{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T10:50:20Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 26.8, "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: 01a0953c-2aef-7650-a462-96d720df0a0b\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: L-cysteine sulphinic acid\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch", "usd": 0.0, "recall": true }, "codex": { "seconds": 77.2, "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: 01a0953c-2ae1-7da0-acfd-8000069bd125\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: L-cysteine sulphinic acid\nRegistry id: vr.tr.l-cysteine-sulphinic-acid\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folde" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:50:42+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-Q2823252", "registryId": "vr.tr.l-cysteine-sulphinic-acid", "name": "L-cysteine sulphinic acid", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q2823252/", "model": { "registry_id": "vr.tr.l-cysteine-sulphinic-acid", "name": "L-cysteine sulphinic acid", "purpose": "Enable an AI agent to recognise L-cysteine sulphinic acid, assess the identity and condition of a sample, and determine its suitability for a specified analytical or biochemical use.", "definition": "L-cysteine sulphinic acid is a sulfur-containing L-α-amino acid with the structure HOOC-CH(NH2)-CH2-S(O)OH, formed by oxidation of L-cysteine and serving as an intermediate in cysteine metabolism and taurine biosynthesis.", "scope_statement": "This model owns the chemical identity, material forms, sample quality, transformations and use constraints of L-cysteine sulphinic acid under registry entry vr.tr.l-cysteine-sulphinic-acid in PHY / PHY.MAT.", "in_scope": [ "Molecular identity, L stereochemistry and sulphinic-acid functionality", "Free-acid, ionisation, hydration and counterion distinctions relevant to sample identity", "Chemical purity, enantiomeric composition and concentration", "Physical condition, solution behaviour and evidence of degradation", "Biochemical relationships and evidence supporting intended laboratory uses", "Form-specific safety information and regulatory identifiers" ], "out_of_scope": [ "L-cysteine and other sulfur oxidation products as independently modelled substances", "Protein-bound cysteine sulphinic-acid residues as complete proteins or peptides", "Commercial formulations, packaging and supplier organisations", "Complete metabolic pathways and the enzymes that catalyse their reactions", "Manufacturing processes and laboratory instruments", "Clinical treatment protocols or inferred therapeutic efficacy" ], "distinguishing_features": [ "Match the free-acid identity to C3H7NO4S, CAS 1115-65-7 and PubChem CID 1549098, while checking that the source record represents the L compound. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/L-Cysteinesulfinic-acid)", "Verify the L configuration at the amino-acid stereocentre; the corresponding systematic name is (2R)-2-amino-3-sulfinopropanoic acid. Formula and ordinary mass measurements alone do not establish this distinction. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/L-Cysteinesulfinic-acid)", "Require structural evidence for the side-chain sulphinic-acid group, distinguishing it from the thiol of cysteine and from neighbouring sulfur oxidation states.", "Establish whether the material is the free amino acid or a cysteine-derived residue covalently incorporated into a peptide.", "Check declared hydration and counterions before treating a supplied material as equivalent to the reference free acid for weighing or concentration calculations." ], "characteristics": [ { "name": "Reference chemical identity", "kind": "category", "unit_or_values": "L-cysteine sulphinic acid; L-cysteinesulfinic acid; 3-sulfino-L-alanine", "why_it_matters": "Normalises spelling and chemical synonyms without merging different stereoisomers." }, { "name": "Reference formula and molar mass", "kind": "measurement", "unit_or_values": "C3H7NO4S; 153.16 g/mol for the reference free acid", "why_it_matters": "Supports identity and amount calculations, subject to correction for the actual supplied form. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/L-Cysteinesulfinic-acid)" }, { "name": "Enantiomeric composition", "kind": "measurement", "unit_or_values": "L fraction or enantiomeric excess in %, with analytical method", "why_it_matters": "Establishes whether the sample meets an L-specific biochemical or analytical requirement." }, { "name": "Material form", "kind": "category", "unit_or_values": "Free acid, hydrate, counterion-containing form or solution; stoichiometry where established", "why_it_matters": "Determines the applicable formula basis and whether reference properties transfer." }, { "name": "Chemical assay and impurity profile", "kind": "measurement", "unit_or_values": "Mass fraction or molar fraction; named impurities; method and reporting basis", "why_it_matters": "Separates actual analyte content from chromatographic area purity and identifies related compounds that could confound an assay." }, { "name": "Water content", "kind": "measurement", "unit_or_values": "Mass % or mol H2O/mol compound, with method", "why_it_matters": "Prevents hydration or absorbed water from biasing gravimetric preparation." }, { "name": "Solution condition", "kind": "state", "unit_or_values": "Solvent, pH, temperature, concentration, preparation time and observed precipitation", "why_it_matters": "Makes solubility, speciation and measured response interpretable." }, { "name": "Thermal behaviour", "kind": "measurement", "unit_or_values": "Transition or decomposition temperature in °C, with method and material form", "why_it_matters": "Prevents a