{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T10:07:25Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 26.3, "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: 01a09515-1131-7303-949d-578c17f6a0df\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: guanidinium thiocyanate\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 0", "usd": 0.0, "recall": true }, "codex": { "seconds": 65.4, "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: 01a09515-1128-7993-a0f8-0814ea747cc9\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: guanidinium thiocyanate\nRegistry id: vr.tr.guanidinium-thiocyanate\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded in" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:53:13+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "visual_identification" ] }, "revisions": [ { "at": "2026-10-07T11:41:19+00:00", "engine": "codex", "fields": [ "definition" ], "answering_review": "727d81c070083c34c9196238a589b996903be3580f7d807f3501c87a4227f2fa" } ], "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T12:16:35+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q904487", "registryId": "vr.tr.guanidinium-thiocyanate", "name": "guanidinium thiocyanate", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q904487/", "model": { "registry_id": "vr.tr.guanidinium-thiocyanate", "name": "guanidinium thiocyanate", "purpose": "Enable an agent to recognise guanidinium thiocyanate, assess the condition and suitability of a particular material lot, and determine compatible uses, handling and disposal.", "definition": "Guanidinium thiocyanate is the salt of the guanidinium cation and thiocyanate anion, with formula C2H6N4S, used as a strong chaotropic protein denaturant in nucleic-acid extraction.", "scope_statement": "This model owns the identity, composition, physical state, quality, functional suitability and handling constraints of guanidinium thiocyanate under registry entry vr.tr.guanidinium-thiococyanate, with corrections to registry references governed by the authoritative registry.", "in_scope": [ "Guanidinium thiocyanate identity, synonyms and verified substance identifiers", "Solid material and solutions explicitly characterised by their guanidinium thiocyanate content", "Lot-specific assay, water content, impurities and application grade", "Physical properties and stability under recorded conditions", "Chaotropic and protein-denaturing suitability for intended applications", "Evidence-backed hazards, incompatibilities, storage and waste constraints" ], "out_of_scope": [ "Complete formulations of proprietary extraction and lysis reagents", "End-to-end nucleic acid extraction or purification protocols", "Guanidinium chloride and other guanidinium salts as separate substances", "Thiocyanate salts with different cations", "Manufacturing plant design and synthesis process execution", "Biological samples, purified nucleic acids and assay results" ], "distinguishing_features": [ "Identity evidence must establish both the guanidinium cation and thiocyanate anion; a guanidinium-only identification cannot distinguish this material from guanidinium chloride.", "The thiocyanate assignment must distinguish the salt from compounds bearing a covalently bound isothiocyanate group.", "A product labelled as a lysis buffer is not identified as the pure substance merely because guanidinium thiocyanate is an ingredient.", "Names such as guanidine thiocyanate or guanidinium isothiocyanate require reconciliation against verified substance identifiers rather than acceptance by wording alone.", "Appearance and dissolution behaviour are supporting observations, not sufficient tests of chemical identity or molecular-biology suitability." ], "characteristics": [ { "name": "Verified chemical identity", "kind": "category", "unit_or_values": "Verified name, formula, CAS number, EC number and PubChem CID, each with evidence", "why_it_matters": "Prevents substitution with a different guanidinium salt or thiocyanate-containing compound." }, { "name": "Material presentation", "kind": "state", "unit_or_values": "Solid; solution with specified solvent; component of a separately modelled formulation", "why_it_matters": "Determines which concentration, physical-property and handling records apply." }, { "name": "Guanidinium thiocyanate assay", "kind": "measurement", "unit_or_values": "% by mass, with analytical method and as-received or dry basis", "why_it_matters": "Distinguishes actual salt content from water and other constituents." }, { "name": "Water content", "kind": "measurement", "unit_or_values": "% by mass, with method and sampling date", "why_it_matters": "Supports mass-based preparation accuracy and evaluation of storage-related changes." }, { "name": "Solution concentration", "kind": "measurement", "unit_or_values": "mol/L or % by mass, with solvent, preparation basis and temperature where relevant", "why_it_matters": "Connects a solution's composition to its intended chaotropic use." }, { "name": "Application grade and impurity profile", "kind": "category", "unit_or_values": "Declared grade, measured impurities, detection limits and acceptance specification", "why_it_matters": "A grade label alone does not establish suitability for a sensitive biological workflow." }, { "name": "Nuclease-related quality evidence", "kind": "relation", "unit_or_values": "Lot-linked RNase or DNase test evidence and stated test conditions", "why_it_matters": "Separates an