{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:35:31Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 22.4, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a094c0-da54-73c1-b368-b5d03ffe36c7\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: chemical ionization\nSense to describe: (none recorded)\nDomain code: PHY.OBJ\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: ", "usd": 0.0, "recall": true }, "codex": { "seconds": 70.3, "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: 01a094c0-da63-7572-af45-c234ba02b0d4\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: chemical ionization\nRegistry id: vr.tr.chemical-ionization\nPlane / domain: PHY / PHY.OBJ\nRegistry definition: (none recorded)\nNames folded into this " } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:48:58+00:00", "fields": [ "agent_conduct", "ethics", "owners" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:31+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q471254", "registryId": "vr.tr.chemical-ionization", "name": "chemical ionization", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q471254/", "model": { "registry_id": "vr.tr.chemical-ionization", "name": "chemical ionization", "purpose": "Enable an agent to recognize chemical ionization, assess whether its reaction conditions support an intended analyte-ion assignment, and decide which method adjustments or verification steps are justified.", "definition": "Chemical ionization is an ionization method used in mass spectrometry in which analyte ions form through reactions with reagent ions, commonly producing less fragmentation than electron ionization.", "scope_statement": "This model owns chemical ionization as a gas-phase ion-molecule process and analytical method, provisionally interpreting vr.tr.chemical-ionization as a process despite its PHY.OBJ placement; its defining boundary follows [IUPAC chemical ionization](https://goldbook.iupac.org/terms/view/C01026).", "in_scope": [ "Formation of analyte ions through reactions with reagent ions", "Reagent-ion generation, composition and reaction pathways", "Positive and negative product-ion modes with explicitly recorded mechanisms", "Reaction-region conditions and analyte delivery requirements", "Ion assignments, method suitability and evidence supporting usable operation" ], "out_of_scope": [ "Construction and maintenance of the complete mass spectrometer", "Mass separation, ion detection and downstream quantification as independent methods", "Chemical substances and reagent supplies as material entities", "Upstream chromatography and sample preparation beyond their ionization interface", "Direct electron ionization, free-electron attachment and chemi-ionization as separate mechanisms" ], "distinguishing_features": [ "Identify a gas-phase ion reacting with an analyte molecule to produce the assigned analyte ion; the instrument's mode label alone is insufficient.", "Distinguish electrons used to generate reagent ions from electrons directly ionizing the analyte.", "Distinguish ion-molecule reactions from ionization involving excited neutral reactants; chemical ionization and chemi-ionization are separate terms under [IUPAC terminology](https://goldbook.iupac.org/terms/view/C01044).", "For negative ions, establish whether formation involves an ion-molecule reaction or free-electron attachment, which the cited IUPAC chemical-ionization definition excludes.", "Identify the reaction regime independently of the process name; atmospheric-pressure chemical ionization is a named implementation described by [IUPAC](https://goldbook.iupac.org/terms/view/12336)." ], "characteristics": [ { "name": "Ionization implementation", "kind": "category", "unit_or_values": "Reduced-pressure CI, atmospheric-pressure CI, other documented implementation, unresolved", "why_it_matters": "Determines which source conditions and method comparisons are applicable." }, { "name": "Product-ion polarity", "kind": "category", "unit_or_values": "Positive, negative, alternating", "why_it_matters": "Constrains candidate ion formulas and reaction pathways." }, { "name": "Reagent composition", "kind": "relation", "unit_or_values": "Linked gas or vapor identities, mixture fractions and impurity specifications", "why_it_matters": "Connects supplied reagents to the ions available to react with the analyte." }, { "name": "Observed reagent-ion population", "kind": "relation", "unit_or_values": "Ion formulas, charge states, relative abundances and acquisition conditions", "why_it_matters": "Tests whether the intended reagent chemistry is actually present." }, { "name": "Reaction-region pressure", "kind": "measurement", "unit_or_values": "Pa, with gauge location, calibration and uncertainty", "why_it_matters": "Supports interpretation of collision conditions and comparisons between runs." }, { "name": "Source temperature", "kind": "measurement", "unit_or_values": "K or °C, with sensor location and setpoint-versus-measured distinction", "why_it_matters": "Helps assess analyte delivery, thermal decomposition and clustering." }, { "name": "Reagent delivery rate", "kind": "measurement", "unit_or_values": "mol/s or standard volumetric flow with reference temperature and pressure", "why_it_matters": "Makes reagent supply reproducible without confusing flow with source pressure." }, { "name": "Assigned reaction channel", "kind": "category", "unit_or_values": "Proton transfer, charge transfer, adduct formation, other supported