{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T10:07:48Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 21.9, "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: 01a09515-2a2a-7f00-bb19-5eb4e1f3a314\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: guanosine pentaphosphate\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": 81.2, "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: 01a09515-2a38-7540-9c86-6dc265b31b78\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: guanosine pentaphosphate\nRegistry id: vr.tr.guanosine-pentaphosphate\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded " } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:57:57+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:32+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q668231", "registryId": "vr.tr.guanosine-pentaphosphate", "name": "guanosine pentaphosphate", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q668231/", "model": { "registry_id": "vr.tr.guanosine-pentaphosphate", "name": "guanosine pentaphosphate", "purpose": "Enable an agent to identify guanosine pentaphosphate, assess the identity and condition of a sample, and judge its suitability for biochemical measurement or use.", "definition": "Guanosine pentaphosphate (pppGpp) is a guanine ribonucleotide bearing a 5′-triphosphate group and a 3′-diphosphate group that functions as an intracellular alarmone in the bacterial stringent response.", "scope_statement": "This model owns vr.tr.guanosine-pentaphosphate in PHY / PHY.MAT, provisionally interpreted as guanosine 3'-diphosphate 5'-triphosphate (pppGpp), including its molecular identity, material forms, analytical quality, stability and context-specific biochemical activity.", "in_scope": [ "Guanosine identity, ribose stereochemistry and the 3'-diphosphate/5'-triphosphate arrangement", "Protonation, counterions, hydration and solution composition of pppGpp materials", "Concentration, purity and discrimination from related guanine nucleotides", "Preparation provenance, storage history and evidence of chemical conversion", "pppGpp-specific biochemical activity with explicit organism and assay context" ], "out_of_scope": [ "Separate models of ppGpp, GTP, GDP and other related nucleotides", "The complete bacterial stringent-response network", "The structure and operation of enzymes that synthesize or hydrolyze pppGpp", "Whole organisms and their stress-response phenotypes", "Commercial reagent products, packaging and manufacturing processes beyond their effects on sample suitability" ], "distinguishing_features": [ "Confirm the 3'-diphosphate and 5'-triphosphate arrangement; counting five phosphates alone does not establish identity. This is the structure associated with the guanosine pentaphosphate synonym in [ChEBI CHEBI:16690](https://www.ebi.ac.uk/chebi/CHEBI%3A16690).", "Distinguish pppGpp from ppGpp by the additional terminal phosphate on the 5' chain, using a method that resolves the two compounds.", "Distinguish pppGpp from GTP by establishing the additional 3'-diphosphate group.", "Require evidence for guanosine and the specified ribose configuration, rather than accepting any nucleotide with five phosphorus atoms.", "Treat measurements labelled '(p)ppGpp' as pooled or ambiguous unless the method reports pppGpp separately." ], "characteristics": [ { "name": "Structural identity", "kind": "category", "unit_or_values": "Guanosine 3'-diphosphate 5'-triphosphate; confirmed, provisional or unresolved", "why_it_matters": "Defines the intended molecule and prevents confusion with phosphate positional isomers." }, { "name": "Identity cross-references", "kind": "relation", "unit_or_values": "Structure-matched ChEBI, PubChem, CAS and EC records where verified", "why_it_matters": "Prevents identifiers for salts, related nucleotides or pooled alarmones from being treated as interchangeable." }, { "name": "Material form", "kind": "category", "unit_or_values": "Protonation convention, counterion identity and stoichiometry, hydration, solid or solution", "why_it_matters": "Determines how weighed material is converted to moles and what accompanies it into an assay." }, { "name": "pppGpp concentration", "kind": "measurement", "unit_or_values": "mol/L, with method, uncertainty and molecular-form basis", "why_it_matters": "Supports reproducible dosing and quantitative comparisons." }, { "name": "Nucleotide impurity profile", "kind": "measurement", "unit_or_values": "Mole fraction or method-qualified chromatographic area percentage for pppGpp, ppGpp, GTP and other resolved species", "why_it_matters": "Related nucleotide impurities can affect interpretation of biochemical results." }, { "name": "Solution environment", "kind": "measurement", "unit_or_values": "pH, temperature in degrees Celsius, buffer and salt concentrations in mmol/L, total and free magnesium where determined", "why_it_matters": "Makes stability and activity observations interpretable under their actual experimental conditions." }, { "name": "Integrity status", "kind": "state", "unit_or_values": "Verified within acceptance limits, conversion detected, untested or indeterminate; with assessment date", "why_it_matters": "Prevents historical purity results