{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:44:31Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 16.8, "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: 01a0956d-9f09-7232-bf51-41d6647fa717\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: oleandomycin\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 re", "usd": 0.0, "recall": true }, "codex": { "seconds": 87.0, "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: 01a0956d-9efc-7731-ae73-ac938eb4586a\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: oleandomycin\nRegistry id: vr.tr.oleandomycin\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:55:52+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "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-Q1076248", "registryId": "vr.tr.oleandomycin", "name": "oleandomycin", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q1076248/", "model": { "registry_id": "vr.tr.oleandomycin", "name": "oleandomycin", "purpose": "Enable an agent to identify oleandomycin, assess the identity, quality and activity of a particular sample, and determine its suitability for a specified use.", "definition": "Oleandomycin is a macrolide antibiotic produced by Streptomyces antibioticus, with a 14-membered lactone ring bearing sugar residues, that inhibits bacterial protein synthesis through interaction with the 50S ribosomal subunit.", "scope_statement": "This model owns vr.tr.oleandomycin in PHY / PHY.MAT: the chemically defined substance and the evidence needed to interpret its material forms, analytical condition and antibacterial activity, with explicit links to salts, derivatives and products.", "in_scope": [ "Oleandomycin molecular identity, stereochemistry and identifier reconciliation.", "Sample composition, purity, grade and oleandomycin content on a stated basis.", "Physical form, solution conditions and evidence of stability or degradation.", "Measured antibacterial activity with organism, assay and reference-standard context.", "Substance-specific handling evidence and jurisdiction-specific restrictions relevant to a proposed use." ], "out_of_scope": [ "Finished medicines, combination products, packaging and their complete formulations.", "Patient diagnosis, prescribing, dosing and treatment selection.", "Standalone models of troleandomycin, erythromycin and covalently modified oleandomycin derivatives.", "Production-organism biology and fermentation-process design.", "Complete models of bacterial species, infections and resistance mechanisms." ], "distinguishing_features": [ "Require a stereochemical structure match to InChIKey RZPAKFUAFGMUPI-QESOVKLGSA-N; the neutral formula C35H61NO12 alone does not establish identity. [ChEBI](https://www.ebi.ac.uk/chebi/CHEBI:16869)", "Distinguish the neutral substance from protonated oleandomycin and counterion-containing material by charge, counterion identification and composition. ChEBI separately identifies its conjugate acid. [ChEBI](https://www.ebi.ac.uk/chebi/CHEBI:16869)", "Reject automatic synonym merging with troleandomycin or oleandomycin 2'-O-phosphate: ChEBI records them as related derivatives. [ChEBI](https://www.ebi.ac.uk/chebi/CHEBI:16869)", "Require an oleandomycin reference comparison to distinguish it from erythromycin; membership in the macrolide antibiotic class is insufficient. [NCATS](https://drugs.ncats.io/substance/P8ZQ646136)", "Inspect composition before mapping historical product names to the pure substance: NCATS describes Sigmamycin as a combination containing oleandomycin and tetracycline. [NCATS](https://drugs.ncats.io/substance/P8ZQ646136)" ], "characteristics": [ { "name": "Chemical identity", "kind": "category", "unit_or_values": "CHEBI:16869; CAS 3922-90-5; InChIKey RZPAKFUAFGMUPI-QESOVKLGSA-N", "why_it_matters": "Provides an identity anchor against which names and sample claims can be checked. [ChEBI](https://www.ebi.ac.uk/chebi/CHEBI:16869)" }, { "name": "Neutral molecular formula and molar mass", "kind": "measurement", "unit_or_values": "C35H61NO12; approximately 687.86 g/mol", "why_it_matters": "Supports mass-to-mole conversion for the neutral parent; salts and solvates require their own composition basis. [NCATS](https://drugs.ncats.io/substance/P8ZQ646136)" }, { "name": "Material form", "kind": "category", "unit_or_values": "Neutral parent, specified salt, specified solvate or hydrate, solution, mixture, unresolved", "why_it_matters": "Determines which identity, concentration and physical-property evidence applies to the sample." }, { "name": "Oleandomycin content", "kind": "measurement", "unit_or_values": "mg/g or mass %, specifying as-received, dry or anhydrous basis and parent-equivalent conversion", "why_it_matters": "Separates actual parent content from total material mass and chromatographic area percentage." }, { "name": "Related substances and residues", "kind": "measurement", "unit_or_values": "Individual and total impurities in mass % or mg/kg; water and residual solvents reported separately", "why_it_matters": "Supports acceptance against a stated specification and detection of compositional change." }, { "name": "Dissolution and solution condition", "kind": "measurement", "unit_or_values": "Solubility in mg/mL at stated solvent, pH and temperature; prepared concentration in mg/mL or mmol/L", "why_it_matters": "Makes stock preparation and assay exposure reproducible without transferring values between