{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:01:59Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 18.5, "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: 01a09546-babc-77e2-ac4c-6ca583611b1e\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: loganin\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 registe", "usd": 0.0, "recall": true }, "codex": { "seconds": 84.2, "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: 01a09546-babe-7431-bda1-6861970d4e78\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: loganin\nRegistry id: vr.tr.loganin\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext " } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:49:25+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:26+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q15426222", "registryId": "vr.tr.loganin", "name": "loganin", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q15426222/", "model": { "registry_id": "vr.tr.loganin", "name": "loganin", "purpose": "Enable an agent to recognize loganin, assess the identity and condition of a supplied sample, and determine its suitability for a specified analytical or research use.", "definition": "Loganin is a naturally occurring iridoid glucoside, structurally the methyl ester of loganic acid, that serves as an intermediate in plant biosynthesis of secologanin and downstream monoterpenoid indole alkaloids.", "scope_statement": "This model owns vr.tr.loganin in PHY / PHY.MAT: the defined loganin molecular entity, its material quality and condition, and evidence governing its use, with explicit boundaries between the substance, plant extracts, related compounds and biological claims.", "in_scope": [ "Molecular identity, stereochemistry, synonyms and reconciled chemical identifiers", "Sample composition, grade, purity, impurities and analytical identity evidence", "Solid and solution states, measured properties and condition-dependent stability", "Isolation or synthesis provenance and links to biological occurrence", "Evidence supporting handling, research suitability and substance-specific restrictions" ], "out_of_scope": [ "Whole plants, botanical taxonomy and cultivation practices", "Complete compositions and claimed benefits of loganin-containing extracts or products", "Manufacturing and extraction processes as independently operated systems", "Separate substance models for loganic acid, loganetin, secologanin and loganin derivatives", "Disease models, treatment protocols and clinical prescribing decisions" ], "distinguishing_features": [ "Require agreement with the stereochemically specified loganin structure; a name or molecular formula alone cannot exclude stereoisomers. ChEBI identifies C17H26O10 and InChIKey AMBQHHVBBHTQBF-UOUCRYGSSA-N. [ChEBI](https://www.ebi.ac.uk/chebi/CHEBI:15771)", "Confirm the β-D-glucoside linkage and retained sugar to distinguish loganin from its functional parent loganetin. [ChEBI](https://www.ebi.ac.uk/chebi/CHEBI:15771)", "Confirm the methyl ester and hydroxyl substitution pattern when assessing possible confusion with loganic acid or 7-deoxyloganin. [ChEBI](https://www.ebi.ac.uk/chebi/CHEBI:15771)", "Require sample-specific separation and identity evidence before treating a plant extract or a peak labelled loganin as isolated loganin.", "Reconcile identifier records through structures: PubChem search identifies (-)-loganin as CID 87691, whereas ChEBI links CID 91727262; their equivalence remains unresolved here. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/Loganin) [ChEBI](https://www.ebi.ac.uk/chebi/CHEBI:15771)" ], "characteristics": [ { "name": "Chemical identity", "kind": "category", "unit_or_values": "Stereochemical structure; formula C17H26O10; CAS 18524-94-2; CHEBI:15771", "why_it_matters": "Anchors recognition to a defined substance rather than a supplier label. [ChEBI](https://www.ebi.ac.uk/chebi/CHEBI:15771)" }, { "name": "Stereochemical confirmation", "kind": "state", "unit_or_values": "Confirmed against reference; partially supported; untested; inconsistent", "why_it_matters": "Prevents formula-compatible isomers from being accepted as loganin." }, { "name": "Loganin content", "kind": "measurement", "unit_or_values": "Mass fraction in % or mg/g, with method, uncertainty and as-received or dry basis", "why_it_matters": "Supports actual quantity calculations without equating chromatographic peak area with mass purity." }, { "name": "Related-compound and residual impurity profile", "kind": "measurement", "unit_or_values": "Identified and unidentified components in % or mg/kg; detection and quantification limits", "why_it_matters": "Distinguishes authentic loganin content from co-isolated substances, residual solvents and possible transformation products." }, { "name": "Material form", "kind": "state", "unit_or_values": "Solid or solution; characterized solid form if known; solvent composition and water content", "why_it_matters": "Connects weighing, dissolution and storage decisions to the material actually supplied." }, { "name": "Solution concentration and dissolved fraction", "kind": "measurement", "unit_or_values": "mg/mL or mmol/L; dissolved fraction in %; solvent, temperature and preparation time", "why_it_matters": "Separates nominal stock concentration