{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T09:37:13Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 15.1, "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: 01a094f9-4dcd-7700-b263-90278a2527de\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: faicar\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001 register", "usd": 0.0, "recall": true }, "codex": { "seconds": 72.6, "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: 01a094f9-4dc8-7b20-893a-7616b0375f68\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: faicar\nRegistry id: vr.tr.faicar\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext fo" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:51:00+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:29+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q2817110", "registryId": "vr.tr.faicar", "name": "faicar", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q2817110/", "model": { "registry_id": "vr.tr.faicar", "name": "faicar", "purpose": "Enable an agent to identify FAICAR, assess the identity and condition of a FAICAR-containing sample, and judge its suitability for studying purine biosynthesis.", "definition": "FAICAR is 5-formamidoimidazole-4-carboxamide ribonucleotide, a formylated nucleotide intermediate in de novo purine biosynthesis that undergoes ring closure to form inosine monophosphate.", "scope_statement": "This model owns vr.tr.faicar as the molecular substance provisionally identified as 5-formamidoimidazole-4-carboxamide ribonucleotide, including its chemical forms, sample quality, analytical recognition and biochemical participation.", "in_scope": [ "FAICAR molecular identity, ribose stereochemistry and 5'-phosphate attachment", "Protonation, counterions, hydration and their effects on reported composition", "FAICAR concentration, purity and distinction from related pathway metabolites", "Formation from AICAR and conversion to inosine monophosphate", "Sample preservation, assay compatibility and handling evidence" ], "out_of_scope": [ "AICAR, IMP and other purine-pathway metabolites as independently owned substances", "ATIC, PurH and PurP enzyme structures and complete catalytic models", "The complete purine biosynthesis pathway and its regulation", "Organism-wide metabolic states or clinical interpretations", "Commercial reagent formulations and laboratory instruments as independent things" ], "distinguishing_features": [ "The proposed identity contains a formamido substituent where AICAR has an amino substituent; identification must resolve this chemical difference.", "The proposed identity includes a ribose-linked 5'-phosphate, distinguishing it from corresponding unphosphorylated compounds.", "FAICAR retains the substituted imidazole structure preceding ring closure to IMP; an IMP signal does not establish FAICAR identity.", "The reference neutral-acid formula is C10H15N4O9P and the PubChem CID is 166760; formula agreement alone does not establish connectivity or stereochemistry. [PubChem FAICAR](https://pubchem.ncbi.nlm.nih.gov/compound/Faicar)" ], "characteristics": [ { "name": "Chemical identity assignment", "kind": "category", "unit_or_values": "FAICAR reference match; tentative match; unresolved", "why_it_matters": "The registry has no definition, so the name-to-structure assignment needs explicit supporting evidence." }, { "name": "Molecular form", "kind": "category", "unit_or_values": "Neutral-acid representation; specified ionic form; specified salt or hydrate; unknown", "why_it_matters": "Formula, molecular mass and preparation calculations depend on the material form." }, { "name": "FAICAR concentration", "kind": "measurement", "unit_or_values": "µmol/L or mmol/L, with method, uncertainty and sampling time", "why_it_matters": "A usable assay requires the concentration of FAICAR itself, not merely the nominal amount of a preparation." }, { "name": "FAICAR purity", "kind": "measurement", "unit_or_values": "Percentage with stated basis and method; separately quantified AICAR and IMP where measured", "why_it_matters": "Neighbouring metabolites can confound identity, reaction rates and endpoint measurements." }, { "name": "Solution conditions", "kind": "state", "unit_or_values": "Measured pH, temperature in °C, solvent, buffer and ionic composition", "why_it_matters": "The chemical form and suitability of a sample must be judged under its actual conditions." }, { "name": "Biochemical role", "kind": "relation", "unit_or_values": "Product of a documented AICAR formylation reaction; substrate of a documented IMP-forming reaction", "why_it_matters": "A pathway relationship must name the organism and enzyme rather than assuming one universal catalyst." }, { "name": "Preservation history", "kind": "state", "unit_or_values": "Preparation time, storage temperature, elapsed storage, freeze-thaw count and latest integrity measurement", "why_it_matters": "A previous identity check does not establish the current composition of the sample." } ], "affordances": [ "Resolve a FAICAR label against a chemical structure and authoritative identifier.", "Compare sample measurements with evidence distinguishing FAICAR from AICAR and IMP.", "Calculate