ion-molecule reaction, unresolved", "why_it_matters": "Links an observed ion to a chemically testable formation hypothesis." }, { "name": "Ionization readiness", "kind": "state", "unit_or_values": "Unverified, conditioning, reference-qualified, drifting, failed", "why_it_matters": "Determines whether sample acquisition or troubleshooting is the justified next action." }, { "name": "Analyte-ion assignment", "kind": "relation", "unit_or_values": "Analyte identity linked to ion formula, charge, measured m/z and supporting evidence", "why_it_matters": "Prevents an adduct or fragment from being mistaken for the neutral molecule." } ], "affordances": [ "Classify a reported ionization event from its reactants and mechanism.", "Compare reagent and polarity choices for a specified analyte and analytical objective.", "Check whether documented source conditions fall within a method's validated operating envelope.", "Propose analyte-ion assignments and identify the additional evidence needed to distinguish them.", "Diagnose changes in reagent-ion populations, background and reference response.", "Recommend a bounded method adjustment or suspend interpretation when ionization evidence is inadequate." ], "agent_conduct": { "may": [ "Explain the principle of chemical ionization and its use in mass spectrometry.", "Run and interpret analyses on instruments the agent is authorized to operate." ], "must_not": [ "Operate instruments outside the laboratory's procedures for reagent gases and vacuum systems.", "Report a compound identification as certain when the spectrum supports it only weakly.", "Assist the analysis of samples for illegal drug production or chemical weapons programmes." ], "requires_human": [ "Reporting results that will be used in legal, forensic or clinical decisions." ] }, "ethics": { "considerations": [ "Analytical results can decide court cases, medical treatment and food safety.", "Laboratory gases and equipment can harm staff if handled carelessly." ], "affected_parties": [ "Laboratory staff", "People affected by forensic and clinical results" ] }, "owners": { "steward": "The laboratory that operates each instrument.", "master_systems": [] }, "what_it_is_for": [ "Chemical ionization is used in analytical laboratories to produce analyte ions for mass spectrometric measurement.", "It can help establish molecular mass or support identification when extensive fragmentation would complicate interpretation.", "Its usefulness depends on reagent chemistry, analyte properties and the selected ion polarity." ], "standards_and_regulation": [ "IEC 61010-1, issued by the International Electrotechnical Commission, provides general safety requirements for laboratory electrical equipment used to perform chemical ionization.", "ISO/IEC 17025, issued jointly by the International Organization for Standardization and the International Electrotechnical Commission, applies when the technique is used within the scope of an accredited testing laboratory." ], "failure_modes_and_hazards": [ "Reagent gases can create fire, toxic exposure or oxygen displacement hazards depending on their identity and containment.", "High voltage and heated instrument components can cause electric shock or burns.", "Incorrect assignments of reagent-related ions or interfering signals can produce misleading analytical conclusions." ], "facets_not_applicable": { "recognition": "Chemical ionization is an ion formation process that cannot be identified directly by visual appearance." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q471254: chemical ionization", "url": "https://www.wikidata.org/wiki/Q471254", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Chemical ionization", "url": "https://en.wikipedia.org/wiki/Chemical_ionization", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "process-identity", "name": "Process identity", "description": "Establish the mechanism represented by the registry entry and its relation to named implementations.", "rationale": "The registry's object placement and instrument mode names must not substitute for identifying the ionization process.", "layers": [ { "id": "mechanistic-boundary", "name": "Mechanistic boundary", "description": "Separate chemical ionization from neighboring routes to charged species.", "findings": [ { "id": "ion-molecule-evidence", "name": "Ion-molecule evidence", "description": "Record the evidence that a reagent ion reacts with a gaseous analyte molecule.", "questions": [ { "text": "Which charged reactant and neutral analyte participate in the proposed ion-forming reaction?", "kind": "definition", "id": "ion-molecule-evidence-q01" }, { "text": "What observation distinguishes this pathway from direct electron ionization, electron attachment or chemi-ionization?", "kind": "boundary", "id": "ion-molecule-evidence-q02" } ] } ] }, { "id": "implementation-lineage", "name": "Implementation lineage", "description": "Connect the general process to source-specific implementations without duplicating their models.", "findings": [ { "id": "named-mode-meaning", "name": "Named mode meaning", "description": "Resolve what an implementation or vendor means by its CI designation.", "questions": [ { "text": "Which source manual or method defines the reported CI mode and its pressure regime?", "kind": "provenance", "id": "named-mode-meaning-q01" }, { "text": "Which features belong to this general process and which belong to a narrower implementation such as