{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T09:10:38Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 21.8, "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: 01a094e0-e9b0-7ae0-b65c-a0ae56ae1cf9\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: digitonin\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001 regis", "usd": 0.0, "recall": true }, "codex": { "seconds": 75.7, "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: 01a094e0-e9be-7812-ad23-81269abbc26e\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: digitonin\nRegistry id: vr.tr.digitonin\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nCont" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:57:13+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:30+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q410968", "registryId": "vr.tr.digitonin", "name": "digitonin", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q410968/", "model": { "registry_id": "vr.tr.digitonin", "name": "digitonin", "purpose": "Enable an agent to identify digitonin, assess a particular preparation, and judge its suitability for cholesterol interaction, membrane permeabilization, or membrane-component solubilization.", "definition": "Digitonin is a steroidal saponin glycoside found in Digitalis plants that complexes with cholesterol and is used as a nonionic detergent to permeabilize or solubilize biological membranes.", "scope_statement": "This model owns digitonin as the chemical substance registered as vr.tr.digitonin in PHY.MAT, including its molecular identity, preparation quality, physical state, conditional membrane activity, and handling constraints.", "in_scope": [ "Digitonin molecular identity and distinction from related Digitalis glycosides", "Lot composition, purity, water content, and analytical evidence", "Solid material, stock solutions, solubility, and aggregation under recorded conditions", "Cholesterol interaction and experimentally established membrane effects", "Storage, exposure controls, and disposition of digitonin preparations" ], "out_of_scope": [ "Digitalis plants and their cultivation", "Digitogenin, digitoxin, and digoxin as independently modeled substances", "Complete cell-permeabilization and organelle-isolation protocols", "Biological specimens and their underlying membrane composition", "Commercial reagent kits, packaging, and purchasing workflows", "Therapeutic claims or clinical treatment regimens" ], "distinguishing_features": [ "Match the molecular structure, not merely a Digitalis-associated name: digitonin is a glycoside with digitogenin attached to five sugars. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/Digitonin)", "Check the identity against formula C56H92O29 and CAS 11024-24-1; the name alone does not establish lot purity. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/Digitonin)", "Distinguish intact digitonin from its aglycone digitogenin through evidence for the attached sugar portion. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/Digitonin)", "Distinguish its cholesterol-interacting, nonionic detergent role from an unspecified detergent designation; membrane activity alone is insufficient to establish chemical identity. [Sigma-Aldrich](https://www.sigmaaldrich.com/US/en/product/sigma/d141)" ], "characteristics": [ { "name": "Chemical identity", "kind": "category", "unit_or_values": "Digitonin; CAS 11024-24-1; PubChem CID 6474107; EC 234-255-6", "why_it_matters": "Supports cross-record matching. Identity references: [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/Digitonin) and [Sigma-Aldrich](https://www.sigmaaldrich.com/US/en/product/sigma/d141)." }, { "name": "Formula and molar mass", "kind": "measurement", "unit_or_values": "C56H92O29; approximately 1229.3 g/mol", "why_it_matters": "Supports concentration calculations when purity and material basis are known. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/Digitonin)" }, { "name": "Assay purity and composition", "kind": "measurement", "unit_or_values": "% with analytical method and basis; related-component profile; water content", "why_it_matters": "Separates nominal weighed material from quantified digitonin and makes lot comparisons meaningful." }, { "name": "Preparation state", "kind": "state", "unit_or_values": "Solid, dissolved, dispersed, or precipitated; solvent and temperature recorded", "why_it_matters": "Determines whether a nominal concentration represents material available in solution." }, { "name": "Solution concentration", "kind": "measurement", "unit_or_values": "mg/mL or mmol/L; distinguish nominal from analytically measured concentration", "why_it_matters": "Connects dose to preparation quality and observed membrane effects." }, { "name": "Solubility and aggregation behavior", "kind": "measurement", "unit_or_values": "Solubility in mg/mL; aggregation threshold in mmol/L if established; solvent, buffer, temperature, and method", "why_it_matters": "Prevents treating condition-dependent solution behavior as a universal material constant." }, { "name": "Thermal behavior", "kind": "measurement", "unit_or_values": "Melting or decomposition temperature in °C with method; boiling point only if established", "why_it_matters": "Distinguishes phase transition from degradation and avoids unsupported heating assumptions." }, { "name": "Membrane response", "kind": "relation", "unit_or_values": "Preparation linked to specimen, exposure conditions, permeability endpoint, and organelle-integrity endpoint", "why_it_matters": "Makes claims of selective permeabilization testable