible with, and what does it degrade into under storage?", "kind": "definition" }, { "id": "incompatibilities-q02", "text": "What storage and handling does that require, and who is competent to do it?", "kind": "action" } ] } ] } ] }, { "id": "hazard-and-regulation", "name": "Hazard classification and regulation", "description": "How Saccharomyces cerevisiae can harm, and what the law says about holding and moving it.", "rationale": "A substance model without its hazard class and its regulatory identity is unusable in exactly the situations that matter.", "layers": [ { "id": "hazard-class", "name": "Hazard classification", "description": "Classified hazards, exposure limits and protective measures.", "findings": [ { "id": "classified-hazards", "name": "Classified hazards and limits", "description": "The classification, the scheme it belongs to, and the limits set.", "questions": [ { "id": "classified-hazards-q01", "text": "How is Saccharomyces cerevisiae classified for hazard, under which scheme, and what exposure limits apply?", "kind": "definition" }, { "id": "classified-hazards-q02", "text": "What protection does handling require, and what must an agent refuse to do without it?", "kind": "action" } ] } ] }, { "id": "regulatory-identity", "name": "Regulatory identity and control", "description": "Registration, restriction and transport rules by jurisdiction.", "findings": [ { "id": "controls", "name": "Controls and jurisdiction", "description": "Where it is restricted and what the restriction attaches to.", "questions": [ { "id": "controls-q01", "text": "Which registrations, restrictions or transport rules cover Saccharomyces cerevisiae, and where?", "kind": "provenance" }, { "id": "controls-q02", "text": "Does the control attach to the substance, its concentration, or its intended use?", "kind": "boundary" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a Saccharomyces cerevisiae 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 Saccharomyces cerevisiae and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae 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 Saccharomyces cerevisiae is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae, 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 Saccharomyces cerevisiae is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 9, "layers": 20, "findings": 22, "questions": 60 } } } }