{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:43:42Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 20.2, "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: 01a0956c-e30f-7802-ab29-72200284c6fd\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: Oil Red O\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 044: 1001 regis", "usd": 0.0, "recall": true }, "codex": { "seconds": 86.3, "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: 01a0956c-e31a-7463-89e1-0a1698b7010c\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: Oil Red O\nRegistry id: vr.tr.oil-red-o\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": "2026-10-06T08:52:08+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:25+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q132442", "registryId": "vr.tr.oil-red-o", "name": "Oil Red O", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q132442/", "model": { "registry_id": "vr.tr.oil-red-o", "name": "Oil Red O", "purpose": "Enable an agent to identify Oil Red O, assess the condition and fitness of a particular grade or preparation, and decide whether it is suitable for an intended lipid-staining use.", "definition": "Oil Red O is a fat-soluble bisazo dye used to visualize neutral lipids in biological specimens by preferentially partitioning into lipid-rich regions.", "scope_statement": "This model owns Oil Red O as the registered chemical substance vr.tr.oil-red-o in PHY / PHY.MAT, including identity, grade, physical condition, preparation-dependent behavior, staining suitability, and handling constraints.", "in_scope": [ "Chemical identity and verified identifiers for Oil Red O", "Dye content, impurities, grade, and lot-specific evidence", "Physical properties and dissolution behavior under recorded conditions", "Condition and suitability of Oil Red O in stock and working preparations", "Lipid-staining performance and limits on interpreting its signal", "Substance-specific handling, storage, and disposal constraints" ], "out_of_scope": [ "Commercial staining kits and their complete formulations", "Full tissue-processing and staining protocols", "Biological specimens and the diseases they may represent", "Microscope hardware and image-analysis software", "Manufacturing processes for azo dyes", "Independent substance models for solvents, counterstains, and alternative dyes" ], "distinguishing_features": [ "Match the name to CAS 1320-06-5, Colour Index 26125, and the synonym Solvent Red 27; a red appearance alone cannot establish identity. [Supplier identity record](https://www.sigmaaldrich.com/US/en/product/sial/o0625)", "Check the declared structure against formula C26H24N4O and molar mass 408.49 g/mol to distinguish similarly named dyes. [Supplier identity record](https://www.sigmaaldrich.com/US/en/product/sial/o0625)", "Distinguish the lipid-localizing lysochrome, reported to produce red-orange staining, from an arbitrary red colorant. [Supplier description](https://www.sigmaaldrich.com/US/en/product/sial/o0625)", "Separate the identified dye from a bottle of Oil Red O solution by checking solvent composition, concentration, and additives.", "Distinguish dye identity from staining qualification: a supplier's certified grade or dye-content specification applies to that product, not automatically to every Oil Red O sample." ], "characteristics": [ { "name": "Verified chemical identity", "kind": "relation", "unit_or_values": "Registry entry linked to verified structure, CAS, Colour Index, EC, and PubChem records", "why_it_matters": "Prevents substitution with another red dye and confusion between compound and supplier substance records." }, { "name": "Dye content and analytical purity", "kind": "measurement", "unit_or_values": "% with assay method, reporting basis, uncertainty, and lot", "why_it_matters": "Dye content and chemical purity need not mean the same thing and affect preparation comparability." }, { "name": "Staining grade", "kind": "category", "unit_or_values": "Certified for a named method, supplier-qualified, unqualified, or unknown", "why_it_matters": "Connects suitability claims to their actual evidence and application." }, { "name": "Preparation concentration", "kind": "measurement", "unit_or_values": "mg/mL, g/L, or explicitly defined % w/v; nominal or measured", "why_it_matters": "Allows preparations to be compared without confusing added powder with dissolved dye." }, { "name": "Solvent environment", "kind": "relation", "unit_or_values": "Solvent identities, proportions, water content, and temperature", "why_it_matters": "Makes dissolution and staining behavior interpretable." }, { "name": "Dissolution and particulate condition", "kind": "state", "unit_or_values": "Solid, dissolved, suspended, visibly precipitated, or