{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:55:52Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 17.8, "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: 01a094d3-5c6b-7193-b3f4-205942fc345a\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: cucurbitine\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001 reg", "usd": 0.0, "recall": true }, "codex": { "seconds": 78.3, "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: 01a094d3-5c60-77f3-b4dd-9c0f22887cd1\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: cucurbitine\nRegistry id: vr.tr.cucurbitine\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": "2026-10-06T08:50:16+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners" ] }, "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-Q2667749", "registryId": "vr.tr.cucurbitine", "name": "cucurbitine", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q2667749/", "model": { "registry_id": "vr.tr.cucurbitine", "name": "cucurbitine", "purpose": "Enable an agent to recognise cucurbitine, assess the identity and condition of a sample, and determine which analytical or experimental uses its evidence supports.", "definition": "Cucurbitine is a non-proteinogenic cyclic amino acid, 3-aminopyrrolidine-3-carboxylic acid, found in pumpkin seeds.", "scope_statement": "This model owns the chemical identity, material state, sample quality and evidence-supported handling of vr.tr.cucurbitine in PHY / PHY.MAT, provisionally anchored to the (3R)-3-aminopyrrolidine-3-carboxylic acid identity while leaving the registry's intended stereochemical breadth explicit.", "in_scope": [ "Molecular connectivity, stereochemistry and identifiers that distinguish cucurbitine from similarly named substances", "Cucurbitine content, chemical purity, enantiomeric composition and associated salt or solvate form", "Physical state, solution conditions, stability and condition-qualified material constants", "Sample provenance and analytical evidence establishing identity and quantity", "Handling constraints and the evidence needed to support proposed experimental uses" ], "out_of_scope": [ "Cucurbita species, seeds and their cultivation as biological entities", "Pumpkin seed extracts, oils and formulated products as complete mixtures", "Cucurbitin seed-storage globulin as a protein", "Cucurbitacins and other separately identified pumpkin constituents", "Extraction or synthesis processes as independently managed workflows", "Clinical treatment protocols and product-level therapeutic authorisations" ], "distinguishing_features": [ "Require the connectivity of 3-aminopyrrolidine-3-carboxylic acid, with amino and carboxyl groups attached at ring carbon 3; a matching molecular formula alone is insufficient. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/Cucurbitine)", "Check stereochemistry explicitly: PubChem CID 442634 and CAS 6807-92-7 identify the (3R) compound, so a racemate or unspecified stereoisomer cannot be silently treated as equivalent. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/Cucurbitine)", "Resolve the name 'cucurbitin' against structure and substance class because it can also denote a globulin that is distinct from this amino acid. [NCBI MeSH](https://www.ncbi.nlm.nih.gov/mesh/67014427)", "Require compound-specific identification in pumpkin-derived material; botanical origin or an extract's biological effect does not establish that the material is isolated cucurbitine.", "Distinguish cucurbitine from cucurbitacins by molecular structure rather than the shared name stem; for example, cucurbitacin C has a different formula and identity. [PubChem: Cucurbitacin C](https://pubchem.ncbi.nlm.nih.gov/compound/Cucurbitacin-C)" ], "characteristics": [ { "name": "Chemical identity", "kind": "category", "unit_or_values": "Non-proteinogenic alpha-amino acid; C5H10N2O2; reference molar mass 130.15 g/mol. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/Cucurbitine)", "why_it_matters": "Anchors recognition and amount calculations to a defined molecule." }, { "name": "Stereochemical identity", "kind": "category", "unit_or_values": "3R confirmed; 3S identified; racemic; mixed; unspecified", "why_it_matters": "Prevents evidence or identifiers for one stereochemical form from being transferred to another." }, { "name": "External identifier correspondence", "kind": "relation", "unit_or_values": "Candidate reference identity: PubChem CID 442634; CAS 6807-92-7; UNII 82AL4JJ8J2, with source and form qualification. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/Cucurbitine)", "why_it_matters": "Connects records without treating an identifier as proof of sample identity or regulatory approval." }, { "name": "Supplied chemical form", "kind": "category", "unit_or_values": "Parent compound; specified salt; hydrate; solvate; solution; unresolved", "why_it_matters": "Controls formula mass, assay basis and comparability with reference data." }, { "name": "Cucurbitine assay", "kind": "measurement", "unit_or_values": "Mass fraction in % or mg/g; solution concentration in mg/mL or mol/L; method, uncertainty and reporting basis required", "why_it_matters": "Distinguishes actual cucurbitine amount from total sample mass or chromatographic area." }, { "name": "Enantiomeric composition", "kind": "measurement", "unit_or_values": "R:S ratio or enantiomeric excess in %, with validated chiral method", "why_it_matters": "Qualifies use where stereochemical identity affects interpretation." }, { "name": "Water, residual