application claim from demonstrated lot quality." }, { "name": "Physical-property evidence", "kind": "measurement", "unit_or_values": "Thermal transitions in °C; solubility with explicit units, solvent and temperature", "why_it_matters": "Supports interpretation of dissolution, crystallisation and thermal behaviour without assuming an ordinary boiling point." }, { "name": "Container and storage condition", "kind": "state", "unit_or_values": "Seal status, exposure history, appearance, storage conditions and assessment date", "why_it_matters": "Connects present condition to confidence in composition and usability." }, { "name": "Applicable hazard and incompatibility record", "kind": "relation", "unit_or_values": "Current supplier SDS and applicable jurisdictional classification for the actual material", "why_it_matters": "Grounds handling and waste decisions in the supplied substance or solution." } ], "affordances": [ "Reconcile a supplier product or lot with the registered chemical identity.", "Compare lot evidence with acceptance criteria for an intended chaotropic application.", "Calculate the required material amount from verified assay and an explicitly defined target concentration.", "Assess whether changes in appearance or exposure history require retesting or quarantine.", "Screen proposed contact materials, cleaning agents and waste streams for documented incompatibilities.", "Trace a solution or aliquot back to its source lot, preparation record and applicable safety information." ], "agent_conduct": { "may": [ "Identify guanidinium thiocyanate from labels, identifiers and safety data sheets.", "Report its hazards and its role in nucleic-acid extraction from official sources.", "Flag waste containing it for correct hazardous-waste segregation." ], "must_not": [ "Mix it or its waste with bleach or acids, which can release toxic gases.", "Dispose of it in drains or ordinary waste.", "Handle it outside a laboratory with appropriate protection.", "Mislabel kits or waste that contain it." ], "requires_human": [ "Changing waste-handling procedures in a laboratory." ] }, "ethics": { "considerations": [ "Mass testing during outbreaks used large volumes of it, putting untrained staff at risk.", "Honest labelling of reagent kits protects workers downstream." ], "affected_parties": [ "Laboratory staff", "Waste handlers", "Cleaners" ] }, "owners": { "steward": "The laboratory or organization that holds the material.", "master_systems": [] }, "visual_identification": [ "Identity rests on the label and safety data sheet, not appearance.", "Often present in extraction kit buffers, named on the kit insert." ], "failure_modes_and_hazards": [ "Harmful by swallowing, skin contact and inhalation.", "Release of toxic gas when mixed with bleach or acids.", "Harmful to aquatic life if released." ], "standards_and_regulation": [ "Globally Harmonized System of Classification and Labelling of Chemicals (GHS), United Nations." ], "what_it_is_for": [ "Guanidinium thiocyanate is encountered in laboratory reagents for extracting RNA and DNA from biological samples.", "Its protein-denaturing action supports sample disruption and inactivation of enzymes that would otherwise degrade nucleic acids." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q904487: guanidinium thiocyanate", "url": "https://www.wikidata.org/wiki/Q904487", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Guanidinium thiocyanate", "url": "https://en.wikipedia.org/wiki/Guanidinium_thiocyanate", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "salt-identity-and-material-boundary", "name": "Salt identity and material boundary", "description": "Establishes which chemical and material instance the entry represents.", "rationale": "Guanidinium salts, thiocyanate compounds and formulated extraction reagents must not collapse into one identity.", "layers": [ { "id": "ionic-identity", "name": "Ionic identity", "description": "Resolves the guanidinium and thiocyanate assignments using chemical evidence.", "findings": [ { "id": "cation-anion-confirmation", "name": "Cation and anion confirmation", "description": "Record evidence sufficient to identify the salt and distinguish nearby chemical identities.", "questions": [ { "text": "Which verified structure and substance identifiers establish the guanidinium cation and thiocyanate anion?", "kind": "definition", "id": "cation-anion-confirmation-q01" }, { "text": "What analytical or supplier evidence distinguishes this lot from guanidinium chloride and other thiocyanate salts?", "kind": "provenance", "id": "cation-anion-confirmation-q02" } ] } ] }, { "id": "substance-solution-formulation", "name": "Substance, solution and formulation", "description": "Separates the salt's identity from the composition of a supplied product.", "findings": [ { "id": "declared-material-boundary", "name": "Declared material boundary", "description": "Identify whether the record describes solid salt, a defined solution or an ingredient within another model.", "questions": [ { "text": "Does the supplied material contain only the declared salt, a specified solvent, or additional functional ingredients?", "kind": "boundary", "id": "declared-material-boundary-q01" }, { "text": "Which formulation record owns detergents, buffers or other additives accompanying guanidinium thiocyanate?", "kind": "boundary", "id": "declared-material-boundary-q02" } ] } ] } ] }, { "id": "composition-and-physical-condition", "name": "Composition and