{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:36:56Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 20.4, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09566-de79-7df3-b25c-616b225139f6\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: nitroxoline\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 reg", "usd": 0.0, "recall": true }, "codex": { "seconds": 74.2, "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: 01a09566-de87-79b2-aac2-56f516f452e4\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: nitroxoline\nRegistry id: vr.tr.nitroxoline\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\n" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:50:01+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:29+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q304570", "registryId": "vr.tr.nitroxoline", "name": "nitroxoline", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q304570/", "model": { "registry_id": "vr.tr.nitroxoline", "name": "nitroxoline", "purpose": "Enable an agent to identify nitroxoline, assess the quality and chemical state of a sample, and determine whether evidence supports its intended handling or use.", "definition": "Nitroxoline is 5-nitroquinolin-8-ol, a synthetic nitro-substituted 8-hydroxyquinoline with metal-chelating and antimicrobial activity, used as an antibacterial medicine for urinary tract infections in some countries.", "scope_statement": "This model owns nitroxoline as the chemical substance registered under vr.tr.nitroxoline in PHY / PHY.MAT, including molecular identity, material quality, condition-dependent properties, biological activity evidence, and applicable handling constraints.", "in_scope": [ "Molecular identity and differentiation from related hydroxyquinolines", "Sample composition, purity, grade, and analytical verification", "Solid-state properties, dissolution, ionization, and metal association", "Nitroxoline-specific biological activity and the conditions supporting each claim", "Substance hazard evidence, storage requirements, and jurisdiction-specific identity" ], "out_of_scope": [ "Finished medicinal products, excipients, packaging, and brand identity", "Patient diagnosis, prescribing, dosing, and treatment selection", "Manufacturing processes and production equipment", "Independent models of nitroxoline derivatives, metabolites, and isolated metal complexes", "Organisms, infections, and assay platforms except as linked experimental context" ], "distinguishing_features": [ "The molecular structure must be quinolin-8-ol bearing a nitro group at position 5; a generic hydroxyquinoline label is insufficient. Identity reference: [PubChem Nitroxoline](https://pubchem.ncbi.nlm.nih.gov/compound/Nitroxoline).", "The neutral parent has formula C9H6N2O3 and molar mass 190.16 g/mol, with CAS 4008-48-4 and PubChem CID 19910; matching identifiers should be corroborated by structure. Reference: [PubChem Nitroxoline](https://pubchem.ncbi.nlm.nih.gov/compound/Nitroxoline).", "Structural analysis must distinguish the 5-nitro substituent from a nitroso substituent and confirm that the 8-hydroxyl group is present.", "An identified nitroxoline constituent does not make an entire tablet, mixture, conjugate, or metal complex equivalent to the parent substance." ], "characteristics": [ { "name": "Structural identity", "kind": "category", "unit_or_values": "Verified connection table and structure identifiers for 5-nitroquinolin-8-ol", "why_it_matters": "Prevents confusion with positional isomers and related quinoline compounds." }, { "name": "Material form", "kind": "category", "unit_or_values": "Neutral parent; ionized species in solution; characterized solid form; mixture containing nitroxoline", "why_it_matters": "Determines which identity, property, and concentration statements apply." }, { "name": "Nitroxoline assay", "kind": "measurement", "unit_or_values": "% w/w with as-is or dry basis; chromatographic area % recorded separately", "why_it_matters": "Supports quantity calculations without treating chromatographic purity as absolute content." }, { "name": "Impurity profile", "kind": "measurement", "unit_or_values": "Individual and total impurities in % w/w or mg/kg, with method and detection limits", "why_it_matters": "Distinguishes intended nitroxoline activity from effects or hazards of contaminants." }, { "name": "Material grade", "kind": "category", "unit_or_values": "Reference standard; research reagent; pharmaceutical substance meeting a named specification; unspecified", "why_it_matters": "Connects suitability to documented specifications and intended use." }, { "name": "Thermal behavior", "kind": "measurement", "unit_or_values": "Melting or decomposition interval in °C with method, atmosphere, and solid form", "why_it_matters": "Supports identity and processing decisions while distinguishing melting from decomposition." }, { "name": "Solubility", "kind": "measurement", "unit_or_values": "mg/mL or mol/L with solvent composition, pH, temperature, and equilibration method", "why_it_matters": "Determines whether a stated preparation concentration is achievable and remains dissolved." }, { "name": "Ionization behavior", "kind": "measurement", "unit_or_values": "pKa values with assigned equilibria, solvent, temperature, and measurement method", "why_it_matters": "Supports interpretation of pH-dependent dissolution and biological exposure." }, { "name": "Metal association", "kind": "relation", "unit_or_values": "Metal species, stoichiometry, free and bound fractions, and supporting evidence", "why_it_matters": "Allows evaluation of whether metal binding changes the material or assay exposure." }, { "name": "Antimicrobial