from verified dissolved loganin." }, { "name": "Thermal behavior", "kind": "measurement", "unit_or_values": "Transition or decomposition temperature in °C with method, pressure and heating rate", "why_it_matters": "Supports condition limits without inventing a boiling point or confusing decomposition with melting." }, { "name": "Stability under specified conditions", "kind": "measurement", "unit_or_values": "Loganin remaining in % over hours or days, with temperature, light, pH and container conditions", "why_it_matters": "Determines whether stored material or prepared solutions remain fit for their intended use." }, { "name": "Source and lot provenance", "kind": "relation", "unit_or_values": "Supplier and lot; isolation or synthesis record; organism and tissue when evidenced; certificate and reference standard", "why_it_matters": "Makes sample quality and botanical attribution traceable." }, { "name": "Handling and regulatory evidence", "kind": "category", "unit_or_values": "Documented classification or unresolved status, with jurisdiction, date, supplier SDS and intended use", "why_it_matters": "Prevents missing hazard information or a research label from being interpreted as established safety or authorization." } ], "affordances": [ "Accept, quarantine or reject a labelled loganin sample against structure and analytical evidence.", "Calculate loganin quantities using measured content and the correct material basis.", "Select a supported dissolution, storage and retest procedure for a specified experiment.", "Compare lots for suitability as an analytical reference, isolated research substance or quantified extract constituent.", "Trace a reported occurrence or experimental effect to the material and evidence that support it." ], "agent_conduct": { "may": [ "Describe loganin and its place in plant iridoid biosynthesis from reliable sources.", "Track samples of it in an authorized laboratory inventory with label and source." ], "must_not": [ "Present plant extracts containing loganin as proven medicines.", "Mislabel a sample or report its purity without analysis.", "Encourage wild collection of source plants beyond sustainable or permitted limits." ], "requires_human": [ "Supplying it for tests on people or animals." ] }, "ethics": { "considerations": [ "Herbal products are often sold with health claims that outrun the evidence.", "Medicinal plants are part of traditional knowledge held by specific communities." ], "affected_parties": [ "Consumers of herbal products", "Researchers", "Traditional knowledge holders" ] }, "owners": { "steward": "Nobody owns the compound; the laboratory or supplier answers for each sample.", "master_systems": [] }, "visual_identification": [ "Usually supplied as a white to off-white solid in a labelled vial.", "Identity is confirmed by analysis, not by appearance." ], "failure_modes_and_hazards": [ "Mislabelled reference standards lead to wrong research results." ], "what_it_is_for": [ "Loganin is encountered in plant chemistry research as an iridoid glucoside involved in pathways leading to secologanin and certain alkaloids.", "Purified samples are used in analytical method development and investigations of plant extracts, biosynthesis and biological activity." ], "standards_and_regulation": [ "The Globally Harmonized System of Classification and Labelling of Chemicals, issued by the United Nations, provides the framework for assessing and communicating any identified hazards of supplied loganin under applicable national implementations." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q15426222: loganin", "url": "https://www.wikidata.org/wiki/Q15426222", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Loganin", "url": "https://en.wikipedia.org/wiki/Loganin", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "loganin-identity", "name": "Loganin identity", "description": "Establish the exact molecular entity represented by the registry entry.", "rationale": "Closely named iridoids and inconsistent database cross-references make label matching insufficient.", "layers": [ { "id": "structure-and-stereochemistry", "name": "Structure and stereochemistry", "description": "Represent the molecular features required for recognition.", "findings": [ { "id": "stereochemical-identity-test", "name": "Stereochemical identity test", "description": "Require a structure-level match that includes the glycoside, ester and stereochemical specification.", "questions": [ { "text": "Which authoritative stereochemical structure defines loganin for vr.tr.loganin?", "kind": "definition", "id": "stereochemical-identity-test-q01" }, { "text": "What evidence distinguishes the sample from an epimer, an aglycone or a related iridoid?", "kind": "measurement", "id": "stereochemical-identity-test-q02" } ] } ] }, { "id": "identifiers-and-neighbours", "name": "Identifiers and neighbours", "description": "Resolve names and database records without merging distinct structures.", "findings": [ { "id": "identifier-reconciliation", "name": "Identifier reconciliation", "description": "Keep identifier equivalence provisional when linked structures have not been compared.", "questions": [ { "text": "Do PubChem CIDs 87691 and 91727262 encode identical stereochemistry, different specificity or distinct