solvent and impurity content", "kind": "measurement", "unit_or_values": "Water in mass %; specified solvents and impurities in mg/kg or mass %, with detection limits", "why_it_matters": "Explains assay differences and determines whether a lot meets its intended use." }, { "name": "Physical and solution state", "kind": "state", "unit_or_values": "Observed phase and appearance; temperature in °C; solvent; concentration; pH where applicable", "why_it_matters": "Makes observations and solution preparations reproducible." }, { "name": "Condition-qualified material constants", "kind": "measurement", "unit_or_values": "Thermal transitions in °C; solubility in g/L; pKa values, each with form, method and conditions; unknown permitted", "why_it_matters": "Supports preparation and storage decisions without inventing missing constants." }, { "name": "Handling and use evidence", "kind": "relation", "unit_or_values": "Lot-specific SDS, jurisdiction-specific classification, restrictions and experimental evidence with dates and sources", "why_it_matters": "Separates documented constraints from missing information and unsupported biological claims." } ], "affordances": [ "Resolve a cucurbitine-labelled record to a structure-qualified identity and flag protein or cucurbitacin name collisions.", "Accept, qualify or quarantine a sample against intended-use requirements for identity, assay and stereochemical composition.", "Calculate cucurbitine amounts using verified chemical form, water content and assay basis.", "Select and document suitable identity, quantitation and chiral measurements.", "Prepare and track solutions using supported solubility, pH and stability information.", "Evaluate whether experimental findings concern isolated cucurbitine or a containing extract before using them to justify further work." ], "agent_conduct": { "may": [ "Describe cucurbitine as an amino acid found in pumpkin seeds, citing reliable sources.", "Track samples in an authorized laboratory inventory with label and source." ], "must_not": [ "Present pumpkin seed products as a proven cure for parasites on the basis of cucurbitine.", "Advise replacing prescribed antiparasitic treatment with seed preparations.", "Report the identity or purity of a sample without analysis." ], "requires_human": [ "Recommending any treatment for a suspected parasite infection." ] }, "ethics": { "considerations": [ "Folk remedies can delay effective treatment of infections, especially in children.", "Traditional uses deserve accurate rather than dismissive description." ], "affected_parties": [ "People with parasite infections", "Children", "Consumers of herbal products" ] }, "owners": { "steward": "Nobody owns the compound; the laboratory or supplier answers for each sample.", "master_systems": [] }, "failure_modes_and_hazards": [ "Relying on seed remedies can leave infections untreated." ], "what_it_is_for": [ "Cucurbitine is encountered in chemical studies of pumpkin seeds and in research on naturally occurring amino acids.", "Authenticated samples can support analytical method development, comparison with plant extracts and experimental investigation of 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 chemical hazards where adopted." ], "visual_identification": [ "A sample label bearing the name cucurbitine or 3-aminopyrrolidine-3-carboxylic acid provides a documentary identification cue.", "The molecular formula C5H10N2O2 on accompanying documentation helps distinguish the substance from similarly named cucurbitacins.", "The appearance of an unlabelled solid or solution cannot distinguish cucurbitine reliably from other chemicals." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q2667749: cucurbitine", "url": "https://www.wikidata.org/wiki/Q2667749", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Cucurbitin", "url": "https://en.wikipedia.org/wiki/Cucurbitin", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "molecular-identity-and-name-resolution", "name": "Molecular identity and name resolution", "description": "Establish which chemical entity the registry name and each sample record denote.", "rationale": "Cucurbitine has a consequential protein name collision and a stereochemically specific reference identity.", "layers": [ { "id": "connectivity-and-stereochemistry", "name": "Connectivity and stereochemistry", "description": "Anchor recognition to the substituted pyrrolidine structure and its configuration.", "findings": [ { "id": "structure-qualified-identity", "name": "Structure-qualified identity", "description": "Record evidence for ring connectivity and configuration separately; do not infer stereochemistry from a non-chiral identity test.", "questions": [ { "text": "What evidence establishes the 3-aminopyrrolidine-3-carboxylic acid connectivity?", "kind": "definition", "id": "structure-qualified-identity-q01" }, { "text": "Does the sample establish the 3R configuration, an enantiomeric mixture or only unspecified stereochemistry?", "kind": "measurement", "id": "structure-qualified-identity-q02" } ] } ] }, { "id": "names-and-identifier-boundaries", "name": "Names and identifier boundaries", "description": "Resolve synonyms and identifier mappings without merging neighbouring substances.", "findings": [ { "id": "cucurbitin-name-collision", "name": "Cucurbitin name collision", "description": "Require source context and structural correspondence before accepting records labelled cucurbitin as evidence about this entry.", "questions": [ { "text": "Does this