physical condition", "description": "Characterises usable salt content and the condition of solids or solutions.", "rationale": "Weighed mass, nominal concentration and visible condition provide different evidence about the material available for use.", "layers": [ { "id": "assay-water-and-impurities", "name": "Assay, water and impurities", "description": "Makes composition claims quantitative and traceable to a lot.", "findings": [ { "id": "effective-salt-content", "name": "Effective salt content", "description": "Record assay basis, water content and relevant impurities before using mass as a measure of salt quantity.", "questions": [ { "text": "What are the measured guanidinium thiocyanate assay and water content, and are they reported on an as-received or dry basis?", "kind": "measurement", "id": "effective-salt-content-q01" }, { "text": "Which impurities were measured, by what methods, and against which application-specific limits?", "kind": "measurement", "id": "effective-salt-content-q02" } ] } ] }, { "id": "phase-dissolution-and-storage", "name": "Phase, dissolution and storage", "description": "Connects observable condition to concentration, temperature and exposure history.", "findings": [ { "id": "condition-dependent-usability", "name": "Condition-dependent usability", "description": "Record physical observations without treating them as conclusive evidence of purity or degradation.", "questions": [ { "text": "At the recorded solvent composition, concentration and temperature, is the material fully dissolved or does solid remain?", "kind": "measurement", "id": "condition-dependent-usability-q01" }, { "text": "What evidence determines whether caking, precipitation or a change in appearance warrants retesting, reconditioning or rejection?", "kind": "action", "id": "condition-dependent-usability-q02" } ] } ] } ] }, { "id": "chaotropic-application-suitability", "name": "Chaotropic application suitability", "description": "Relates material quality and composition to its intended protein-denaturing or nucleic-acid-processing role.", "rationale": "Chemical identity alone cannot establish functional performance or compatibility with a downstream assay.", "layers": [ { "id": "functional-use-conditions", "name": "Functional use conditions", "description": "Records the conditions under which the salt's intended chaotropic function is supported.", "findings": [ { "id": "application-qualified-performance", "name": "Application-qualified performance", "description": "Treat functional suitability as conditional on concentration, matrix and supporting evidence.", "questions": [ { "text": "What evidence supports the intended denaturing or nuclease-inactivating function at the proposed concentration and sample conditions?", "kind": "provenance", "id": "application-qualified-performance-q01" }, { "text": "Which performance requirements belong to this material specification, and which depend on the complete extraction formulation or protocol?", "kind": "boundary", "id": "application-qualified-performance-q02" } ] } ] }, { "id": "grade-and-downstream-carryover", "name": "Grade and downstream carryover", "description": "Connects lot qualification and residual salt to the requirements of subsequent operations.", "findings": [ { "id": "sensitive-workflow-acceptance", "name": "Sensitive workflow acceptance", "description": "Record evidence needed to accept a lot and evaluate carryover into a specified downstream method.", "questions": [ { "text": "Which lot-specific tests support the claimed molecular-biology grade, including any RNase or DNase specifications?", "kind": "provenance", "id": "sensitive-workflow-acceptance-q01" }, { "text": "What residual guanidinium thiocyanate limit and verification method apply to the intended downstream assay?", "kind": "measurement", "id": "sensitive-workflow-acceptance-q02" } ] } ] } ] }, { "id": "chemical-safety-and-disposition", "name": "Chemical safety and disposition", "description": "Records applicable hazard evidence, contact restrictions and disposition requirements.", "rationale": "Safe decisions require guanidinium thiocyanate-specific compatibility evidence and knowledge of the actual solution or waste composition.", "layers": [ { "id": "hazard-and-reactive-contact", "name": "Hazard and reactive contact", "description": "Resolves handling constraints and proposed chemical contacts against current evidence.", "findings": [ { "id": "documented-contact-restrictions", "name": "Documented contact restrictions", "description": "Require explicit compatibility assessment for cleaning agents and other chemicals that may contact the material.", "questions": [ { "text": "Which current SDS and jurisdictional classification apply to this supplier's solid or solution?", "kind": "provenance", "id": "documented-contact-restrictions-q01" }, { "text": "What do authoritative compatibility sources require for contact with hypochlorite bleach, acids and other proposed cleaning or treatment agents?", "kind": "action", "id": "documented-contact-restrictions-q02" } ] } ] }, { "id": "storage-and-waste-disposition", "name": "Storage and waste disposition", "description": "Maintains identity and composition information through storage, quarantine and waste routing.", "findings": [ { "id": "traceable-material-disposition", "name": "Traceable material disposition", "description": "Base retention or disposal on documented material condition and the composition of any resulting