entities?", "kind": "boundary", "id": "identifier-reconciliation-q01" }, { "text": "Which read source supports each accepted CAS, EC, synonym and structure mapping?", "kind": "provenance", "id": "identifier-reconciliation-q02" } ] } ] } ] }, { "id": "loganin-content-and-authentication", "name": "Loganin content and authentication", "description": "Determine what a supplied sample contains and how confidently it is identified.", "rationale": "A loganin-labelled peak, an enriched extract and a quantitatively characterized standard support different actions.", "layers": [ { "id": "analytical-identification", "name": "Analytical identification", "description": "Connect identification claims to methods and appropriate reference materials.", "findings": [ { "id": "orthogonal-identity-evidence", "name": "Orthogonal identity evidence", "description": "Assess chromatographic and spectroscopic agreement while recording unresolved isomer discrimination.", "questions": [ { "text": "Which reference-standard, MS and NMR comparisons support the loganin assignment?", "kind": "measurement", "id": "orthogonal-identity-evidence-q01" }, { "text": "Can the chosen method distinguish loganin from relevant co-eluting compounds and stereoisomers?", "kind": "boundary", "id": "orthogonal-identity-evidence-q02" } ] } ] }, { "id": "content-and-impurities", "name": "Content and impurities", "description": "Quantify loganin separately from water, solvents and other constituents.", "findings": [ { "id": "usable-loganin-quantity", "name": "Usable loganin quantity", "description": "Base quantity and suitability decisions on validated content measurements and impurity limits.", "questions": [ { "text": "Is the reported purity a mass assay, chromatographic area percentage or another measurement, and on what basis?", "kind": "measurement", "id": "usable-loganin-quantity-q01" }, { "text": "Which residual solvents, related compounds or unidentified peaks could invalidate the intended use?", "kind": "action", "id": "usable-loganin-quantity-q02" } ] } ] } ] }, { "id": "loganin-form-and-stability", "name": "Loganin form and stability", "description": "Track the conditions under which a loganin sample remains usable.", "rationale": "Stock preparation and storage require evidence for the actual solvent, material form and exposure conditions.", "layers": [ { "id": "solid-and-solution-properties", "name": "Solid and solution properties", "description": "Record measured material properties with conditions and uncertainty.", "findings": [ { "id": "condition-specific-properties", "name": "Condition-specific properties", "description": "Distinguish documented dissolution and thermal behavior from assumed constants.", "questions": [ { "text": "What loganin solubility or dissolved concentration was measured in the intended solvent at the intended temperature?", "kind": "measurement", "id": "condition-specific-properties-q01" }, { "text": "Does thermal analysis establish melting, solvent loss or decomposition for this material form?", "kind": "measurement", "id": "condition-specific-properties-q02" } ] } ] }, { "id": "storage-and-transformation", "name": "Storage and transformation", "description": "Assess loss of loganin identity or content during storage and use.", "findings": [ { "id": "validated-use-window", "name": "Validated use window", "description": "Set storage and solution-use limits from measured stability, including investigation of possible glycoside or ester cleavage.", "questions": [ { "text": "Under the proposed pH, temperature and light conditions, what change in loganin content and impurity profile occurs over time?", "kind": "measurement", "id": "validated-use-window-q01" }, { "text": "What evidence sets the retest date, stock-solution use window and criteria for disposal?", "kind": "action", "id": "validated-use-window-q02" } ] } ] } ] }, { "id": "loganin-origin-and-biological-context", "name": "Loganin origin and biological context", "description": "Connect loganin samples to their origin and carefully bounded biological evidence.", "rationale": "Occurrence in a plant and activity of an extract do not independently establish the provenance or effects of an isolated loganin sample.", "layers": [ { "id": "material-provenance", "name": "Material provenance", "description": "Trace isolated or synthesized loganin to verifiable records.", "findings": [ { "id": "source-to-sample-trace", "name": "Source-to-sample trace", "description": "Separate literature occurrence records from the documented origin of the current lot.", "questions": [ { "text": "Was this lot isolated, synthesized or obtained through another route, and which records establish that route?", "kind": "provenance", "id": "source-to-sample-trace-q01" }, { "text": "If botanical origin is claimed, which species, tissue and authenticated specimen support it?", "kind": "provenance", "id": "source-to-sample-trace-q02" } ] } ] }, { "id": "biological-role-evidence", "name": "Biological role evidence", "description": "Attach pathway and activity claims to the experiments that support them.", "findings": [ { "id": "bounded-biological-attribution", "name": "Bounded biological attribution", "description": "Record the tested material, biological system and endpoint before attributing