from being assumed to describe the current sample." }, { "name": "Biochemical activity evidence", "kind": "relation", "unit_or_values": "Target, organism, assay endpoint, concentration range and supporting experiment", "why_it_matters": "Keeps pppGpp-specific observations separate from claims about the broader alarmone family." }, { "name": "Handling classification", "kind": "category", "unit_or_values": "Form-specific SDS and jurisdiction-specific classification, or explicitly unknown", "why_it_matters": "Supports handling decisions without assuming a biological metabolite or its formulation is hazard-free." } ], "affordances": [ "Match a candidate record or sample to the defined pppGpp structure.", "Calculate assay additions using verified concentration and material-form information.", "Select and interpret an analytical method that separates pppGpp from related nucleotides.", "Accept, requalify or exclude a sample using application-specific purity and integrity criteria.", "Evaluate reported biochemical effects against pppGpp-specific controls and experimental conditions.", "Choose storage and handling conditions supported for the actual preparation." ], "agent_conduct": { "may": [ "Describe pppGpp as a bacterial alarmone in the stringent response, citing sources.", "Report how it was measured and how it was distinguished from ppGpp." ], "must_not": [ "Report pppGpp and ppGpp as one compound when the distinction matters.", "Present findings on bacterial stress signalling as ready antibacterial treatments.", "Report measurements without method and limits.", "Release engineered bacterial strains outside containment." ], "requires_human": [ "Publishing results that depend on an unverified standard.", "Releasing modified strains." ] }, "ethics": { "considerations": [ "Research on bacterial persistence bears on antibiotic resistance and must be reported carefully.", "Laboratory strains need containment to protect others." ], "affected_parties": [ "Researchers", "Patients affected by resistant infections", "Laboratory staff" ] }, "owners": { "steward": "The laboratory that holds the sample or strain.", "master_systems": [] }, "visual_identification": [ "Not identifiable by sight; handled as solutions or small solids.", "Identity is settled by chromatography or mass spectrometry." ], "failure_modes_and_hazards": [ "Degradation into related nucleotides during handling.", "Confusion between alarmone forms in data." ], "what_it_is_for": [ "Guanosine pentaphosphate occurs inside bacteria as a signaling nucleotide involved in the stringent response to nutrient limitation and other stresses.", "It is studied in microbiology and biochemistry to investigate stress regulation, nucleotide metabolism and the enzymes that synthesize or degrade alarmones." ], "standards_and_regulation": [ "The Globally Harmonized System of Classification and Labelling of Chemicals, issued by the United Nations, provides the framework for assessing hazards and communicating any applicable classifications for laboratory chemical preparations containing this compound." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q668231: guanosine pentaphosphate", "url": "https://www.wikidata.org/wiki/Q668231", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Guanosine pentaphosphate", "url": "https://en.wikipedia.org/wiki/Guanosine_pentaphosphate", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "molecular-identity", "name": "Molecular identity", "description": "Establish what the registry name denotes at the level of nucleotide structure.", "rationale": "The name alone does not resolve phosphate topology or distinguish a specific molecule from collective alarmone terminology.", "layers": [ { "id": "phosphate-topology", "name": "Phosphate topology", "description": "Identify the guanosine scaffold and phosphate attachment positions.", "findings": [ { "id": "structural-assignment", "name": "Structural assignment", "description": "Record evidence for the intended 3'-diphosphate/5'-triphosphate structure rather than relying on total phosphate count.", "questions": [ { "text": "Does the structure explicitly show guanosine bearing a 3'-diphosphate and a 5'-triphosphate?", "kind": "definition", "id": "structural-assignment-q01" }, { "text": "What evidence establishes phosphate attachment positions and ribose stereochemistry?", "kind": "measurement", "id": "structural-assignment-q02" } ] } ] }, { "id": "identifier-boundaries", "name": "Identifier boundaries", "description": "Connect registry and chemical identifiers without merging distinct chemical entities.", "findings": [ { "id": "name-and-record-alignment", "name": "Name and record alignment", "description": "Retain distinctions between pppGpp, ppGpp, collective '(p)ppGpp' terminology and records for particular ionic forms.", "questions": [ { "text": "Which structure-bearing source supports interpreting this registry entry specifically as pppGpp?", "kind": "provenance", "id": "name-and-record-alignment-q01" }, { "text": "Does each proposed identifier describe this molecule, a particular salt or a broader nucleotide grouping?", "kind": "boundary", "id": "name-and-record-alignment-q02" } ] } ] } ] }, { "id": "material-form-and-dosing", "name": "Material