occurrence of 'cucurbitin' denote the amino acid or the seed-storage globulin?", "kind": "boundary", "id": "cucurbitin-name-collision-q01" }, { "text": "Which inspected identifier record establishes the same stereochemistry and chemical form as the proposed match?", "kind": "provenance", "id": "cucurbitin-name-collision-q02" } ] } ] } ] }, { "id": "sample-composition-and-origin", "name": "Sample composition and origin", "description": "Describe what a cucurbitine lot contains and how its provenance supports that description.", "rationale": "An isolated compound, a salt and a pumpkin extract cannot share an unqualified assay or evidence record.", "layers": [ { "id": "chemical-form-and-assay-basis", "name": "Chemical form and assay basis", "description": "Connect reported content to the actual material weighed or dissolved.", "findings": [ { "id": "parent-equivalent-content", "name": "Parent-equivalent content", "description": "Distinguish supplied-form mass from cucurbitine-equivalent mass and make water, counterion and solvent contributions explicit.", "questions": [ { "text": "Is the supplied material the parent compound or a specified salt, hydrate or solvate?", "kind": "definition", "id": "parent-equivalent-content-q01" }, { "text": "Is the assay reported as received, on a dry basis or as parent-compound equivalents?", "kind": "measurement", "id": "parent-equivalent-content-q02" } ] } ] }, { "id": "botanical-or-synthetic-provenance", "name": "Botanical or synthetic provenance", "description": "Track source material and lot history without treating origin as identity proof.", "findings": [ { "id": "origin-linked-impurity-evidence", "name": "Origin-linked impurity evidence", "description": "Record botanical extraction or synthetic provenance alongside measured residual matrix components and process impurities.", "questions": [ { "text": "Which records identify the source organism and tissue, or synthetic route, for this lot?", "kind": "provenance", "id": "origin-linked-impurity-evidence-q01" }, { "text": "What measurements distinguish isolated cucurbitine from a containing extract and quantify relevant residual components?", "kind": "measurement", "id": "origin-linked-impurity-evidence-q02" } ] } ] } ] }, { "id": "physical-state-and-solution-behaviour", "name": "Physical state and solution behaviour", "description": "Capture conditions governing the material's observed state and preparation.", "rationale": "Cucurbitine's amino-acid functionality makes solution conditions relevant, while unverified constants cannot support handling decisions.", "layers": [ { "id": "solid-state-and-thermal-evidence", "name": "Solid state and thermal evidence", "description": "Qualify solid-state observations and thermal events by sample form and method.", "findings": [ { "id": "thermal-event-interpretation", "name": "Thermal event interpretation", "description": "Keep melting, decomposition and solvent loss distinct rather than assigning an ambiguous literature temperature as a universal constant.", "questions": [ { "text": "Which chemical form, water content and measurement conditions accompany the reported thermal event?", "kind": "provenance", "id": "thermal-event-interpretation-q01" }, { "text": "Does the measurement demonstrate melting, decomposition, desolvation or an unresolved combination?", "kind": "measurement", "id": "thermal-event-interpretation-q02" } ] } ] }, { "id": "dissolution-and-storage", "name": "Dissolution and storage", "description": "Relate solution preparation and usable lifetime to measured conditions.", "findings": [ { "id": "condition-qualified-solution-usability", "name": "Condition-qualified solution usability", "description": "Record solvent, pH, concentration and temperature alongside dissolution and stability observations.", "questions": [ { "text": "At the intended pH, solvent and temperature, what cucurbitine concentration is demonstrably dissolved?", "kind": "measurement", "id": "condition-qualified-solution-usability-q01" }, { "text": "What evidence supports the storage conditions and retest interval for this solid or solution?", "kind": "action", "id": "condition-qualified-solution-usability-q02" } ] } ] } ] }, { "id": "analytical-recognition-and-quantitation", "name": "Analytical recognition and quantitation", "description": "Establish whether measurements identify cucurbitine and quantify it in the relevant matrix.", "rationale": "Formula matches, non-chiral purity results and seed-extract peak assignments answer different questions.", "layers": [ { "id": "orthogonal-identity-evidence", "name": "Orthogonal identity evidence", "description": "Combine complementary measurements to resolve connectivity and configuration.", "findings": [ { "id": "identity-test-coverage", "name": "Identity test coverage", "description": "State which alternatives each analytical result excludes and which remain unresolved.", "questions": [ { "text": "Which reference-standard comparison or structural measurements distinguish cucurbitine from same-formula alternatives?", "kind": "measurement", "id": "identity-test-coverage-q01" }, { "text": "Which chiral measurement independently supports the claimed enantiomeric composition?", "kind": "measurement", "id": "identity-test-coverage-q02" } ] } ] }, { "id": "matrix-specific-assay", "name": "Matrix-specific assay", "description": "Qualify quantitation for isolated material, solutions or seed-derived mixtures.", "findings": [ { "id": "traceable-cucurbitine-quantity", "name": "Traceable