decomposition event from being reported as an ordinary melting or boiling point." }, { "name": "Storage and degradation status", "kind": "state", "unit_or_values": "Storage history, retest date, related-compound changes and acceptance decision", "why_it_matters": "Links continued suitability to evidence about the actual sample." }, { "name": "Biochemical role evidence", "kind": "relation", "unit_or_values": "Compound linked to reaction, enzyme or assay endpoint, with organism and conditions", "why_it_matters": "Keeps biochemical interpretation tied to a demonstrated experimental context." }, { "name": "Applicable safety classification", "kind": "category", "unit_or_values": "Verified classification, jurisdiction, material form, source date or unresolved", "why_it_matters": "Prevents an absent classification or a mismatched supplier record from being interpreted as evidence of safety." } ], "affordances": [ "Resolve chemical synonyms and identifiers while flagging stereochemical or material-form mismatches.", "Assess whether identity, purity and water-content evidence support an intended use.", "Calculate weighed amounts or solution concentrations using the verified material form and assay basis.", "Select analytical checks that distinguish the target from related sulfur compounds and stereoisomers.", "Evaluate whether a stored solid or prepared solution needs retesting before use.", "Associate biochemical observations and handling decisions with their supporting evidence and conditions." ], "agent_conduct": { "may": [ "Describe L-cysteine sulphinic acid and its role in cysteine metabolism and taurine synthesis from reliable sources.", "Record its use and storage in a laboratory the agent is authorized to manage." ], "must_not": [ "Present it as a supplement or treatment without clinical evidence.", "Diagnose a metabolic disorder in a particular person from metabolite results.", "Confuse it with similarly named sulfur compounds in records or orders." ], "requires_human": [ "Interpreting a patient's metabolic test results." ] }, "ethics": { "considerations": [ "Metabolic research can be overstated into health claims that mislead patients." ], "affected_parties": [ "Researchers and students", "Patients with metabolic disorders" ] }, "owners": { "steward": "Nobody owns the compound; the laboratory that holds a sample answers for it.", "master_systems": [ "Chemical inventories and safety data sheet systems" ] }, "failure_modes_and_hazards": [ "Confusion with related sulfur amino acids can corrupt experimental records." ], "what_it_is_for": [ "L-cysteine sulphinic acid is encountered in biochemical studies of sulfur amino acid metabolism and taurine biosynthesis.", "It is used as a research material or analytical reference when investigating enzymes and metabolites associated with cysteine oxidation." ], "standards_and_regulation": [ "The Globally Harmonized System of Classification and Labelling of Chemicals, issued by the United Nations, provides the framework for evaluating hazards and communicating any applicable classifications for supplied L-cysteine sulphinic acid materials." ], "visual_identification": [ "A sample label should explicitly identify L-cysteine sulphinic acid, since appearance alone cannot distinguish it from similar laboratory chemicals.", "The identity documentation should specify the L form and the sulphinic acid group, distinguishing it from unspecified stereochemical forms and more highly oxidized cysteic acid." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q2823252: L-cysteine sulphinic acid", "url": "https://www.wikidata.org/wiki/Q2823252", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Cysteine sulfinic acid", "url": "https://en.wikipedia.org/wiki/Cysteine_sulfinic_acid", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "chemical-identity-and-boundaries", "name": "Chemical identity and boundaries", "description": "Recognise the specific L amino acid and prevent confusion with closely named sulfur compounds.", "rationale": "A near-match in spelling, formula or oxidation terminology can identify a different experimental material.", "layers": [ { "id": "structure-and-stereochemistry", "name": "Structure and stereochemistry", "description": "Establish connectivity and the amino-acid stereocentre.", "findings": [ { "id": "l-sulphinic-acid-identity", "name": "L sulphinic-acid identity", "description": "Record evidence that both the sulphinic-acid functionality and L configuration belong to the material being identified.", "questions": [ { "text": "What structural evidence establishes the sulphinic-acid side chain rather than another sulfur-containing group?", "kind": "definition", "id": "l-sulphinic-acid-identity-q01" }, { "text": "What chiral measurement or traceable reference establishes the L configuration and limits the D fraction?", "kind": "measurement", "id": "l-sulphinic-acid-identity-q02" } ] } ] }, { "id": "identifier-and-entity-matching", "name": "Identifier and entity matching", "description": "Resolve names and external records against the registry boundary.", "findings": [ { "id": "equivalent-name-boundary", "name": "Equivalent-name boundary", "description": "Treat spelling variants as candidate synonyms while checking whether each record describes the free compound, a supplied form or a covalently bound residue.", "questions": [ { "text": "Which authoritative records connect the sulphinic and sulfinic spellings to this exact stereochemical identity?", "kind": "provenance", "id": "equivalent-name-boundary-q01" }, { "text": "Does the encountered name denote the free amino acid, a salt or hydrate, a racemate, or a peptide-bound residue?", "kind": "boundary", "id": "equivalent-name-boundary-q02" } ] } ] } ] }, { "id": "material-form-and-amount", "name": "Material