material forms." }, { "name": "Thermal behavior", "kind": "measurement", "unit_or_values": "Melting or decomposition event in °C with method; boiling point only if experimentally meaningful at a stated pressure", "why_it_matters": "Distinguishes measured phase behavior from decomposition or unsupported catalogue values." }, { "name": "Antibacterial activity", "kind": "measurement", "unit_or_values": "MIC in µg/mL or validated potency units/mg, with strain, method and reference standard", "why_it_matters": "Relates sample performance to a defined biological test rather than assuming activity from chemical identity." }, { "name": "Storage qualification", "kind": "state", "unit_or_values": "Within validated conditions, excursion under review, retest required, failed, unknown", "why_it_matters": "Connects storage history and stability evidence to whether a sample remains usable." }, { "name": "Applicable hazard and use evidence", "kind": "relation", "unit_or_values": "Links to form-specific SDS, classification record, exposure-limit source and dated jurisdictional authorization", "why_it_matters": "Prevents identifier registration, historical marketing or missing hazard data from being treated as permission to use." } ], "affordances": [ "Resolve a supplier or registry record to oleandomycin using structure and material-form evidence.", "Calculate oleandomycin-equivalent concentration from verified composition and assay basis.", "Select identity, content and impurity checks suitable for the intended sample use.", "Compare antibacterial measurements only when their strain, method and concentration bases are compatible.", "Assess whether a stored sample requires retesting before use.", "Identify the handling documentation and current authorization evidence required for a proposed application." ], "agent_conduct": { "may": [ "Describe oleandomycin and its history as a human and veterinary antibiotic.", "Report its current authorization status, which varies by country." ], "must_not": [ "Recommend it or a dose for a person or animal.", "Advise its use as a growth promoter in livestock where that is banned.", "Supply it outside the regulated medicines chain." ], "requires_human": [ "Any decision to treat a person or animal with it." ] }, "ethics": { "considerations": [ "Antibiotic misuse in people and animals breeds resistance.", "Residues in food can affect consumers." ], "affected_parties": [ "Patients and animals", "Consumers", "The public at risk of resistance" ] }, "owners": { "steward": "The authorization holder; medicines and veterinary regulators control its use.", "master_systems": [ "Medicines and veterinary product registers" ] }, "visual_identification": [ "Usually a white powder or tablets; identified by label and analysis." ], "failure_modes_and_hazards": [ "Can interact with other medicines and cause liver effects.", "Overuse drives macrolide resistance." ], "what_it_is_for": [ "Oleandomycin is encountered in antibiotic research, pharmaceutical reference collections and analytical work involving macrolide compounds.", "It may be studied for chemical identity, purity, antibacterial activity and bacterial resistance.", "Its historical therapeutic role provides context for pharmaceutical literature and records." ], "standards_and_regulation": [ "The Anatomical Therapeutic Chemical classification maintained by the WHO Collaborating Centre for Drug Statistics Methodology classifies oleandomycin under J01FA05 among macrolide antibacterials." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q1076248: oleandomycin", "url": "https://www.wikidata.org/wiki/Q1076248", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Oleandomycin", "url": "https://en.wikipedia.org/wiki/Oleandomycin", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "oleandomycin-identity", "name": "Oleandomycin identity", "description": "Recognize the specific chemical entity and resolve ambiguous names or identifiers.", "rationale": "Macrolide class labels, product names and related-derivative names cannot establish oleandomycin identity.", "layers": [ { "id": "parent-structure", "name": "Parent structure", "description": "Anchor recognition in molecular connectivity and stereochemistry.", "findings": [ { "id": "structure-match", "name": "Structure match", "description": "Record whether the claimed entity and analytical evidence match the reference oleandomycin structure.", "questions": [ { "text": "Does the candidate structure match the reference oleandomycin connectivity and all specified stereocenters?", "kind": "definition", "id": "structure-match-q01" }, { "text": "Which reference-standard comparison or orthogonal analytical evidence supports the sample's identity?", "kind": "measurement", "id": "structure-match-q02" } ] } ] }, { "id": "identifier-boundaries", "name": "Identifier boundaries", "description": "Separate parent identifiers from salt, derivative and product records.", "findings": [ { "id": "name-resolution", "name": "Name resolution", "description": "Require structure-aware reconciliation before accepting a name or identifier as equivalent.", "questions": [ { "text": "Which source establishes that each CAS, PubChem, EC or supplier identifier refers to this exact chemical entity?", "kind": "provenance", "id": "name-resolution-q01" }, { "text": "Does a record labelled oleandomycin phosphate describe a counterion-containing salt or covalent