{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T09:06:41Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 22.1, "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: 01a094dd-6710-7723-a108-3bbbe98edb73\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: depurination\nSense to describe: (none recorded)\nDomain code: ACT.PRC\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001 re", "usd": 0.0, "recall": true }, "codex": { "seconds": 69.0, "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: 01a094dd-6709-72f3-9baa-98dd31d8a86a\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: depurination\nRegistry id: vr.tr.depurination\nPlane / domain: ACT / ACT.PRC\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:16:20+00:00", "fields": [ "agent_conduct", "ethics", "owners" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:33+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q903582", "registryId": "vr.tr.depurination", "name": "depurination", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q903582/", "model": { "registry_id": "vr.tr.depurination", "name": "depurination", "purpose": "Enable an agent to recognize, quantify and assess depurination events and choose evidence-supported responses to purine loss from nucleic-acid substrates.", "definition": "Depurination is the cleavage of the N-glycosidic bond linking a purine base to its sugar in a nucleoside, nucleotide, or nucleic acid, releasing the base and, in a nucleic acid, leaving an abasic site.", "scope_statement": "This ACT / ACT.PRC model owns depurination as a chemical process: cleavage of a purine-sugar N-glycosidic bond, its substrate and reaction conditions, evidence of purine release, and immediate products; downstream repair and biological outcomes are linked processes.", "in_scope": [ "Identification of the purine-bearing substrate and the bond whose cleavage constitutes depurination", "Spontaneous, chemically promoted or catalyzed purine removal, with the route explicitly recorded", "Reaction conditions, exposure history and context-specific kinetics", "Released purines and residual sugar-containing products, including apurinic sites in nucleic-acid chains", "Measurement validity, competing explanations and decisions about preserving or processing affected material" ], "out_of_scope": [ "Depyrimidination, which removes a pyrimidine base", "Deamination and oxidation that modify a base without necessarily removing it", "Phosphodiester backbone cleavage as a distinct reaction", "Complete base-excision repair pathways and their regulation", "Purine biosynthesis, salvage and degradation after base release", "Organism-level disease or mutation models beyond documented links to the reaction" ], "distinguishing_features": [ "The departing group must be a purine base or an identified purine derivative; pyrimidine loss is a different process.", "The defining bond loss is between the purine and its sugar, rather than between successive residues of the nucleic-acid backbone.", "In a nucleic-acid chain, the immediate residue lacks its purine; an observed strand break alone does not establish that depurination occurred.", "An abasic-site signal alone does not identify the missing base or establish the route that removed it.", "Depurination describes a transformation; an apurinic site describes a resulting molecular state." ], "characteristics": [ { "name": "Substrate class", "kind": "category", "unit_or_values": "DNA; RNA; purine nucleoside; purine nucleotide; other specified purine-bearing substrate", "why_it_matters": "Determines which reaction evidence, product description and kinetic comparisons apply." }, { "name": "Departing purine identity", "kind": "category", "unit_or_values": "Adenine; guanine; specified modified purine; unresolved", "why_it_matters": "Distinguishes depurination from other base-loss reactions and supports product accounting." }, { "name": "Affected residue context", "kind": "relation", "unit_or_values": "Parent molecule, residue coordinate, neighboring sequence and strand or structural context where known", "why_it_matters": "Allows localized events to be distinguished from bulk averages." }, { "name": "Reaction route", "kind": "category", "unit_or_values": "Uncatalyzed hydrolysis; acid-promoted hydrolysis; catalyst-mediated removal; unresolved, with evidence", "why_it_matters": "Prevents equivalent products from being treated as evidence of identical causes." }, { "name": "Reaction environment", "kind": "measurement", "unit_or_values": "pH; temperature in °C; duration in s; buffer and solute concentrations in mol/L; water availability where relevant", "why_it_matters": "Makes reaction extent and rates interpretable in their actual experimental or storage context." }, { "name": "Purine-loss extent", "kind": "measurement", "unit_or_values": "mol released purine/mol initial target purine, or sites per specified number of nucleotides; denominator required", "why_it_matters": "Separates reaction extent from sample size and from remaining abasic-site abundance." }, { "name": "Observed reaction rate", "kind": "measurement", "unit_or_values": "mol/L/s, or s^-1 for a justified first-order