form and amount", "description": "Connect the molecular reference identity to the material actually weighed or dissolved.", "rationale": "Hydration, counterions and solution conditions can change the interpretation of amounts and properties.", "layers": [ { "id": "solid-form-and-composition", "name": "Solid form and composition", "description": "Establish the composition basis of a supplied solid.", "findings": [ { "id": "hydration-and-assay-basis", "name": "Hydration and assay basis", "description": "Require water content, counterion information and assay basis before converting sample mass into analyte amount.", "questions": [ { "text": "What evidence establishes hydration, counterions and any residual solvent in this lot?", "kind": "measurement", "id": "hydration-and-assay-basis-q01" }, { "text": "Is the reported assay expressed as supplied, on a dry basis or as free-acid equivalent?", "kind": "definition", "id": "hydration-and-assay-basis-q02" } ] } ] }, { "id": "solution-speciation-and-solubility", "name": "Solution speciation and solubility", "description": "Describe dissolved material under explicit chemical and physical conditions.", "findings": [ { "id": "conditioned-solution-properties", "name": "Conditioned solution properties", "description": "Record solubility and ionisation evidence with pH, solvent and temperature instead of assigning universal solution behaviour.", "questions": [ { "text": "What concentration is demonstrably dissolved in the specified solvent at the recorded pH and temperature?", "kind": "measurement", "id": "conditioned-solution-properties-q01" }, { "text": "Which measured or sourced acid-base data support the assigned solution species?", "kind": "provenance", "id": "conditioned-solution-properties-q02" }, { "text": "What material-form and assay corrections are required to prepare the intended concentration?", "kind": "action", "id": "conditioned-solution-properties-q03" } ] } ] } ] }, { "id": "analytical-quality-and-stability", "name": "Analytical quality and stability", "description": "Determine whether a sample contains the intended compound at an acceptable quality and remains suitable over time.", "rationale": "Related sulfur compounds and untracked changes can distort identity, concentration and biochemical readouts.", "layers": [ { "id": "related-compound-discrimination", "name": "Related-compound discrimination", "description": "Assess analytical separation and identification of plausible confounders.", "findings": [ { "id": "selective-analyte-assay", "name": "Selective analyte assay", "description": "Require an assay capable of distinguishing the target from relevant related compounds; assess stereochemistry separately where necessary.", "questions": [ { "text": "Does the method distinguish L-cysteine sulphinic acid from cysteine, cysteic acid and other relevant sample components?", "kind": "measurement", "id": "selective-analyte-assay-q01" }, { "text": "What reference materials, detection limits and response corrections support the reported purity?", "kind": "provenance", "id": "selective-analyte-assay-q02" } ] } ] }, { "id": "storage-and-preparation-history", "name": "Storage and preparation history", "description": "Relate current analytical condition to handling and elapsed time.", "findings": [ { "id": "evidence-based-retest", "name": "Evidence-based retest", "description": "Base storage limits and retesting decisions on evidence for the relevant solid or solution form.", "questions": [ { "text": "How have analyte content and related-compound levels changed under the recorded storage or solution conditions?", "kind": "measurement", "id": "evidence-based-retest-q01" }, { "text": "What evidence supports the permissible preparation age and the decision to use, retest or reject this sample?", "kind": "action", "id": "evidence-based-retest-q02" } ] } ] } ] }, { "id": "biochemical-context-and-use", "name": "Biochemical context and use", "description": "Connect the free compound to biochemical reactions and experimental observations.", "rationale": "Metabolite and assay roles require conditions and evidence before they can guide an experiment.", "layers": [ { "id": "reaction-participation", "name": "Reaction participation", "description": "Record supported formation and consumption relationships.", "findings": [ { "id": "supported-metabolic-links", "name": "Supported metabolic links", "description": "Represent reaction participation through identified substrates, products and catalysts rather than treating a pathway label as proof.", "questions": [ { "text": "Which primary evidence establishes formation or consumption of this compound in the specified organism or enzyme system?", "kind": "provenance", "id": "supported-metabolic-links-q01" }, { "text": "How was the free compound distinguished from other sulfur metabolites or oxidised peptide residues?", "kind": "boundary", "id": "supported-metabolic-links-q02" } ] } ] }, { "id": "experimental-role-and-interpretation", "name": "Experimental role and interpretation", "description": "Determine what an assay using or detecting this compound can establish.", "findings": [ { "id": "use-specific-acceptance", "name": "Use-specific acceptance", "description": "Connect reagent quality, concentration and controls to the intended biochemical endpoint.", "questions": [ { "text": "What role does the compound have in this experiment: analyte, calibration material, substrate or applied test substance?", "kind": "definition", "id": "use-specific-acceptance-q01" }, { "text": "Which purity, stereochemical, concentration and control requirements must be met before interpreting the