rather than intrinsic guarantees." }, { "name": "Hazard and handling status", "kind": "category", "unit_or_values": "Applicable SDS classifications, jurisdiction, revision date, exposure limits if established, and required controls", "why_it_matters": "Grounds handling decisions in the actual supplied preparation and current documentation." } ], "affordances": [ "Authenticate a preparation against digitonin identity references and lot-specific analytical evidence.", "Compare lots for a specified membrane assay using both purity and functional acceptance criteria.", "Evaluate a proposed stock solution against documented dissolution and stability evidence.", "Assess whether measured exposure conditions support selective permeabilization or broader solubilization.", "Evaluate digitonin for cholesterol precipitation or complexation using a defined analytical endpoint.", "Determine handling, storage, and disposal requirements from applicable preparation-specific documentation." ], "agent_conduct": { "may": [ "Identify digitonin as a saponin detergent used to permeabilize membranes, citing sources.", "Report grade, storage and safety data of a held stock." ], "must_not": [ "Assist anyone in using it to harm people or animals.", "Recommend it or foxglove material as a remedy.", "Handle it without regard to its safety data.", "Dispose of it in drains or general waste." ], "requires_human": [ "Ordering, transferring or disposing of stock.", "Using it in studies involving animals." ] }, "ethics": { "considerations": [ "It is toxic and comes from a poisonous plant, so careless handling harms workers.", "Foxglove poisoning happens when plants are mistaken for edible ones." ], "affected_parties": [ "Laboratory workers", "People and animals near foxglove", "Waste handlers" ] }, "owners": { "steward": "The laboratory that holds the stock.", "master_systems": [ "Laboratory chemical inventories" ] }, "visual_identification": [ "A white powder supplied in labelled containers; not identifiable by sight.", "Its source plant, foxglove, has tall spikes of tubular purple or white flowers." ], "failure_modes_and_hazards": [ "Toxic exposure through ingestion or inhalation of dust.", "Variable purity giving inconsistent results." ], "standards_and_regulation": [ "Globally Harmonized System of Classification and Labelling of Chemicals (GHS), United Nations." ], "what_it_is_for": [ "Digitonin is encountered in cell biology and biochemistry laboratories as a reagent for working with cholesterol-containing membranes.", "Researchers use it to permeabilize cells or extract membrane components when the preparation must retain features needed for subsequent analysis." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q410968: digitonin", "url": "https://www.wikidata.org/wiki/Q410968", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Digitonin", "url": "https://en.wikipedia.org/wiki/Digitonin", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "digitonin-identity", "name": "Digitonin identity", "description": "Establish which molecular entity the registered name denotes.", "rationale": "Similar Digitalis-derived names and variable reagent descriptions can conceal a different substance or mixture.", "layers": [ { "id": "molecular-recognition", "name": "Molecular recognition", "description": "Recognize digitonin through structure and concordant identifiers.", "findings": [ { "id": "intact-glycoside-identity", "name": "Intact glycoside identity", "description": "Require evidence that identifies the intact digitonin glycoside rather than only its origin or aglycone.", "questions": [ { "text": "Which structural reference defines digitonin's stereochemistry and sugar connectivity?", "kind": "definition", "id": "intact-glycoside-identity-q01" }, { "text": "Which analytical observations distinguish intact digitonin from digitogenin and related glycosides?", "kind": "measurement", "id": "intact-glycoside-identity-q02" } ] } ] }, { "id": "registry-and-neighbour-boundaries", "name": "Registry and neighbour boundaries", "description": "Keep identifiers and adjacent chemical entities distinct.", "findings": [ { "id": "identifier-concordance", "name": "Identifier concordance", "description": "Reconcile registry, supplier, and chemical database records without treating every database number as a compound identifier.", "questions": [ { "text": "Do the CAS, EC, structure, and compound database record refer to the same digitonin entity?", "kind": "provenance", "id": "identifier-concordance-q01" }, { "text": "Does a cited identifier denote digitonin itself, a supplier substance record, or a formulated solution?", "kind": "boundary", "id": "identifier-concordance-q02" } ] } ] } ] }, { "id": "digitonin-preparation-quality", "name": "Digitonin preparation quality", "description": "Describe the composition and performance evidence of an actual preparation.", "rationale": "A digitonin label does not establish concentration accuracy or interchangeable membrane activity across lots.", "layers": [ { "id": "composition-and-assay", "name": "Composition and assay", "description": "Establish what fraction of the material is digitonin and how that was measured.", "findings": [ { "id": "purity-basis", "name": "Purity basis", "description": "Interpret assay values alongside water, residual solvents, and related components.", "questions": [ { "text": "Is the reported purity a mass fraction, chromatographic area percentage, or another assay result?", "kind": "measurement", "id": "purity-basis-q01" }, { "text": "Which related saponins, degradation products, water, or