an effect or pathway role to loganin.", "questions": [ { "text": "Did the experiment test characterized loganin, a mixture or an extract, and at what measured concentration?", "kind": "boundary", "id": "bounded-biological-attribution-q01" }, { "text": "Which primary experiment supports the asserted biological effect or conversion involving loganin in the stated organism?", "kind": "provenance", "id": "bounded-biological-attribution-q02" } ] } ] } ] }, { "id": "loganin-handling-and-use", "name": "Loganin handling and use", "description": "Determine supported handling and use decisions for the specific material.", "rationale": "Natural occurrence and experimental biological activity cannot substitute for hazard evidence, grade requirements or applicable authorization.", "layers": [ { "id": "hazard-evidence", "name": "Hazard evidence", "description": "Track documented hazards and explicit information gaps for solid loganin and its solutions.", "findings": [ { "id": "material-specific-handling-basis", "name": "Material-specific handling basis", "description": "Tie handling decisions to applicable documentation, including solvent hazards for prepared solutions.", "questions": [ { "text": "Which current SDS and supporting evidence apply to this loganin lot and physical form?", "kind": "provenance", "id": "material-specific-handling-basis-q01" }, { "text": "Are GHS classifications and exposure limits documented, explicitly unestablished or simply absent from the available records?", "kind": "definition", "id": "material-specific-handling-basis-q02" } ] } ] }, { "id": "fitness-for-intended-use", "name": "Fitness for intended use", "description": "Evaluate whether the sample and evidence meet the requirements of a concrete proposed use.", "findings": [ { "id": "use-eligibility-decision", "name": "Use eligibility decision", "description": "Require suitable identity, content, stability and applicable regulatory evidence before accepting a lot for use.", "questions": [ { "text": "What identity, assay uncertainty and impurity criteria must this loganin lot meet for the proposed analytical or research task?", "kind": "action", "id": "use-eligibility-decision-q01" }, { "text": "Which jurisdiction-specific records establish whether the proposed use is permitted, restricted or unresolved?", "kind": "provenance", "id": "use-eligibility-decision-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "This description is based on recall; no sources were consulted.", "Verify analytical purity, stereochemical identity and measured physical properties for the particular sample.", "Hazard classification, exposure limits and jurisdiction-specific regulatory status require checking; none are asserted here." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of loganin 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": "18524-94-2", "note": "Identifier for loganin." }, { "scheme": "Molecular formula", "value_or_pattern": "C17H26O10", "note": "Describes composition but does not uniquely distinguish stereoisomers." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of loganin 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": [ "Reference compound for identifying and quantifying loganin in plant extracts.", "Research on iridoid and monoterpenoid indole alkaloid biosynthesis.", "Experimental investigation of biological activity." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of loganin 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": "390.38", "unit": "g/mol" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of loganin 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": [ "Hydrolysis can cleave the glycosidic bond or the methyl ester, changing the substance being measured.", "Biological effects observed in experimental systems do not establish safety or therapeutic efficacy in humans." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of loganin 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": "Loganic acid", "difference": "Has a free carboxylic acid group where loganin has a methyl ester." }, { "name": "Secologanin", "difference": "Has an oxidatively opened iridoid carbocyclic ring and is a downstream biosynthetic product of loganin." }, { "name": "Loganetin", "difference": "Is the aglycone corresponding to loganin and lacks its glucose residue." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of loganin this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "How should PubChem CIDs 87691 and 91727262 be reconciled against the full stereochemical definition, and which EC identifier is independently verified?", "Which validated analytical methods resolve loganin from the related iridoids and stereoisomers likely to occur in the relevant sample matrices?", "What reliable measurements establish solid form, water content, solvent-dependent solubility and thermal behavior without conflating melting with decomposition?", "What primary stability data establish loganin degradation pathways and defensible storage or solution-use limits under the intended conditions?", "Which current hazard, exposure-limit and regulatory records apply, and which biological claims remain limited to specific preclinical experiments?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 16, "questions": 26 } }