endpoint?", "kind": "action", "id": "use-specific-acceptance-q02" } ] } ] } ] }, { "id": "handling-and-regulatory-evidence", "name": "Handling and regulatory evidence", "description": "Associate handling decisions and regulatory identity with the exact material and jurisdiction.", "rationale": "Safety information for a hydrate, mixture or neighbouring chemical cannot automatically establish requirements for every form.", "layers": [ { "id": "form-specific-safety", "name": "Form-specific safety", "description": "Assess whether available hazard and handling evidence applies to the sample.", "findings": [ { "id": "applicable-safety-record", "name": "Applicable safety record", "description": "Keep safety classifications and handling instructions traceable to the represented form and source revision.", "questions": [ { "text": "Which current safety data sheet matches this sample's chemical identity, hydration and formulation?", "kind": "provenance", "id": "applicable-safety-record-q01" }, { "text": "What handling and disposal measures does that evidence support for the intended quantity and operation?", "kind": "action", "id": "applicable-safety-record-q02" } ] } ] }, { "id": "jurisdiction-and-data-gaps", "name": "Jurisdiction and data gaps", "description": "Separate established identifiers and restrictions from unresolved regulatory information.", "findings": [ { "id": "verified-regulatory-status", "name": "Verified regulatory status", "description": "Record jurisdiction-specific identifiers, classifications and limits only when their applicability is established.", "questions": [ { "text": "Which official records verify the applicable EC or inventory identifier and classification for this exact substance?", "kind": "provenance", "id": "verified-regulatory-status-q01" }, { "text": "Is any exposure limit substance-specific, a general limit applicable to the operation, or still unverified?", "kind": "boundary", "id": "verified-regulatory-status-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 a recall-based description; no sources were consulted.", "Verify stereospecific CAS, PubChem, and EC identifiers before assigning registry records.", "Physical constants, storage stability, purity specifications, and formal hazard classifications require checking for the exact supplied form." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of L-cysteine sulphinic acid 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": "Molecular formula", "value_or_pattern": "C3H7NO4S", "note": "Formula of the unsalted compound; does not distinguish stereoisomers." }, { "scheme": "Chemical synonym", "value_or_pattern": "L-cysteine sulfinic acid", "note": "Alternative spelling of L-cysteine sulphinic acid; also called L-cysteinesulfinic acid." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of L-cysteine sulphinic acid 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": [ "Research on cysteine oxidation and sulfur amino acid metabolism.", "Biochemical studies of cysteine dioxygenase, which produces it from L-cysteine.", "Studies of cysteine sulfinic acid decarboxylase and the pathway producing hypotaurine and taurine.", "Experimental research on excitatory amino acid signaling." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of L-cysteine sulphinic acid 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": "153.16", "unit": "g/mol" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of L-cysteine sulphinic acid 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": [ "Further oxidation of the sulfinic acid group produces cysteic acid, changing chemical identity and potentially confounding assays.", "Confusion with cysteine, cysteic acid, or a racemic preparation can invalidate experiments requiring this specific metabolite.", "Its excitatory amino acid activity requires consideration in biological experiments; this does not establish a formal hazard classification." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of L-cysteine sulphinic acid 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": [ "Sulphinic and sulfinic are spelling variants and do not identify different substances." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of L-cysteine sulphinic acid 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": "L-cysteine", "difference": "Has a thiol group, -SH, instead of the oxidized sulfinic acid group, -S(O)OH." }, { "name": "L-cysteic acid", "difference": "Has a sulfonic acid group, -SO3H, containing one more oxygen atom." }, { "name": "Hypotaurine", "difference": "Is the decarboxylation product and lacks the amino acid carboxyl group." }, { "name": "Taurine", "difference": "Lacks the carboxyl group and contains a sulfonic acid group rather than a sulfinic acid group." }, { "name": "D-cysteine sulphinic acid", "difference": "Has the opposite configuration at the amino acid stereocenter." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of L-cysteine sulphinic acid this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which hydrate or salt forms are documented, and what water-content and assay corrections are justified for each?", "What reliable measurements establish pKa values, condition-specific solubility and thermal behaviour, including whether decomposition precludes a meaningful boiling point?", "What degradation products and rates occur under relevant solid-storage and aqueous-assay conditions?", "Which validated methods best separate the target from related sulfur compounds and independently quantify its enantiomeric composition?", "Which current official identifiers, hazard classifications and exposure limits apply to the exact material in the intended jurisdiction?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 17, "questions": 28 } }