form and dosing", "description": "Describe the actual pppGpp preparation sufficiently to determine composition and dose.", "rationale": "A nominal mass or concentration is insufficient when counterions, water and assay constituents are unspecified.", "layers": [ { "id": "ionic-and-solid-form", "name": "Ionic and solid form", "description": "Track the form used for composition and mass calculations.", "findings": [ { "id": "mass-basis", "name": "Mass basis", "description": "Associate formula and molar mass with the specified protonation, counterions and hydration of the preparation.", "questions": [ { "text": "Which counterions, water content and protonation convention are included in the stated material composition?", "kind": "definition", "id": "mass-basis-q01" }, { "text": "Is the assigned pppGpp amount measured directly or calculated from a mass corrected for purity and material form?", "kind": "measurement", "id": "mass-basis-q02" } ] } ] }, { "id": "solution-composition", "name": "Solution composition", "description": "Record the chemical environment accompanying a pppGpp dose.", "findings": [ { "id": "assay-ready-stock", "name": "Assay-ready stock", "description": "Describe stock concentration, buffer, pH and salts together with their contributions to the final assay.", "questions": [ { "text": "What are the measured pppGpp concentration, pH, buffer composition and magnesium content of the stock?", "kind": "measurement", "id": "assay-ready-stock-q01" }, { "text": "What dilution delivers the intended pppGpp concentration while meeting the assay's buffer and ion requirements?", "kind": "action", "id": "assay-ready-stock-q02" } ] } ] } ] }, { "id": "analytical-discrimination", "name": "Analytical discrimination", "description": "Establish whether a measurement identifies and quantifies pppGpp specifically.", "rationale": "Signals from related nucleotides, mixtures or sample preparation can be mistaken for pppGpp.", "layers": [ { "id": "specificity-and-resolution", "name": "Specificity and resolution", "description": "Assess separation and identity evidence against plausible nucleotide interferents.", "findings": [ { "id": "resolved-pppgpp-signal", "name": "Resolved pppGpp signal", "description": "Require method-specific evidence that the reported signal belongs to pppGpp.", "questions": [ { "text": "Can the method distinguish pppGpp from ppGpp, GTP and plausible phosphate positional isomers?", "kind": "measurement", "id": "resolved-pppgpp-signal-q01" }, { "text": "Which authentic standards, retention data, mass-spectral evidence or structural measurements support the assignment?", "kind": "provenance", "id": "resolved-pppgpp-signal-q02" } ] } ] }, { "id": "quantitation-and-recovery", "name": "Quantitation and recovery", "description": "Evaluate concentration and purity estimates in the relevant sample matrix.", "findings": [ { "id": "qualified-abundance", "name": "Qualified abundance", "description": "Record calibration, recovery, uncertainty and impurity reporting basis instead of treating peak area as absolute amount.", "questions": [ { "text": "What calibration, detection limits and matrix-effect corrections support the pppGpp amount reported?", "kind": "measurement", "id": "qualified-abundance-q01" }, { "text": "What recovery and preparation controls test whether pppGpp was lost or converted before measurement?", "kind": "measurement", "id": "qualified-abundance-q02" } ] } ] } ] }, { "id": "integrity-and-handling", "name": "Integrity and handling", "description": "Connect preparation history and handling conditions to the current usability of pppGpp.", "rationale": "The starting identity of a preparation does not establish its composition after storage or experimental handling.", "layers": [ { "id": "preparation-and-storage-history", "name": "Preparation and storage history", "description": "Track conditions and residual constituents that may affect pppGpp integrity.", "findings": [ { "id": "current-sample-integrity", "name": "Current sample integrity", "description": "Link lot provenance and exposure history to direct evidence of retained pppGpp content.", "questions": [ { "text": "What preparation, purification, storage-temperature and freeze-thaw history applies to this sample?", "kind": "provenance", "id": "current-sample-integrity-q01" }, { "text": "Do repeat analyses show loss of pppGpp or growth of ppGpp, GTP or other products under the intended handling conditions?", "kind": "measurement", "id": "current-sample-integrity-q02" } ] } ] }, { "id": "use-and-handling-decisions", "name": "Use and handling decisions", "description": "Set evidence-based acceptance and handling requirements for the actual preparation.", "findings": [ { "id": "preparation-specific-permission", "name": "Preparation-specific suitability", "description": "Combine assay acceptance limits with applicable handling information without inventing shelf life or hazard classifications.", "questions": [ { "text": "What purity, concentration and integrity limits must this pppGpp preparation meet before use?", "kind": "action", "id": "preparation-specific-permission-q01" }, { "text": "Which current SDS and local requirements apply to its salt form, solvent