activity endpoint", "kind": "measurement", "unit_or_values": "MIC or other named endpoint in mg/L or µmol/L, with organism, strain, medium, and protocol", "why_it_matters": "Makes activity claims comparable only where experimental conditions support comparison." }, { "name": "Storage condition and stability", "kind": "state", "unit_or_values": "Storage history, container, temperature, light and moisture exposure, retest date, and degradation evidence", "why_it_matters": "Determines whether previous analytical results still describe the available material." }, { "name": "Applicable hazard and regulatory record", "kind": "relation", "unit_or_values": "Dated source, jurisdiction, substance identifier, classification, exposure limit if established, and applicability", "why_it_matters": "Prevents transferring product-specific or foreign requirements to the wrong substance context." } ], "affordances": [ "Match a registry or supplier record to nitroxoline using structural and identifier evidence.", "Assess whether a lot meets a named purity and grade specification for an intended use.", "Calculate nitroxoline quantities from verified assay values and the correct material form.", "Evaluate preparation feasibility using condition-matched solubility, pH, and stability evidence.", "Compare biological activity results while retaining organism, medium, metal content, and endpoint context.", "Select documented handling, storage, and disposal requirements applicable to the actual material." ], "agent_conduct": { "may": [ "Identify nitroxoline from analytical data and report a sample's grade and storage history.", "Explain its authorized use as a urinary antibacterial where it is approved, citing the source." ], "must_not": [ "Recommend a dose or course of nitroxoline for a person's infection.", "Present it as authorized in a country where it is not.", "Supply or suggest using expired or unlabelled material as a medicine.", "Release antibacterial material into drains or the environment." ], "requires_human": [ "Any decision to use it to treat a person or animal.", "Disposing of quantities of the active substance." ] }, "ethics": { "considerations": [ "Misuse of antibacterials drives resistance that harms people beyond the patient.", "Patients may trust online advice over a prescriber who knows their history." ], "affected_parties": [ "Patients", "Prescribers and pharmacists", "Laboratory workers" ] }, "owners": { "steward": "The pharmacy, manufacturer or laboratory holding it; the medicines regulator authorizes medicinal use.", "master_systems": [ "National medicines registers" ] }, "visual_identification": [ "A yellow crystalline powder, which does not settle identity on its own.", "Medicinal products carry a label with the active substance and strength.", "Identity is settled by spectroscopy or chromatography against a reference standard." ], "failure_modes_and_hazards": [ "Inappropriate use contributes to antibacterial resistance.", "Wrong or counterfeit products leave an infection untreated.", "It discolours urine, which can alarm patients who were not told." ], "standards_and_regulation": [ "Globally Harmonized System of Classification and Labelling of Chemicals (GHS), United Nations." ], "what_it_is_for": [ "Nitroxoline is encountered as a pharmaceutical substance and as an antibacterial medicine for urinary tract infections in some countries.", "Laboratory research examines its antimicrobial activity and its ability to bind metal ions.", "Assessing a sample for a specified use requires distinguishing the pure compound from a formulated medicine and checking identity, purity and chemical condition." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q304570: nitroxoline", "url": "https://www.wikidata.org/wiki/Q304570", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Nitroxoline", "url": "https://en.wikipedia.org/wiki/Nitroxoline", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "nitroxoline-identity", "name": "Nitroxoline identity", "description": "Establish the exact molecular entity and its relationship to the registered substance.", "rationale": "Related quinoline names and chemically modified forms can otherwise be merged into one misleading identity.", "layers": [ { "id": "substitution-pattern", "name": "Substitution pattern", "description": "Resolve the quinoline scaffold and positions of the hydroxyl and nitro groups.", "findings": [ { "id": "parent-structure-verification", "name": "Parent structure verification", "description": "Require evidence that the assigned molecule is 5-nitroquinolin-8-ol.", "questions": [ { "text": "Does the recorded structure place the hydroxyl group at position 8 and the nitro group at position 5?", "kind": "definition", "id": "parent-structure-verification-q01" }, { "text": "Which analytical or reference evidence distinguishes this material from positional isomers and nitroso analogues?", "kind": "provenance", "id": "parent-structure-verification-q02" } ] } ] }, { "id": "identifier-and-entity-boundaries", "name": "Identifier and entity boundaries", "description": "Connect substance identifiers while separating the parent from products and derivatives.", "findings": [ { "id": "registry-identity-crosswalk", "name": "Registry identity crosswalk", "description": "Reconcile vr.tr.nitroxoline with authoritative identifiers and explicitly scoped related entities.", "questions": [ { "text": "Which read sources establish the CAS, PubChem, and any EC identifiers for the same molecular entity?", "kind": "provenance", "id": "registry-identity-crosswalk-q01" }, { "text": "Does the record describe nitroxoline itself, a formulation containing it, or a distinct conjugate or isolated