unassessed", "why_it_matters": "Supports assessment of whether apparent staining could include deposited particles." }, { "name": "Thermal behavior", "kind": "measurement", "unit_or_values": "°C with event type, method, pressure where relevant, and decomposition flag", "why_it_matters": "Avoids treating a decomposition-associated transition as a clean melting or boiling point." }, { "name": "Optical response", "kind": "measurement", "unit_or_values": "Absorption wavelength in nm and absorbance with solvent, concentration, and path length", "why_it_matters": "Supports preparation checks and method-specific readout selection." }, { "name": "Staining control performance", "kind": "state", "unit_or_values": "Pass, fail, or indeterminate against recorded positive and negative control criteria", "why_it_matters": "Makes reagent suitability an observed result rather than an assumption." }, { "name": "Applicable hazard evidence", "kind": "relation", "unit_or_values": "Current SDS linked to material form, supplier, jurisdiction, and revision date", "why_it_matters": "Keeps powder-specific constraints distinct from hazards introduced by a solvent preparation." } ], "affordances": [ "Resolve an Oil Red O label to verified chemical and supplier records.", "Compare lots for an intended staining method using assay and qualification evidence.", "Calculate a nominal preparation concentration while retaining dye-content and dissolution uncertainty.", "Assess a stock or working preparation for precipitation and method-specific usability.", "Qualify lipid-staining observations using reagent controls and specimen-processing history.", "Select handling, storage, and waste-routing actions supported by the applicable material documentation." ], "agent_conduct": { "may": [ "Explain Oil Red O as a lipid stain used in histology and cell biology.", "Report hazards and handling information from safety data sheets." ], "must_not": [ "Present a stain result as a diagnosis without a qualified reviewer.", "Dispose of solvent-based stain solutions into drains.", "Use the dye in food or cosmetics.", "Handle stain powders without the protection the safety data sheet requires." ], "requires_human": [ "Using stained slides in a clinical diagnosis for a patient." ] }, "ethics": { "considerations": [ "Laboratory findings feed patient and research decisions; errors matter.", "Solvent and dye waste can harm the environment." ], "affected_parties": [ "Patients whose samples are stained", "Laboratory workers", "Researchers" ] }, "owners": { "steward": "The laboratory or business that holds it; chemical safety authorities regulate supply and use.", "master_systems": [] }, "visual_identification": [ "A dark red powder; stains lipid droplets bright red under the microscope.", "Usually prepared as a solution in an organic solvent." ], "failure_modes_and_hazards": [ "Flammable solvents in stain solutions.", "Staining artefacts leading to misread results.", "Skin and eye irritation." ], "standards_and_regulation": [ "Globally Harmonized System of Classification and Labelling of Chemicals (GHS), United Nations." ], "what_it_is_for": [ "This dye is encountered in histology and cell biology laboratories for visualizing neutral lipid deposits in biological specimens.", "It is commonly used with frozen tissue sections and cultured cells when specimen preparation preserves the lipids of interest.", "The resulting staining supports assessment of lipid distribution and accumulation in research and diagnostic investigations." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q132442: Oil Red O", "url": "https://www.wikidata.org/wiki/Q132442", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Oil Red O", "url": "https://en.wikipedia.org/wiki/Oil_Red_O", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "oil-red-o-identity", "name": "Oil Red O identity", "description": "Establish which chemical the name denotes and separate it from related dyes and formulated products.", "rationale": "Color, trade names, and staining purpose are insufficient to establish Oil Red O identity.", "layers": [ { "id": "chemical-name-resolution", "name": "Chemical name resolution", "description": "Connect the registry entry to independently identifiable chemical records.", "findings": [ { "id": "identifier-agreement", "name": "Identifier agreement", "description": "Record whether identifiers and structural evidence consistently identify the same dye.", "questions": [ { "text": "Which authoritative records connect Oil Red O, Solvent Red 27, and the declared chemical structure?", "kind": "definition", "id": "identifier-agreement-q01" }, { "text": "Do CAS, EC, Colour Index, and PubChem records agree, and is each PubChem identifier a CID or an