residual solvents are quantified?", "kind": "measurement", "id": "purity-basis-q02" } ] } ] }, { "id": "lot-fitness", "name": "Lot fitness", "description": "Connect traceable preparation history to a defined digitonin use.", "findings": [ { "id": "functional-lot-acceptance", "name": "Functional lot acceptance", "description": "Separate chemical identity acceptance from suitability for a particular membrane or cholesterol assay.", "questions": [ { "text": "Which certificate and preparation history support the identity and grade of this lot?", "kind": "provenance", "id": "functional-lot-acceptance-q01" }, { "text": "What reference assay and acceptance threshold establish this lot's fitness for the intended digitonin application?", "kind": "action", "id": "functional-lot-acceptance-q02" } ] } ] } ] }, { "id": "digitonin-physical-state", "name": "Digitonin physical state", "description": "Track dissolution, aggregation, and physical changes that affect usable digitonin.", "rationale": "Weighed digitonin and digitonin available in a working solution need not be equivalent.", "layers": [ { "id": "dissolution-and-aggregation", "name": "Dissolution and aggregation", "description": "Describe concentration and solution behavior under explicit conditions.", "findings": [ { "id": "available-solution-concentration", "name": "Available solution concentration", "description": "Distinguish nominal loading, dissolved material, aggregates, and visible precipitate.", "questions": [ { "text": "What solvent, buffer, temperature, and equilibration conditions support the stated dissolved concentration?", "kind": "measurement", "id": "available-solution-concentration-q01" }, { "text": "What evidence distinguishes undissolved digitonin from aggregation or precipitation after dilution?", "kind": "measurement", "id": "available-solution-concentration-q02" } ] } ] }, { "id": "thermal-and-storage-behavior", "name": "Thermal and storage behavior", "description": "Assess whether preparation and storage preserve usable digitonin.", "findings": [ { "id": "state-change-versus-degradation", "name": "State change versus degradation", "description": "Record physical and chemical evidence separately when a preparation changes during heating or storage.", "questions": [ { "text": "Which reported thermal values distinguish melting from decomposition for the characterized material?", "kind": "measurement", "id": "state-change-versus-degradation-q01" }, { "text": "Which storage duration, temperature, and solvent conditions preserve the stock's concentration and assay performance?", "kind": "action", "id": "state-change-versus-degradation-q02" } ] } ] } ] }, { "id": "cholesterol-dependent-function", "name": "Cholesterol-dependent function", "description": "Represent cholesterol interaction and its consequences for membrane experiments.", "rationale": "Digitonin interacts with membrane cholesterol and can permeabilize or solubilize membranes; useful selectivity must be established under the intended conditions. [Sigma-Aldrich](https://www.sigmaaldrich.com/US/en/product/sigma/d141)", "layers": [ { "id": "sterol-interaction", "name": "Sterol interaction", "description": "Characterize the chemical interaction separately from whole-cell outcomes.", "findings": [ { "id": "cholesterol-complexation", "name": "Cholesterol complexation", "description": "Digitonin is used as a cholesterol-precipitating reagent; the model must retain the conditions and analytical endpoint of that use. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/Digitonin)", "questions": [ { "text": "Under which solvent, concentration, and temperature conditions is cholesterol complexation or precipitation demonstrated?", "kind": "measurement", "id": "cholesterol-complexation-q01" }, { "text": "Which other sterols or sample components interfere with the intended cholesterol measurement?", "kind": "boundary", "id": "cholesterol-complexation-q02" } ] } ] }, { "id": "membrane-selectivity", "name": "Membrane selectivity", "description": "Describe the experimentally supported window between useful access and excessive membrane disruption.", "findings": [ { "id": "permeabilization-window", "name": "Permeabilization window", "description": "Treat selective permeabilization as an observed relationship among the preparation, membrane system, and exposure conditions.", "questions": [ { "text": "At what digitonin concentration, exposure time, temperature, and specimen loading is the required permeability achieved?", "kind": "measurement", "id": "permeabilization-window-q01" }, { "text": "Which paired measurements establish target-membrane access and retention of the required organelle integrity?", "kind": "measurement", "id": "permeabilization-window-q02" }, { "text": "What observed endpoint requires reducing exposure or rejecting the preparation for this use?", "kind": "action", "id": "permeabilization-window-q03" } ] } ] }, { "id": "solubilization-and-assay-effects", "name": "Solubilization and assay effects", "description": "Separate membrane-component extraction from preservation of downstream function.", "findings": [ { "id": "extraction-fitness", "name": "Extraction fitness", "description": "Assess whether digitonin exposure yields material compatible with the intended biochemical measurement.", "questions": [ { "text": "Which measurements establish extraction yield and preservation of the target protein or complex's required activity?", "kind": "measurement", "id": "extraction-fitness-q01" }, { "text": "Does residual digitonin alter the downstream readout, and what evidence