model; conditions and uncertainty required", "why_it_matters": "Supports comparisons and predictions only when the kinetic model and conditions are compatible." }, { "name": "Residual backbone state", "kind": "state", "unit_or_values": "Intact at affected site; cleaved; mixed population; unmeasured", "why_it_matters": "Separates initial base loss from subsequent strand damage." }, { "name": "Evidence status", "kind": "state", "unit_or_values": "Directly observed purine release; localized product evidence; indirect assay inference; unresolved", "why_it_matters": "Controls how confidently an agent can attribute damage or recommend further processing." } ], "affordances": [ "Classify whether an observed molecular change meets the depurination boundary.", "Record affected purines, substrate context and immediate products without conflating reaction and lesion.", "Compare measured reaction extents or rates under explicitly matched conditions.", "Select complementary measurements to distinguish purine release, abasic-site accumulation and strand cleavage.", "Evaluate handling or storage changes against measured depurination under relevant conditions.", "Route affected material to a separate repair, recovery or disposal workflow using application-specific acceptance criteria." ], "agent_conduct": { "may": [ "Explain depurination and its role in DNA damage and sequencing from scientific sources.", "Note its effect on sample quality in laboratory records." ], "must_not": [ "Misreport how sample degradation affects test results.", "Present damaged DNA results as reliable without stating the limits.", "Use DNA samples beyond the consent under which they were taken." ], "requires_human": [ "Relying on degraded DNA results for decisions about a person." ] }, "ethics": { "considerations": [ "Degraded samples can lead to wrong identifications or diagnoses.", "Genetic material carries private information about people and their relatives." ], "affected_parties": [ "Patients and donors", "People identified by DNA evidence", "Researchers" ] }, "owners": { "steward": "Nobody owns the process; laboratories answer for their samples and results.", "master_systems": [] }, "what_it_is_for": [ "Depurination is encountered in nucleic acid chemistry, DNA damage research and studies of biological repair.", "It is relevant when assessing the integrity of biological samples, stored nucleic acids and material intended for sequencing.", "Researchers examine purine loss and resulting abasic sites to understand degradation and its effects on downstream measurements." ], "failure_modes_and_hazards": [ "Unrepaired abasic sites in DNA can interfere with replication and contribute to mutations.", "Depurination can promote nucleic acid strand breakage and reduce sample integrity.", "Damage in analytical samples can cause sequencing errors, loss of usable material or biased results." ], "facets_not_applicable": { "interfaces": "No universal standard or regulation applies specifically to depurination, while sample quality requirements depend on the analytical application.", "recognition": "Depurination is a molecular process that cannot be identified visually and requires analytical evidence of purine loss or abasic sites." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q903582: depurination", "url": "https://www.wikidata.org/wiki/Q903582", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Depurination", "url": "https://en.wikipedia.org/wiki/Depurination", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "purine-loss-identity", "name": "Purine-loss identity", "description": "Establish the molecular event and the substrate on which it occurred.", "rationale": "An agent must identify a specific purine-sugar bond loss before assigning the process label.", "layers": [ { "id": "defining-bond-change", "name": "Defining bond change", "description": "Separate base release from other forms of nucleic-acid alteration.", "findings": [ { "id": "purine-release-boundary", "name": "Purine release boundary", "description": "DNA depurination cleaves the purine-deoxyribose glycosidic bond without requiring initial phosphodiester backbone disruption. [Depurination decreases fidelity of DNA synthesis in vitro](https://www.nature.com/articles/270537a0)", "questions": [ { "text": "Which purine-sugar bond was cleaved, and how was the departing base identified?", "kind": "definition", "id": "purine-release-boundary-q01" }, { "text": "What evidence distinguishes this event from depyrimidination, base modification or direct backbone cleavage?", "kind": "boundary", "id": "purine-release-boundary-q02" } ] } ] }, { "id": "substrate-and-site", "name": "Substrate and site", "description": "Locate the event within a chemically specified substrate.", "findings": [ { "id": "purine-bearing-substrate", "name": "Purine-bearing substrate", "description": "Record sugar type, base identity, molecular context and any prior base modification; do not transfer observations between substrate classes without justification.", "questions": [ { "text": "Is the substrate DNA, RNA, a free nucleoside or nucleotide, or another specified purine-bearing