and any isotopic label?", "kind": "provenance", "id": "preparation-specific-permission-q02" } ] } ] } ] }, { "id": "biochemical-role-and-conversion", "name": "Biochemical role and conversion", "description": "Represent pppGpp-specific interactions and conversions within explicitly bounded biological systems.", "rationale": "An effect attributed to the alarmone family may not establish the activity of pppGpp itself.", "layers": [ { "id": "formation-and-turnover", "name": "Formation and turnover", "description": "Record reactions that produce or consume pppGpp, with enzyme and organism context.", "findings": [ { "id": "conversion-aware-interpretation", "name": "Conversion-aware interpretation", "description": "Conversion can change the active nucleotide during an experiment: an E. coli enzyme was shown to remove the 5'-terminal phosphate from pppGpp to yield ppGpp. [Primary study](https://pubmed.ncbi.nlm.nih.gov/8394006/).", "questions": [ { "text": "Which demonstrated synthesis and hydrolysis reactions apply in the organism or preparation being modeled?", "kind": "provenance", "id": "conversion-aware-interpretation-q01" }, { "text": "Was pppGpp-to-ppGpp conversion measured or controlled during the experiment?", "kind": "measurement", "id": "conversion-aware-interpretation-q02" } ] } ] }, { "id": "target-and-response-evidence", "name": "Target and response evidence", "description": "Separate direct molecular effects from broader stress-response associations.", "findings": [ { "id": "pppgpp-specific-effect", "name": "pppGpp-specific effect", "description": "Attach each claimed effect to a target, organism, concentration and assay that distinguish pppGpp from related nucleotides.", "questions": [ { "text": "Does the evidence demonstrate direct pppGpp binding or activity, or only an association with a combined '(p)ppGpp' pool?", "kind": "boundary", "id": "pppgpp-specific-effect-q01" }, { "text": "Which ppGpp, GTP and vehicle controls establish the specificity of the observed response?", "kind": "measurement", "id": "pppgpp-specific-effect-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "This description uses recalled knowledge; no sources were consulted.", "Verify database identifiers, protonation state, counterions and hydration before assigning a formula or molar mass to a supplied preparation.", "Specific regulatory targets and the relative roles of pppGpp and ppGpp vary among organisms." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of guanosine pentaphosphate 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": "Biochemical abbreviation", "value_or_pattern": "pppGpp", "note": "Distinguishes guanosine pentaphosphate from guanosine tetraphosphate, ppGpp." }, { "scheme": "Descriptive chemical nomenclature", "value_or_pattern": "guanosine 3′-diphosphate 5′-triphosphate", "note": "Specifies the phosphate groups attached to the ribose; the five phosphates do not form a single chain." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of guanosine pentaphosphate 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": [ "Acts as an endogenous signal that helps bacteria adjust growth and metabolism during nutrient limitation and other stresses.", "Used in biochemical research on stringent-response enzymes and nucleotide-binding regulatory proteins." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of guanosine pentaphosphate 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": [ "Enzymatic degradation or interconversion during sample handling can distort measurements of cellular pppGpp.", "Failure to distinguish pppGpp from ppGpp can obscure their different concentrations and biological effects." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of guanosine pentaphosphate 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": "Guanosine tetraphosphate (ppGpp)", "difference": "Has a 5′-diphosphate group rather than a 5′-triphosphate group, while retaining the 3′-diphosphate group." }, { "name": "Guanosine triphosphate (GTP)", "difference": "Has the 5′-triphosphate group but lacks the additional 3′-diphosphate group." }, { "name": "(p)ppGpp", "difference": "Is collective notation for ppGpp and pppGpp rather than the name of this single molecular species." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of guanosine pentaphosphate this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry's originating record unambiguously identify guanosine 3'-diphosphate 5'-triphosphate, and which CAS, PubChem and EC identifiers match that precise entity?", "Which salt and hydration forms have verified composition, solubility and thermal data, and are meaningful melting or boiling measurements available rather than decomposition observations?", "What storage duration, pH, temperature and freeze-thaw limits are supported by measured pppGpp stability for each relevant preparation?", "Which analytical methods reliably quantify pppGpp separately from ppGpp and other nucleotides in the intended biological matrices?", "Which biological effects are established specifically for pppGpp, and what form-specific hazard classifications or exposure limits, if any, are documented?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 15, "questions": 25 } }