complex?", "kind": "boundary", "id": "registry-identity-crosswalk-q02" } ] } ] } ] }, { "id": "nitroxoline-material-quality", "name": "Nitroxoline material quality", "description": "Determine what a particular lot contains and whether its specification supports the intended use.", "rationale": "A nitroxoline label alone does not establish active content, impurity burden, or pharmaceutical suitability.", "layers": [ { "id": "content-and-impurities", "name": "Content and impurities", "description": "Separate quantitative nitroxoline content from chromatographic purity and other constituents.", "findings": [ { "id": "lot-composition-evidence", "name": "Lot composition evidence", "description": "Record validated content measurements together with related substances, water, and residual solvents.", "questions": [ { "text": "What is the nitroxoline mass fraction, on which reporting basis, and with what analytical uncertainty?", "kind": "measurement", "id": "lot-composition-evidence-q01" }, { "text": "Which related quinoline impurities, residual solvents, water, or inorganic residues were measured, and at what detection limits?", "kind": "measurement", "id": "lot-composition-evidence-q02" } ] } ] }, { "id": "grade-and-release", "name": "Grade and release", "description": "Tie material acceptance to a named specification and traceable lot evidence.", "findings": [ { "id": "intended-use-qualification", "name": "Intended-use qualification", "description": "Assess suitability using the actual lot record and specification rather than the substance name.", "questions": [ { "text": "Which certificate, reference standard, and specification establish this lot's claimed grade?", "kind": "provenance", "id": "intended-use-qualification-q01" }, { "text": "Do the verified results permit release for the proposed analytical, research, or pharmaceutical use?", "kind": "action", "id": "intended-use-qualification-q02" } ] } ] } ] }, { "id": "nitroxoline-physical-and-solution-state", "name": "Nitroxoline physical and solution state", "description": "Describe the conditions under which measured properties apply to the available material.", "rationale": "Solid form, dissolution, ionization, and metal association can affect preparation and interpretation of nitroxoline experiments.", "layers": [ { "id": "solid-and-thermal-state", "name": "Solid and thermal state", "description": "Characterize the solid without assuming an unverified polymorph, hydrate, or thermal constant.", "findings": [ { "id": "solid-form-and-transition-evidence", "name": "Solid form and transition evidence", "description": "Associate solid-state observations and thermal events with a characterized sample.", "questions": [ { "text": "What evidence identifies the sample's crystalline or amorphous state and any solvent or water incorporation?", "kind": "measurement", "id": "solid-form-and-transition-evidence-q01" }, { "text": "Does the reported thermal event represent melting, decomposition, or both, and under which conditions?", "kind": "measurement", "id": "solid-form-and-transition-evidence-q02" } ] } ] }, { "id": "dissolution-and-speciation", "name": "Dissolution and speciation", "description": "Track dissolved concentration and chemical forms under the actual solvent and medium conditions.", "findings": [ { "id": "condition-dependent-availability", "name": "Condition-dependent availability", "description": "Distinguish nominal added nitroxoline from dissolved, ionized, or metal-associated material.", "questions": [ { "text": "What concentration remains dissolved at the specified solvent composition, pH, temperature, and elapsed time?", "kind": "measurement", "id": "condition-dependent-availability-q01" }, { "text": "What evidence establishes ionization or metal association under these conditions, and how much unbound nitroxoline remains?", "kind": "measurement", "id": "condition-dependent-availability-q02" } ] } ] } ] }, { "id": "nitroxoline-biological-evidence", "name": "Nitroxoline biological evidence", "description": "Organize substance-level activity claims with their experimental context and evidential limits.", "rationale": "Nitroxoline activity cannot be interpreted reliably from an endpoint detached from exposure conditions or extrapolated directly into clinical efficacy.", "layers": [ { "id": "antimicrobial-assay-context", "name": "Antimicrobial assay context", "description": "Make organism-specific activity measurements interpretable and comparable.", "findings": [ { "id": "activity-and-exposure-record", "name": "Activity and exposure record", "description": "Attach each antimicrobial result to the tested material, organism, method, and exposure.", "questions": [ { "text": "Which organism and strain, inoculum, medium, pH, incubation time, and endpoint define this result?", "kind": "measurement", "id": "activity-and-exposure-record-q01" }, { "text": "Were dissolved exposure, solvent effects, and medium metal content controlled sufficiently to attribute the result to nitroxoline?", "kind": "provenance", "id": "activity-and-exposure-record-q02" } ] } ] }, { "id": "mechanism-and-translation", "name": "Mechanism and translation", "description": "Separate measured biological effects, proposed mechanisms, and evidence for practical use.", "findings": [ { "id": "claim-evidence-boundaries", "name": "Claim evidence boundaries", "description": "Keep mechanistic hypotheses and investigational uses distinguishable from demonstrated outcomes.", "questions": [ { "text": "Which primary experiments support each proposed mechanism, including any contribution from metal binding?", "kind": "provenance", "id": "claim-evidence-boundaries-q01" }, { "text": "Does each claim