cucurbitine quantity", "description": "Require calibration, specificity and recovery evidence appropriate to the sample rather than treating peak area as mass purity.", "questions": [ { "text": "What standard identity, assigned content and calibration support the reported cucurbitine amount?", "kind": "provenance", "id": "traceable-cucurbitine-quantity-q01" }, { "text": "How were matrix interference, recovery, quantitation limits and uncertainty assessed?", "kind": "measurement", "id": "traceable-cucurbitine-quantity-q02" } ] } ] } ] }, { "id": "handling-and-biological-evidence", "name": "Handling and biological evidence", "description": "Connect proposed actions to applicable handling information and correctly attributed experimental results.", "rationale": "Seed origin does not establish isolated-compound safety, and whole-extract activity cannot establish cucurbitine-specific efficacy.", "layers": [ { "id": "form-specific-handling-constraints", "name": "Form-specific handling constraints", "description": "Record applicable hazard information for the actual supplied material.", "findings": [ { "id": "supported-handling-decision", "name": "Supported handling decision", "description": "Separate documented classifications and restrictions from unavailable data; absence of a classification is not a measured safety result.", "questions": [ { "text": "Which current SDS or authoritative classification covers this cucurbitine form in the relevant jurisdiction?", "kind": "provenance", "id": "supported-handling-decision-q01" }, { "text": "What controls and disposal instructions does that evidence support for the planned operation?", "kind": "action", "id": "supported-handling-decision-q02" } ] } ] }, { "id": "compound-specific-activity-attribution", "name": "Compound-specific activity attribution", "description": "Assess whether biological observations concern characterised cucurbitine or a containing preparation.", "findings": [ { "id": "activity-claim-boundary", "name": "Activity claim boundary", "description": "Keep compound-level effects tied to tested identity, purity, dose, organism and endpoint, with extract and clinical claims separately bounded.", "questions": [ { "text": "Was the tested agent characterised cucurbitine, a specified salt or a multicomponent seed preparation?", "kind": "boundary", "id": "activity-claim-boundary-q01" }, { "text": "Which dose, controls, organism and endpoint support the claimed effect, and what proposed use would exceed that evidence?", "kind": "action", "id": "activity-claim-boundary-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": [ "Confirm that the registry intends the amino acid rather than the similarly named seed-storage protein.", "Verify natural stereochemistry and stereochemistry-specific CAS or PubChem identifiers before assigning them.", "Anthelmintic research does not establish clinical efficacy or safety of the isolated substance; physical constants and hazard classifications are omitted because they are not confidently recalled." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of cucurbitine 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": "IUPAC chemical nomenclature", "value_or_pattern": "3-aminopyrrolidine-3-carboxylic acid", "note": "This name specifies connectivity without assigning stereochemistry." }, { "scheme": "Molecular formula", "value_or_pattern": "C5H10N2O2", "note": "Formula of the neutral parent compound; not a unique substance identifier." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of cucurbitine 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": [ "Investigated as a constituent of pumpkin seeds in research on their reported anthelmintic activity." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of cucurbitine 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": "130.15", "unit": "g/mol" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of cucurbitine 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": "Cucurbitacins", "difference": "Cucurbitacins are tetracyclic triterpenoids; cucurbitine is a small cyclic amino acid." }, { "name": "Cucurbitin seed-storage protein", "difference": "The storage protein is a macromolecule; cucurbitine here denotes a discrete amino acid, although similar naming can cause confusion." }, { "name": "Proline", "difference": "Proline has its carboxyl group at position 2 of the pyrrolidine ring; cucurbitine has amino and carboxyl groups at position 3." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of cucurbitine this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does vr.tr.cucurbitine intend specifically the 3R compound or stereochemically unspecified connectivity, and does an existing Vercy world model already own that exact concept?", "Which primary measurements establish melting versus decomposition, solubility, ionisation constants and storage stability for clearly identified cucurbitine forms?", "Which validated methods and reference materials reliably measure cucurbitine content and enantiomeric composition in isolated lots and pumpkin-derived matrices?", "What verified EC identity, jurisdiction-specific GHS classification and substance-specific exposure limits exist, if any, for the intended chemical form?", "Which biological effects have been demonstrated using characterised isolated cucurbitine, and what remains attributable only to seed extracts or insufficiently characterised preparations?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 15, "questions": 25 } }