SID?", "kind": "provenance", "id": "identifier-agreement-q02" } ] } ] }, { "id": "dye-product-boundary", "name": "Dye and product boundary", "description": "Separate the substance from neighboring dyes, grades, and ready-to-use solutions.", "findings": [ { "id": "material-being-identified", "name": "Material being identified", "description": "Determine whether an observed item is the dye, a grade of the dye, or a formulation containing it.", "questions": [ { "text": "Does this label identify Oil Red O powder, a stock solution, a working stain, or a kit component?", "kind": "boundary", "id": "material-being-identified-q01" }, { "text": "What evidence excludes confusion with Sudan III, Sudan IV, or another red solvent dye?", "kind": "definition", "id": "material-being-identified-q02" } ] } ] } ] }, { "id": "dye-grade-and-composition", "name": "Dye grade and composition", "description": "Describe what a particular Oil Red O lot contains and what its qualification demonstrates.", "rationale": "A chemically matching name does not establish equivalent dye strength or staining fitness.", "layers": [ { "id": "assay-and-impurities", "name": "Assay and impurities", "description": "Capture lot-specific composition with the meaning of each reported assay.", "findings": [ { "id": "effective-dye-content", "name": "Effective dye content", "description": "Keep dye-content measurements, purity measurements, and unspecified material fractions distinct.", "questions": [ { "text": "What dye content and chemical purity are reported for this lot, using which methods and reporting bases?", "kind": "measurement", "id": "effective-dye-content-q01" }, { "text": "Which impurities, residual solvents, or unidentified fractions are documented, and could they affect staining?", "kind": "provenance", "id": "effective-dye-content-q02" } ] } ] }, { "id": "stain-qualification", "name": "Stain qualification", "description": "Limit certification and suitability claims to the applications actually evaluated.", "findings": [ { "id": "qualification-coverage", "name": "Qualification coverage", "description": "Connect a grade or certification claim to its method, lot coverage, and acceptance criteria.", "questions": [ { "text": "Which staining method and performance criteria does the certification or supplier qualification cover?", "kind": "provenance", "id": "qualification-coverage-q01" }, { "text": "What additional comparison is required before this lot can replace the lot used in an established method?", "kind": "action", "id": "qualification-coverage-q02" } ] } ] } ] }, { "id": "physical-and-solution-behavior", "name": "Physical and solution behavior", "description": "Represent Oil Red O properties with the conditions needed to apply them.", "rationale": "Powder properties and solvent-dependent behavior govern whether a usable stain can be prepared.", "layers": [ { "id": "solid-state-properties", "name": "Solid-state properties", "description": "Describe the received solid and the evidence for its thermal characteristics.", "findings": [ { "id": "solid-and-thermal-evidence", "name": "Solid and thermal evidence", "description": "Distinguish observed physical condition from literature properties and unresolved thermal behavior.", "questions": [ { "text": "What appearance, physical form, and signs of contamination or change are recorded for the received material?", "kind": "measurement", "id": "solid-and-thermal-evidence-q01" }, { "text": "Which reported thermal transitions involve decomposition, and is any boiling-point claim experimentally supported?", "kind": "provenance", "id": "solid-and-thermal-evidence-q02" } ] } ] }, { "id": "solvent-dependent-properties", "name": "Solvent-dependent properties", "description": "Capture dissolution and optical measurements in a specified solvent environment.", "findings": [ { "id": "conditional-dissolution-and-absorption", "name": "Conditional dissolution and absorption", "description": "Treat solubility and spectral observations as conditional measurements rather than universal constants.", "questions": [ { "text": "At what solvent composition and temperature was the reported dissolved concentration established?", "kind": "measurement", "id": "conditional-dissolution-and-absorption-q01" }, { "text": "What absorption spectrum was measured, with which concentration, path length, solvent blank, and particulate checks?", "kind": "measurement", "id": "conditional-dissolution-and-absorption-q02" } ] } ] } ] }, { "id": "working-stain-condition", "name": "Working stain condition", "description": "Track the Oil Red O component through preparation, dilution, storage, and usability assessment.", "rationale": "The nominal amount of dye added does not establish the condition of the stain at use.", "layers": [ { "id": "preparation-lineage", "name": "Preparation lineage", "description": "Connect stock and working preparations to their originating dye lot and preparation record.", "findings": [ { "id": "concentration-traceability", "name": "Concentration traceability", "description": "Record how concentration was calculated and whether it represents powder added or dye dissolved.", "questions": [ { "text": "Which dye lot, weighed amount, solvent composition, final volume, and preparation date produced this stock?", "kind": "provenance", "id": "concentration-traceability-q01" }, { "text": "Does the stated working concentration account for dilution, dye content, and any undissolved material?", "kind": "measurement", "id": "concentration-traceability-q02" } ] } ] }, { "id": "precipitation-and-use-status", "name": "Precipitation and use status", "description": "Assess physical changes and method-specific evidence for continued usability.", "findings": [ { "id": "preparation-acceptability", "name": "Preparation acceptability", "description": "Record particulate observations, treatment history, and the criteria for accepting or rejecting a preparation.", "questions": [ { "text": "What precipitation, deposits, or optical changes appeared after preparation, dilution, or storage?", "kind": "measurement", "id": "preparation-acceptability-q01" }, { "text": "Under the applicable method, should this preparation be filtered, requalified, remade, or discarded?", "kind": "action", "id": "preparation-acceptability-q02" } ] } ] } ] }, { "id": "lipid-staining-fitness", "name": "Lipid-staining fitness", "description": "Define when Oil Red O staining is informative and how its signal can be misinterpreted.", "rationale": "Reagent performance, lipid preservation, and readout validation jointly determine what a staining result supports.", "layers": [ { "id": "target-and-specimen-compatibility", "name": "Target and specimen compatibility", "description": "Link intended lipid detection to evidence about the target and specimen-processing history.", "findings": [ { "id": "accessible-lipid-target", "name": "Accessible lipid target", "description": "Require evidence that the intended lipid target remains available and is detectable by the selected method.", "questions": [ { "text": "Which lipid classes or lipid-containing structures does the selected Oil Red O method demonstrably detect?", "kind": "boundary", "id": "accessible-lipid-target-q01" }, { "text": "Could fixation, dehydration, embedding, or solvent exposure have removed or redistributed the target lipid?", "kind": "provenance", "id": "accessible-lipid-target-q02" } ] } ] }, { "id": "signal-controls-and-interpretation", "name": "Signal controls and interpretation", "description": "Separate reagent qualification and observed color from justified biological or quantitative conclusions.", "findings": [ { "id": "credible-staining-signal", "name": "Credible staining signal", "description": "Assess controls, particulate artifacts, background, and any calibration supporting interpretation.", "questions": [ { "text": "Do positive, negative, and reagent controls distinguish lipid-associated staining from background or dye deposits?", "kind": "measurement", "id": "credible-staining-signal-q01" }, { "text": "What calibration, extraction recovery, normalization, and linear-range evidence supports any conversion of signal into lipid quantity?", "kind": "measurement", "id": "credible-staining-signal-q02" }, { "text": "Which conclusions remain unsupported by this Oil Red O result alone?", "kind": "boundary", "id": "credible-staining-signal-q03" } ] } ] } ] }, { "id": "handling-and-lifecycle", "name": "Handling and lifecycle", "description": "Connect actions on Oil Red O to material-specific safety evidence and storage history.", "rationale": "The dye powder and its solvent preparations require separately grounded handling decisions.", "layers": [ { "id": "form-specific-hazards", "name": "Form-specific hazards", "description": "Identify applicable classifications and exposure controls for the actual material being handled.", "findings": [ { "id": "applicable-safety-record", "name": "Applicable safety record", "description": "Keep documented hazards, missing data, and formulation-derived hazards distinguishable.", "questions": [ { "text": "Which current SDS and jurisdiction apply to this Oil Red O powder or preparation, and what classifications do they state?", "kind": "provenance", "id": "applicable-safety-record-q01" }, { "text": "What controls address dye dust, solvent exposure, and spills for the intended operation, and are any exposure limits specifically established?", "kind": "action", "id": "applicable-safety-record-q02" } ] } ] }, { "id": "storage-and-retirement", "name": "Storage and