molecule?", "kind": "definition", "id": "purine-bearing-substrate-q01" }, { "text": "Which residue coordinates, sequence context and pre-existing purine modifications are established rather than inferred?", "kind": "provenance", "id": "purine-bearing-substrate-q02" } ] } ] } ] }, { "id": "reaction-route-and-exposure", "name": "Reaction route and exposure", "description": "Represent the circumstances that produced purine loss and the evidence supporting causal attribution.", "rationale": "A shared product does not justify assuming a shared mechanism or a transferable rate.", "layers": [ { "id": "route-attribution", "name": "Route attribution", "description": "Distinguish the observed transformation from its proposed cause.", "findings": [ { "id": "catalysis-evidence", "name": "Catalysis evidence", "description": "Record whether purine removal is attributed to background hydrolysis, chemical promotion or a specified catalyst, with controls supporting that attribution.", "questions": [ { "text": "What observations support the assigned reaction route beyond merely detecting an abasic product?", "kind": "provenance", "id": "catalysis-evidence-q01" }, { "text": "Which catalyst-free, untreated or otherwise matched controls distinguish the proposed cause from background purine loss?", "kind": "measurement", "id": "catalysis-evidence-q02" } ] } ] }, { "id": "exposure-and-kinetics", "name": "Exposure and kinetics", "description": "Connect measured purine loss to a defined condition history.", "findings": [ { "id": "condition-specific-rate", "name": "Condition-specific rate", "description": "Treat a reported rate as conditional on substrate, environment, sampling interval and fitted kinetic model; retain the underlying time-course evidence.", "questions": [ { "text": "What pH, temperature, buffer composition and exposure durations applied before and during measurement?", "kind": "measurement", "id": "condition-specific-rate-q01" }, { "text": "What time-course data and normalization justify the reported rate or half-life?", "kind": "measurement", "id": "condition-specific-rate-q02" }, { "text": "Within which tested conditions may this rate be used to predict further purine loss?", "kind": "boundary", "id": "condition-specific-rate-q03" } ] } ] } ] }, { "id": "products-and-detection", "name": "Products and detection", "description": "Account for released bases and residual products while evaluating assay specificity.", "rationale": "Neither abasic-site abundance nor fragmentation alone uniquely measures depurination.", "layers": [ { "id": "product-accounting", "name": "Product accounting", "description": "Track immediate base-loss products separately from their subsequent conversion.", "findings": [ { "id": "base-loss-versus-chain-breakage", "name": "Base loss versus chain breakage", "description": "Depurination and subsequent cleavage at apurinic sites require separate observations; defined oligonucleotide experiments have characterized these successive transformations. [Mechanistic studies on depurination and apurinic site chain breakage](https://pubmed.ncbi.nlm.nih.gov/7800492/)", "questions": [ { "text": "Which released purines and residual apurinic products were measured at each sampling time?", "kind": "measurement", "id": "base-loss-versus-chain-breakage-q01" }, { "text": "Was backbone cleavage already present, produced during analysis, or observed after the initial purine-loss interval?", "kind": "boundary", "id": "base-loss-versus-chain-breakage-q02" } ] } ] }, { "id": "assay-specificity", "name": "Assay specificity", "description": "Determine what each analytical signal can establish about purine loss.", "findings": [ { "id": "depurination-attribution", "name": "Depurination attribution", "description": "Record whether an assay detects released purines, abasic residues or strand breaks, and identify alternative processes and handling artifacts that could generate the signal.", "questions": [ { "text": "What analyte does the assay measure, with what calibration, detection limit and uncertainty?", "kind": "measurement", "id": "depurination-attribution-q01" }, { "text": "How are pyrimidine-derived abasic sites, pre-existing free purines and sample-preparation damage excluded or quantified?", "kind": "boundary", "id": "depurination-attribution-q02" }, { "text": "Which independent measurement would resolve the remaining ambiguity about purine loss?", "kind": "action", "id": "depurination-attribution-q03" } ] } ] } ] }, { "id": "material-state-and-response", "name": "Material state and response", "description": "Translate established depurination evidence into decisions about the affected material.", "rationale": "Reaction recognition must support decisions while preserving uncertainty about downstream effects.", "layers": [ { "id": "remaining-substrate-usability", "name": "Remaining substrate usability", "description": "Assess material against the requirements of its intended use.", "findings": [ { "id": "application-specific-damage-assessment", "name": "Application-specific damage assessment", "description": "Keep measured purine loss, remaining lesion burden, backbone integrity and performance in the