concern a biochemical assay, planktonic growth, biofilm behavior, an animal model, or a human outcome?", "kind": "boundary", "id": "claim-evidence-boundaries-q02" } ] } ] } ] }, { "id": "nitroxoline-handling-and-permitted-use", "name": "Nitroxoline handling and permitted use", "description": "Connect the material's condition and intended use to substantiated handling and regulatory requirements.", "rationale": "Research material, bulk pharmaceutical substance, and finished medicines require distinct evidence even when they contain the same parent molecule.", "layers": [ { "id": "hazards-and-preservation", "name": "Hazards and preservation", "description": "Determine applicable hazards and preservation conditions for the actual form and lot.", "findings": [ { "id": "handling-and-stability-basis", "name": "Handling and stability basis", "description": "Base handling and continued use on dated safety information and relevant stability evidence.", "questions": [ { "text": "Which current safety data sheet and underlying evidence establish hazard classifications, exposure controls, and any applicable exposure limits?", "kind": "provenance", "id": "handling-and-stability-basis-q01" }, { "text": "What storage or solution-hold conditions are supported, and what deviations require retesting or rejection?", "kind": "action", "id": "handling-and-stability-basis-q02" } ] } ] }, { "id": "jurisdiction-and-use-status", "name": "Jurisdiction and use status", "description": "Resolve legal and quality requirements without confusing substance identity with product authorization.", "findings": [ { "id": "applicable-use-determination", "name": "Applicable use determination", "description": "Link proposed activities to dated, jurisdiction-specific records for the appropriate entity.", "questions": [ { "text": "Which authoritative records establish requirements for this substance and intended activity in the relevant jurisdiction?", "kind": "provenance", "id": "applicable-use-determination-q01" }, { "text": "Does an asserted authorization apply to bulk nitroxoline, a specific finished medicine, or only an investigational use?", "kind": "boundary", "id": "applicable-use-determination-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; no sources were consulted.", "Confirm current national authorizations, prescribing restrictions and susceptibility guidance before interpreting medicinal uses.", "Verify grade-specific purity, physical constants and chemical hazard classifications against authoritative substance records; these are omitted here." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of nitroxoline 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": "4008-48-4", "note": "Identifies nitroxoline as a chemical substance." }, { "scheme": "Molecular formula", "value_or_pattern": "C9H6N2O3", "note": "Formula of the neutral compound; not a unique structural identifier." }, { "scheme": "WHO ATC classification", "value_or_pattern": "J01XX07", "note": "Nitroxoline, classified among other antibacterials." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of nitroxoline 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": [ "Active pharmaceutical ingredient in oral medicines for urinary tract infections where authorized.", "Research compound in studies of metal chelation, antimicrobial activity and potential anticancer activity." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of nitroxoline 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": "190.16", "unit": "g/mol" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of nitroxoline 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": [ "Antibacterial treatment may fail when the infecting organism is not susceptible.", "Medicinal use can cause gastrointestinal adverse effects, including nausea.", "Hypersensitivity reactions can occur." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of nitroxoline 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": [ "Medicinal authorization, availability and approved indications differ between countries." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of nitroxoline 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": "8-hydroxyquinoline", "difference": "Nitroxoline has an additional nitro group at position 5 of the 8-hydroxyquinoline structure." }, { "name": "Nitrofurantoin", "difference": "Both are associated with urinary tract infection treatment, but nitrofurantoin is a nitrofuran compound with a different structure and pharmacology." }, { "name": "Nitroxoline-containing medicine", "difference": "Nitroxoline is the active chemical substance; a medicine containing it has a specified dose, formulation and excipients." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of nitroxoline this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which authoritative EC identifier, hazard classifications, and occupational exposure limits, if any, apply to nitroxoline in the target jurisdictions?", "Which primary measurements establish melting versus decomposition behavior, and is a meaningful boiling-point measurement available before decomposition?", "Which solid forms, pKa values, solubility measurements, and metal-binding equilibria are sufficiently characterized for the intended preparation conditions?", "Which impurity specifications, analytical methods, and stability data support research-grade versus pharmaceutical-grade lot acceptance?", "Which primary studies and current regulatory records establish the boundaries between antimicrobial assay activity, proposed mechanisms, investigational applications, and authorized medicinal use?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 17, "questions": 27 } }