phosphorylation, and what structural evidence resolves it?", "kind": "boundary", "id": "name-resolution-q02" } ] } ] } ] }, { "id": "oleandomycin-sample-composition", "name": "Oleandomycin sample composition", "description": "Describe how much oleandomycin a sample contains and what accompanies it.", "rationale": "Sample mass, parent-equivalent content and analytical purity can differ and support different decisions.", "layers": [ { "id": "form-and-content", "name": "Form and content", "description": "Establish material form and the basis of quantitative claims.", "findings": [ { "id": "parent-equivalent-content", "name": "Parent-equivalent content", "description": "Tie concentration calculations to counterion, water, solvent and assay information.", "questions": [ { "text": "What neutral, salt, hydrated, solvated or mixed form was actually supplied?", "kind": "definition", "id": "parent-equivalent-content-q01" }, { "text": "How much oleandomycin parent equivalent is present per gram, and is the result reported as received or on a corrected basis?", "kind": "measurement", "id": "parent-equivalent-content-q02" } ] } ] }, { "id": "purity-and-grade", "name": "Purity and grade", "description": "Relate impurity evidence and declared grade to a specific application.", "findings": [ { "id": "sample-acceptance", "name": "Sample acceptance", "description": "Evaluate the lot using documented limits rather than a standalone purity percentage.", "questions": [ { "text": "Which methods quantify oleandomycin, related compounds, water and residual solvents, and what remains unresolved?", "kind": "measurement", "id": "sample-acceptance-q01" }, { "text": "Does the lot meet the documented specification for its proposed use, including any required microbiological quality?", "kind": "action", "id": "sample-acceptance-q02" } ] } ] } ] }, { "id": "oleandomycin-physical-stability", "name": "Oleandomycin physical state and stability", "description": "Assess the supplied material and prepared solutions under recorded conditions.", "rationale": "Physical-property and storage claims need to follow the actual oleandomycin form and preparation.", "layers": [ { "id": "phase-and-dissolution", "name": "Phase and dissolution", "description": "Record physical behavior with material-form and measurement context.", "findings": [ { "id": "usable-solution-state", "name": "Usable solution state", "description": "Establish whether the intended concentration is dissolved and supported by applicable property evidence.", "questions": [ { "text": "What solubility has been measured for this oleandomycin form in the intended solvent at the specified pH and temperature?", "kind": "measurement", "id": "usable-solution-state-q01" }, { "text": "Do thermal data describe melting, decomposition or another event, and which sample form and method produced them?", "kind": "provenance", "id": "usable-solution-state-q02" } ] } ] }, { "id": "storage-and-degradation", "name": "Storage and degradation", "description": "Link elapsed time and environmental exposure to retained content and activity.", "findings": [ { "id": "remaining-suitability", "name": "Remaining suitability", "description": "Use stability evidence to decide whether stored solid or solution remains qualified.", "questions": [ { "text": "What data establish acceptable time, temperature, light, moisture and solution-pH conditions for this preparation?", "kind": "provenance", "id": "remaining-suitability-q01" }, { "text": "After the recorded storage history or excursion, do content, impurity and activity results justify use or require retesting?", "kind": "action", "id": "remaining-suitability-q02" } ] } ] } ] }, { "id": "oleandomycin-antibacterial-performance", "name": "Oleandomycin antibacterial performance", "description": "Represent biological activity as evidence tied to a defined experimental system.", "rationale": "Chemical content alone does not establish performance against a particular bacterial strain.", "layers": [ { "id": "target-and-assay-context", "name": "Target and assay context", "description": "Separate mechanistic evidence from growth-inhibition observations.", "findings": [ { "id": "activity-evidence", "name": "Activity evidence", "description": "NCATS associates oleandomycin with bacterial 50S ribosomal inhibition; individual results still require their own experimental context. [NCATS](https://drugs.ncats.io/substance/P8ZQ646136)", "questions": [ { "text": "Does the cited experiment measure ribosomal effects, protein synthesis, growth inhibition or killing?", "kind": "definition", "id": "activity-evidence-q01" }, { "text": "Which organism, strain, medium, inoculum and exposure conditions support the reported oleandomycin effect?", "kind": "provenance", "id": "activity-evidence-q02" } ] } ] }, { "id": "potency-and-susceptibility", "name": "Potency and susceptibility", "description": "Make potency and susceptibility comparisons conditional on compatible evidence.", "findings": [ { "id": "interpretable-performance", "name": "Interpretable performance", "description": "Keep potency, MIC and susceptibility interpretation distinct, with explicit standards and uncertainty.", "questions": [ { "text": "What MIC or potency was measured, with what replicates, uncertainty, reference standard and parent-equivalent concentration?", "kind": "measurement", "id": "interpretable-performance-q01" }, { "text": "Is an applicable