intended application as distinct assessments.", "questions": [ { "text": "What purine-loss burden, site distribution and backbone state are established for this material?", "kind": "measurement", "id": "application-specific-damage-assessment-q01" }, { "text": "Which application-specific evidence or acceptance criterion determines whether the material remains usable?", "kind": "action", "id": "application-specific-damage-assessment-q02" } ] } ] }, { "id": "intervention-and-handoff", "name": "Intervention and handoff", "description": "Choose supported measures to limit additional loss or manage its products.", "findings": [ { "id": "response-selection", "name": "Response selection", "description": "Link handling changes to evidence about further depurination and hand off lesion processing to the appropriate repair or recovery model.", "questions": [ { "text": "Which tested change in exposure, storage or processing reduces additional purine loss for this substrate?", "kind": "action", "id": "response-selection-q01" }, { "text": "What evidence supports preservation, repair, remeasurement or rejection of the affected material?", "kind": "action", "id": "response-selection-q02" }, { "text": "Which proposed outcomes require a separate repair, replication or biological-effect model?", "kind": "boundary", "id": "response-selection-q03" } ] } ] } ] }, { "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 unqualified term most commonly concerns purine loss from DNA, but also applies to other purine-containing substrates.", "Spontaneous, acid-catalysed and enzymatic depurination describe mechanisms or conditions, not mutually exclusive formal classes.", "No numerical biological rate is supplied because rates depend strongly on experimental conditions." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of depurination 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": [ "Spontaneous hydrolytic depurination", "Acid-catalysed depurination", "Enzymatic depurination" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of depurination 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": [ "Studying spontaneous DNA damage and base-excision repair.", "Producing abasic DNA substrates for biochemical experiments.", "Controlled purine removal followed by strand cleavage in chemical DNA sequencing.", "Assessing DNA degradation during storage and chemical processing." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of depurination 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": "Depurination rate constant", "typical_range": "Strongly dependent on temperature, pH, substrate and molecular environment; no universal range.", "unit": "s⁻¹" }, { "quantity": "Abasic-site frequency", "typical_range": "Depends on exposure and repair; abasic-site measurements alone do not establish depurination as the cause.", "unit": "sites per nucleotide" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of depurination 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": [ "Unrepaired abasic sites can block DNA replication or promote mutagenic bypass.", "Abasic sites can undergo subsequent reactions that break the nucleic-acid backbone.", "Acidic conditions and elevated temperatures can accelerate unwanted depurination during DNA handling.", "Depurination can damage oligonucleotides during chemical synthesis.", "Certain ribosome-inactivating toxins remove a specific adenine from ribosomal RNA, impairing protein synthesis." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of depurination 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": "Depyrimidination", "difference": "Removes a pyrimidine base rather than a purine base." }, { "name": "Deamination", "difference": "Removes an amino group from a base rather than detaching the base from its sugar." }, { "name": "Abasic site", "difference": "The base-free position left in a nucleic acid is a structural lesion; depurination is one process that produces it." }, { "name": "Nucleic-acid strand cleavage", "difference": "Breaks the sugar-phosphate backbone; depurination initially breaks the base-sugar bond." }, { "name": "Base-excision repair", "difference": "A repair pathway that removes damaged bases and restores DNA; depurination itself is a base-removal event." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of depurination this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should the registry apply depurination broadly to purine nucleosides, nucleotides, DNA and RNA, or reserve this entry for a narrower substrate scope?", "Should enzyme-mediated excision of normal or modified purines be represented as depurination routes here or linked to narrower catalytic-process entries?", "Which primary datasets support quantitative rate comparisons across substrate classes, purine modifications and environmental conditions?", "Which assay combinations can distinguish purine-derived abasic sites from other abasic products in the intended sample types?", "What application-specific thresholds connect measured purine loss to a justified preservation, repair or rejection decision?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 14, "questions": 25 } }