establishes an acceptable residual level?", "kind": "action", "id": "extraction-fitness-q02" } ] } ] } ] }, { "id": "digitonin-handling-constraints", "name": "Digitonin handling constraints", "description": "Attach evidence-based handling decisions to digitonin powder and its preparations.", "rationale": "Descriptions of mild detergency do not establish occupational safety, and solution hazards also depend on the solvent.", "layers": [ { "id": "hazard-evidence", "name": "Hazard evidence", "description": "Resolve applicable classifications and exposure information for the material in hand.", "findings": [ { "id": "preparation-specific-hazards", "name": "Preparation-specific hazards", "description": "Keep digitonin hazard evidence distinct from solvent hazards and undocumented assumptions about toxicity.", "questions": [ { "text": "Which current supplier SDS and jurisdiction establish the hazard classification of this digitonin preparation?", "kind": "provenance", "id": "preparation-specific-hazards-q01" }, { "text": "Are digitonin-specific exposure limits established, absent, or simply not yet checked?", "kind": "provenance", "id": "preparation-specific-hazards-q02" } ] } ] }, { "id": "handling-and-disposition", "name": "Handling and disposition", "description": "Translate the preparation's state and documentation into practical controls.", "findings": [ { "id": "powder-stock-and-waste-controls", "name": "Powder, stock, and waste controls", "description": "Select controls for weighing, solution preparation, storage, and contaminated waste using the actual preparation and use context.", "questions": [ { "text": "What documented controls apply when weighing digitonin powder or preparing stocks in the selected solvent?", "kind": "action", "id": "powder-stock-and-waste-controls-q01" }, { "text": "How do digitonin, solvent, and biological contaminants jointly determine the applicable waste route?", "kind": "action", "id": "powder-stock-and-waste-controls-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "This is recalled information, not a source-verified record.", "Check product-specific purity, solubility and effective permeabilization conditions before applying a protocol.", "Verify current hazard classifications and jurisdiction-specific requirements against the relevant supplier safety data sheet." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of digitonin 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": "CAS Registry Number", "value_or_pattern": "110-27-0", "note": "Identifies digitonin; commercial preparations can differ in purity." }, { "scheme": "Molecular formula", "value_or_pattern": "C56H92O29", "note": "Composition of the digitonin molecule, not a unique structural identifier." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of digitonin 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": [ "Selective permeabilization of cholesterol-rich plasma membranes in cell biology experiments.", "Solubilization of membrane proteins and protein complexes for biochemical analysis.", "Preparation of permeabilized cells for mitochondrial function assays.", "Precipitation of cholesterol as a digitonin complex in classical analytical methods." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of digitonin 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": "Molar mass", "typical_range": "Approximately 1229.3", "unit": "g/mol" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of digitonin 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": [ "Can disrupt cell membranes and cause haemolysis.", "Excessive concentration or exposure can damage intracellular membranes and compromise experimental selectivity.", "Membrane cholesterol content affects susceptibility, so a treatment effective for one cell type may fail in another.", "Insufficient dissolution or variation in preparation purity can produce inconsistent experimental results." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of digitonin 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": "Digitoxigenin", "difference": "Digitoxigenin is a cardiac glycoside aglycone; digitonin is a sugar-bearing steroidal saponin." }, { "name": "Digitoxin", "difference": "Digitoxin is a cardiac glycoside acting on sodium-potassium ATPase; digitonin is principally used for its cholesterol-dependent membrane effects." }, { "name": "Digitogenin", "difference": "Digitogenin is the steroidal aglycone of digitonin; digitonin additionally contains its attached sugar chain." }, { "name": "Saponin", "difference": "Saponin names a broad class of glycosides; digitonin is a particular member with a defined molecular structure." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of digitonin this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which structural reference resolves legacy or conflicting digitonin database identifiers without conflating compound and supplier substance records?", "How much do related saponins, water content, and preparation method vary across available grades, and which differences change functional potency?", "What measured solubility, aggregation, thermal behavior, and stock stability apply under the intended working conditions?", "Which specimen-specific exposure window achieves the required permeability while preserving the organelles or protein complexes relevant to the task?", "What current jurisdiction-specific hazard classification, exposure-limit status, and disposal requirements apply to the selected preparation?" ], "statistics": { "bundles": 6, "layers": 12, "findings": 17, "questions": 29 } }