retirement", "description": "Determine whether retained material remains usable and how spent material should be routed.", "findings": [ { "id": "remaining-fitness-and-waste-route", "name": "Remaining fitness and waste route", "description": "Use documented storage conditions, qualification results, and waste composition to decide the next action.", "questions": [ { "text": "What storage conditions and usable-life evidence apply separately to this powder, stock solution, and working stain?", "kind": "provenance", "id": "remaining-fitness-and-waste-route-q01" }, { "text": "Which disposal route applies to the dye, spent solvent stain, and contaminated materials under local requirements?", "kind": "action", "id": "remaining-fitness-and-waste-route-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 description is recalled knowledge; no sources were consulted.", "Verify identifiers, purity, dye content, and suitability against the specific supplier's documentation before publication or experimental use.", "Melting point, absorption maximum, exposure limits, and jurisdiction-specific hazard classifications are omitted because they require verification." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of Oil Red O 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": "1320-06-5", "note": "Identifier for Oil Red O; prepared staining solutions also contain solvents." }, { "scheme": "Colour Index Generic Name", "value_or_pattern": "C.I. Solvent Red 27", "note": "Colour Index designation for the dye." }, { "scheme": "Colour Index Constitution Number", "value_or_pattern": "26125", "note": "Constitution number associated with Oil Red O." }, { "scheme": "Molecular formula", "value_or_pattern": "C26H24N4O", "note": "Formula of the dye molecule, not of a formulated staining reagent." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of Oil Red O 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": [ "Staining neutral lipid deposits in frozen tissue sections.", "Visualizing intracellular lipid droplets in cultured cells.", "Assessing lipid accumulation during experimental adipocyte differentiation.", "Visualizing lipid-rich lesions in experimental atherosclerosis studies." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of Oil Red O 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": "408.49", "unit": "g/mol" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of Oil Red O 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": [ "Routine paraffin-processing solvents can extract lipids, making conventional processed sections unsuitable for demonstrating the original neutral lipid distribution.", "Dye precipitation can produce deposits that resemble stained lipid droplets.", "Staining intensity depends on preparation and imaging conditions and is not automatically an absolute measure of lipid mass.", "Oil Red O staining alone does not identify individual lipid species.", "Alcohol-containing staining formulations may be flammable; hazards must be assessed for the actual formulation." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of Oil Red O 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": "Sudan IV", "difference": "A related lipid-soluble azo dye with a different chemical identity; shared lipid-staining use does not make the dyes interchangeable." }, { "name": "Nile red", "difference": "A fluorescent lipid probe, whereas Oil Red O is ordinarily read through visible red coloration in bright-field imaging." }, { "name": "Oil Red O staining solution", "difference": "A formulation containing the dye and solvents; concentration, solvent composition, and preparation determine its staining performance and hazards." }, { "name": "Triglycerides", "difference": "Neutral lipids that can take up the dye; they are staining targets rather than the colorant." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of Oil Red O this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which authoritative compound record confirms the PubChem CID and reconciles structural representations and synonyms for the registry entry?", "How do dye-content assays, chemical purity, impurity profiles, and staining qualification compare across available Oil Red O grades?", "Which solubility, absorption, and thermal measurements have sufficient method and condition detail to serve as reference properties?", "For each intended specimen and readout, what lipid selectivity, processing compatibility, control criteria, and quantitative calibration are experimentally supported?", "What current jurisdiction-specific hazard classifications, exposure-limit evidence, and validated storage lifetimes apply to the selected powder and solvent preparations?" ], "statistics": { "bundles": 7, "layers": 13, "findings": 18, "questions": 31 } }