APCI?", "kind": "boundary", "id": "named-mode-meaning-q02" } ] } ] } ] }, { "id": "reagent-reaction-system", "name": "Reagent reaction system", "description": "Represent the chain from supplied reagents to reactive ions and analyte products.", "rationale": "A reagent label does not establish the actual ion population or dominant reaction.", "layers": [ { "id": "reagent-ion-production", "name": "Reagent-ion production", "description": "Identify how the reacting ions are generated and verified.", "findings": [ { "id": "effective-reagent-population", "name": "Effective reagent population", "description": "Link reagent composition and primary excitation to observed reagent ions.", "questions": [ { "text": "Which gases or vapors are supplied, and how are their initial ions generated?", "kind": "definition", "id": "effective-reagent-population-q01" }, { "text": "Which reagent ions are observed under the actual operating conditions, and in what relative abundances?", "kind": "measurement", "id": "effective-reagent-population-q02" } ] } ] }, { "id": "analyte-reaction-pathways", "name": "Analyte reaction pathways", "description": "Describe competing routes from neutral analyte to detected product ions.", "findings": [ { "id": "supported-reaction-channel", "name": "Supported reaction channel", "description": "Separate proposed reaction equations from experimentally supported assignments.", "questions": [ { "text": "What balanced reaction accounts for the assigned ion, including charge and any transferred species?", "kind": "definition", "id": "supported-reaction-channel-q01" }, { "text": "Which measured or published evidence supports this channel over competing transfer, association or fragmentation pathways?", "kind": "provenance", "id": "supported-reaction-channel-q02" } ] } ] } ] }, { "id": "reaction-environment", "name": "Reaction environment", "description": "Capture conditions governing reagent-analyte encounters and delivery of intact analyte.", "rationale": "Identical reagent names can produce different outcomes under different source and delivery conditions.", "layers": [ { "id": "collision-conditions", "name": "Collision conditions", "description": "Record the physical conditions of the region where reactions occur.", "findings": [ { "id": "reaction-region-envelope", "name": "Reaction-region envelope", "description": "Keep measured conditions, instrument setpoints and inferred conditions distinct.", "questions": [ { "text": "What pressure, temperature and reagent flow characterize the reaction region, and where are they measured?", "kind": "measurement", "id": "reaction-region-envelope-q01" }, { "text": "What evidence bounds reaction time or ion residence time for this source configuration?", "kind": "provenance", "id": "reaction-region-envelope-q02" } ] } ] }, { "id": "analyte-entry", "name": "Analyte entry", "description": "Assess whether the intended analyte reaches the reaction region in a suitable form.", "findings": [ { "id": "gas-phase-availability", "name": "Gas-phase availability", "description": "Track delivery losses and transformations that could be mistaken for ionization behavior.", "questions": [ { "text": "How does the analyte enter the gas phase, and what evidence indicates that it survives delivery intact?", "kind": "provenance", "id": "gas-phase-availability-q01" }, { "text": "Which delivery or temperature adjustment could test suspected condensation, decomposition or incomplete vaporization?", "kind": "action", "id": "gas-phase-availability-q02" } ] } ] } ] }, { "id": "product-ion-interpretation", "name": "Product-ion interpretation", "description": "Connect measured signals to ion identities and bounded conclusions about the analyte.", "rationale": "An observed peak does not by itself identify a neutral molecule or establish its ionization route.", "layers": [ { "id": "ion-assignment", "name": "Ion assignment", "description": "Evaluate molecular, adduct and fragment assignments against available evidence.", "findings": [ { "id": "formula-and-neutral-link", "name": "Formula and neutral link", "description": "Record the explicit transformation connecting an ion formula to a proposed neutral analyte.", "questions": [ { "text": "Which ion formula and charge fit the measured m/z and isotope pattern within stated uncertainty?", "kind": "measurement", "id": "formula-and-neutral-link-q01" }, { "text": "What transferred group, adduct or neutral loss must be accounted for before inferring the neutral mass?", "kind": "definition", "id": "formula-and-neutral-link-q02" } ] } ] }, { "id": "interpretive-limits", "name": "Interpretive limits", "description": "Prevent weak response or limited fragmentation from supporting excessive conclusions.", "findings": [ { "id": "assignment-discrimination", "name": "Assignment discrimination", "description": "Identify unresolved alternatives and useful discriminating experiments.", "questions": [ { "text": "Which alternative analytes, background ions or reaction products remain consistent with the observed signal?", "kind": "boundary", "id": "assignment-discrimination-q01" }, { "text": "Would a reagent change, polarity change, reference standard or tandem mass spectrum distinguish the remaining assignments?", "kind": "action", "id": "assignment-discrimination-q02" } ] } ] } ] }, { "id": "method-control", "name": "Method control", "description": "Determine whether the chemical-ionization method is ready for use and how deviations should be investigated.", "rationale": "Usable operation requires