oleandomycin-specific interpretive criterion available, or must the result remain an uninterpreted experimental measurement?", "kind": "boundary", "id": "interpretable-performance-q02" } ] } ] } ] }, { "id": "oleandomycin-handling-and-use", "name": "Oleandomycin handling and use", "description": "Connect the particular material and intended activity to applicable handling and authorization evidence.", "rationale": "An antibiotic identity or historical product record does not establish present handling requirements or permitted applications.", "layers": [ { "id": "handling-and-disposal", "name": "Handling and disposal", "description": "Resolve controls for the actual solid, solution or mixture being handled.", "findings": [ { "id": "documented-controls", "name": "Documented controls", "description": "Record supported hazard classifications and waste procedures, retaining missing information explicitly.", "questions": [ { "text": "Which current SDS and classification source cover this oleandomycin form, concentration and jurisdiction, and do they identify an applicable exposure limit?", "kind": "provenance", "id": "documented-controls-q01" }, { "text": "What documented containment and disposal procedure applies to oleandomycin-containing stock, assay liquid and contaminated materials?", "kind": "action", "id": "documented-controls-q02" } ] } ] }, { "id": "application-eligibility", "name": "Application eligibility", "description": "Distinguish material qualification from authorization of a product or use.", "findings": [ { "id": "dated-use-evidence", "name": "Dated use evidence", "description": "Require current, jurisdiction-specific evidence for any regulated application and link detailed product decisions to the product model.", "questions": [ { "text": "What dated authority establishes the status of the proposed research, human, veterinary or other application in the relevant jurisdiction?", "kind": "provenance", "id": "dated-use-evidence-q01" }, { "text": "Does the proposed action require evidence about a specific formulation, product authorization or clinical context beyond this substance model?", "kind": "boundary", "id": "dated-use-evidence-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 account is based on recall; no sources were consulted.", "Confirm identifiers and distinguish the parent compound from salts and acetylated derivatives before linking records.", "Current medicinal availability, jurisdiction-specific authorization, physical constants and hazard classifications require verification." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of oleandomycin 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": "3922-90-5", "note": "Identifies oleandomycin itself; salts and derivatives require separate identity checks." }, { "scheme": "Molecular formula", "value_or_pattern": "C35H61NO12", "note": "Formula of the neutral parent compound; does not uniquely specify its stereochemistry." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of oleandomycin 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": [ "Historical antibacterial treatment of infections caused by susceptible bacteria.", "Research on macrolide biosynthesis, antibiotic resistance and bacterial protein synthesis." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of oleandomycin 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 of the neutral parent compound", "typical_range": "Approximately 687.86", "unit": "g/mol" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of oleandomycin 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": [ "Bacterial resistance can prevent antibacterial activity, including resistance associated with modification of the ribosomal target.", "Cross-resistance with other macrolide antibiotics can limit effectiveness." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of oleandomycin 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": "Troleandomycin", "difference": "Troleandomycin is the triacetyl derivative of oleandomycin, rather than the unmodified parent antibiotic." }, { "name": "Erythromycin", "difference": "Both are 14-membered macrolide antibiotics, but they have different chemical structures, including different neutral sugar residues." }, { "name": "Oleandomycin phosphate", "difference": "The phosphate salt is distinguished from the parent compound by its counterion and corresponding composition." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of oleandomycin this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which PubChem CID and EC identifier resolve to the exact stereochemical parent, and how should conflicting or form-specific registry mappings be reconciled?", "Which authoritative specifications and reference standards establish identity, parent content, potency and impurity limits for each intended grade?", "What experimentally supported solubility, ionization, thermal and stability data apply separately to the neutral substance, supplied salts and prepared solutions?", "Which oleandomycin-specific susceptibility methods, interpretive criteria and resistance evidence support present-day interpretation without borrowing criteria from other macrolides?", "What current form-specific GHS classifications, occupational exposure limits, disposal requirements and jurisdictional use authorizations can be verified?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 16, "questions": 26 } }