waste.", "questions": [ { "text": "Which documented storage conditions, container requirements and expiry or retest criteria apply to this lot or prepared solution?", "kind": "action", "id": "traceable-material-disposition-q01" }, { "text": "Which approved waste route accepts the actual guanidinium thiocyanate concentration, solvents, additives and biological contaminants present?", "kind": "action", "id": "traceable-material-disposition-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 recalled knowledge; no sources were consulted.", "Verify product-specific hazard classifications, purity specifications and any occupational exposure limits against authoritative records.", "The concentration range describes common working formulations, not an intrinsic material constant; thermal properties and additional registry identifiers require verification." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of guanidinium thiocyanate 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": [ "Reagent-grade material", "Molecular-biology-grade material" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of guanidinium thiocyanate 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": "593-84-0", "note": "Identifies guanidinium thiocyanate, also commonly called guanidine thiocyanate or guanidine isothiocyanate." }, { "scheme": "Molecular formula", "value_or_pattern": "CH6N4S", "note": "One guanidinium cation, CH6N3+, paired with one thiocyanate anion, SCN−." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of guanidinium thiocyanate this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-standards-and-regulation", "name": "Standards and regulation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "United Nations Globally Harmonized System of Classification and Labelling of Chemicals (GHS): framework for communicating chemical hazards.", "European Union CLP Regulation (EC) No 1272/2008: classification, labelling and packaging requirements.", "US Occupational Safety and Health Administration Hazard Communication Standard, 29 CFR 1910.1200: workplace hazard communication and safety data sheets." ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of guanidinium thiocyanate 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": [ "Disruption of cells and denaturation of proteins during RNA extraction.", "Inactivation of ribonucleases to help preserve extracted RNA.", "Chaotropic component of silica-based DNA and RNA purification buffers.", "Component of acid guanidinium thiocyanate-phenol-chloroform RNA extraction reagents." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of guanidinium thiocyanate 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": "118.16", "unit": "g/mol" }, { "quantity": "Concentration in concentrated nucleic-acid extraction buffers", "typical_range": "Approximately 4-6, depending on formulation", "unit": "mol/L" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of guanidinium thiocyanate 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": [ "Harmful exposure can occur through ingestion, skin contact or inhalation of dust; handling requires the applicable product safety data sheet.", "Contact with acids can release toxic gases.", "Mixing guanidinium thiocyanate-containing waste with hypochlorite bleach can generate highly toxic reaction products.", "Residual reagent carried into purified nucleic acids can inhibit downstream enzymatic reactions.", "Crystallization or incomplete dissolution can alter buffer composition and impair extraction performance." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of guanidinium thiocyanate 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": [ "Hazard labels, safety data sheet requirements and waste-disposal obligations depend on jurisdiction and product formulation." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of guanidinium thiocyanate 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": "Guanidinium chloride", "difference": "Contains chloride instead of thiocyanate; both are chaotropic salts, but their properties and suitable extraction formulations differ." }, { "name": "Guanidine", "difference": "The neutral base rather than the guanidinium salt paired with thiocyanate." }, { "name": "Guanidine isothiocyanate", "difference": "A conventional synonym for this reagent, not a separate substance in this usage." }, { "name": "Guanidinium thiocyanate-phenol extraction reagent", "difference": "A formulated mixture containing the salt and other components, rather than the individual chemical substance." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of guanidinium thiocyanate this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which authoritative sources confirm the identifier set and resolve the guanidine thiocyanate and guanidinium isothiocyanate naming conventions?", "Which thermal-transition and solubility measurements are reliable, and under what conditions does decomposition prevent reporting a meaningful boiling point?", "What evidence establishes water uptake, storage stability and appropriate retest intervals for relevant solids and solutions?", "Which grade specifications, impurity limits and carryover thresholds are validated for the intended nucleic acid workflows?", "Which current classifications, exposure limits if established, incompatibility evidence and disposal requirements apply in the intended jurisdiction?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 17, "questions": 25 } }