evidence that reagent chemistry and analyte response remain appropriate to the analytical task.", "layers": [ { "id": "qualification-evidence", "name": "Qualification evidence", "description": "Define method-specific evidence for accepting the ionization state.", "findings": [ { "id": "reference-and-blank-behavior", "name": "Reference and blank behavior", "description": "Use reference ions and backgrounds to qualify operation without inventing universal thresholds.", "questions": [ { "text": "Which reference compound, reagent-ion ratios, response measures and blank signals define acceptable CI operation for this method?", "kind": "measurement", "id": "reference-and-blank-behavior-q01" }, { "text": "Which validation record supplies their acceptance limits and applicable source configuration?", "kind": "provenance", "id": "reference-and-blank-behavior-q02" } ] } ] }, { "id": "deviation-response", "name": "Deviation response", "description": "Connect observed chemical changes to bounded troubleshooting actions.", "findings": [ { "id": "chemistry-drift-triage", "name": "Chemistry drift triage", "description": "Investigate reagent supply, contamination and operating-condition changes before accepting altered spectra.", "questions": [ { "text": "Do changes in reagent-ion ratios, adduct patterns or background coincide with changes in gas supply, moisture, temperature or pressure?", "kind": "measurement", "id": "chemistry-drift-triage-q01" }, { "text": "Which approved diagnostic adjustment should be made next, and what reference result must pass before sample interpretation resumes?", "kind": "action", "id": "chemistry-drift-triage-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": [ "The conventional sense is a mass-spectrometric method, so classification as a physical object should be reviewed.", "Negative-ion chemical ionization includes mechanisms such as electron capture and ion-molecule reactions; terminology should be checked for the intended subtype.", "Source pressures, reagent choices and fragmentation depend strongly on implementation; conventional reduced-pressure chemical ionization and atmospheric-pressure chemical ionization should not share an undifferentiated operating range." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of chemical ionization this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Positive-ion chemical ionization", "Negative-ion chemical ionization", "Atmospheric-pressure chemical ionization" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of chemical ionization 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": [ "Supporting molecular-mass assignment through protonated, deprotonated or reagent-adduct ions.", "Characterizing volatile compounds using gas chromatography-mass spectrometry.", "Sensitive detection of electron-capturing compounds, including many halogenated pollutants, using negative-ion methods.", "Analyzing suitable compounds by liquid chromatography-mass spectrometry with atmospheric-pressure chemical ionization." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of chemical ionization 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": [ "Reagent-gas identity, purity and source conditions can change ion populations and spectral reproducibility.", "Adduct formation and competing reaction pathways can complicate molecular-mass assignment.", "Excessive fragmentation or weak analyte ion formation can occur when reaction energetics are unsuitable.", "Source contamination can increase background and reduce sensitivity.", "Depending on the instrument and reagent, operation involves high voltage, heated surfaces, compressed gases and flammable or toxic reagent gases." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of chemical ionization 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": "Electron ionization", "difference": "Electron ionization forms analyte ions directly through electron collisions; chemical ionization uses reagent-mediated reactions." }, { "name": "Electrospray ionization", "difference": "Electrospray transfers ions from charged liquid droplets, whereas chemical ionization relies on reactions involving reagent ions." }, { "name": "Photoionization", "difference": "Direct photoionization uses photon absorption to ionize an analyte; chemical ionization uses chemical reactions." }, { "name": "Chemical ionization source", "difference": "The source is the instrument component that implements the method; chemical ionization is the process." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of chemical ionization this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should the registry's PHY.OBJ placement be corrected to represent an ionization process or analytical method, and does an existing world model already own that concept?", "Does this entry encompass all gas-phase chemical-ionization implementations, or is its intended usage specifically conventional reduced-pressure mass-spectrometric CI?", "How should instrument documentation that labels free-electron attachment as negative chemical ionization be represented alongside the stricter mechanistic definition?", "Which reagent-analyte combinations have sufficient evidence to support selection rules, including competing reactions and unfavorable cases?", "Which implementation-specific validation sources establish operating envelopes, diagnostic ion ratios and acceptance limits?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 15, "questions": 25 } }