preparation amounts using the documented chemical form and measured purity.", "Assess whether a sample is suitable as an IMP cyclohydrolase substrate under specified assay conditions.", "Track FAICAR production or consumption while preserving organism, enzyme and sampling context.", "Request reanalysis or withhold use when identity, preservation or handling evidence is insufficient." ], "agent_conduct": { "may": [ "Identify FAICAR as an intermediate of purine synthesis and report it with its source and evidence.", "Describe its role in the pathway and the enzyme step that converts it, citing literature." ], "must_not": [ "Report a measurement of FAICAR in a sample without stating the method and its limits.", "Present it as a supplement or therapy for people.", "Confuse it with related nucleotides such as AICAR when stating results.", "Infer a person's metabolic disorder from FAICAR data without clinical review." ], "requires_human": [ "Interpreting metabolite data that bears on a patient's diagnosis.", "Publishing findings that depend on an unverified FAICAR standard." ] }, "ethics": { "considerations": [ "Metabolic findings can lead to diagnoses that affect patients and families.", "Errors in research reagents can waste effort and mislead later studies." ], "affected_parties": [ "Patients with metabolic disorders", "Researchers", "Laboratory staff" ] }, "owners": { "steward": "The laboratory that holds the sample or reference material.", "master_systems": [] }, "visual_identification": [ "Not identifiable by appearance; in practice a solution or small solid sample in a labelled vial.", "Identity is settled by mass spectrometry or chromatography against a reference." ], "failure_modes_and_hazards": [ "Degradation or misidentification of the reagent gives false experimental results.", "Confusion with similarly named nucleotides in reports." ], "what_it_is_for": [ "FAICAR is encountered in biochemical research on the final stages of de novo purine biosynthesis.", "Researchers study it in enzyme assays and metabolic analyses to investigate its conversion to inosine monophosphate.", "Its role as a pathway intermediate makes sample identity and stability relevant to interpreting experimental results." ], "standards_and_regulation": [ "The Globally Harmonized System of Classification and Labelling of Chemicals, issued by the United Nations, provides the framework for evaluating hazards and communicating any applicable classifications for supplied FAICAR materials." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q2817110: faicar", "url": "https://www.wikidata.org/wiki/Q2817110", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: 5-Formamidoimidazole-4-carboxamide ribotide", "url": "https://en.wikipedia.org/wiki/5-Formamidoimidazole-4-carboxamide_ribotide", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "faicar-identity", "name": "FAICAR identity", "description": "Establish what chemical entity the registry name denotes and which material forms represent it.", "rationale": "The registry supplies neither a definition nor structural evidence, and acronym matching alone cannot settle identity.", "layers": [ { "id": "name-and-structure", "name": "Name and structure", "description": "Connect the registered name to a chemically explicit reference.", "findings": [ { "id": "reference-identity", "name": "Reference identity", "description": "PubChem identifies FAICAR as a formamidoimidazole carboxamide ribonucleotide with CID 166760; linking that identity to this registry entry remains a provenance task. [PubChem FAICAR](https://pubchem.ncbi.nlm.nih.gov/compound/Faicar)", "questions": [ { "text": "Which originating registry record or external identifier confirms that vr.tr.faicar denotes this FAICAR structure?", "kind": "provenance", "id": "reference-identity-q01" }, { "text": "Does the assigned structure preserve the formamido group, ribose stereochemistry and 5'-phosphate attachment?", "kind": "definition", "id": "reference-identity-q02" } ] } ] }, { "id": "forms-and-neighbours", "name": "Forms and neighbours", "description": "Separate representations of FAICAR from chemically different metabolites.", "findings": [ { "id": "form-boundary", "name": "Chemical form boundary", "description": "The model must distinguish protonation and salt descriptions from changes in connectivity, phosphorylation or stereochemistry.", "questions": [ { "text": "Which protonation state, counterions and hydration state describe the actual FAICAR material?", "kind": "definition", "id": "form-boundary-q01" }, { "text": "Does a candidate synonym denote FAICAR itself, an unphosphorylated analogue, AICAR or another substance?", "kind": "boundary", "id": "form-boundary-q02" } ] } ] } ] }, { "id": "purine-intermediate-role", "name": "Purine intermediate role", "description": "Represent FAICAR's immediate formation and consumption reactions.", "rationale": "Its usefulness as a biochemical intermediate depends on reaction context and catalyst identity.", "layers": [ { "id": "faicar-formation", "name": "FAICAR formation", "description": "Record the reaction that supplies FAICAR in the system under examination.", "findings": [ { "id": "aicar-formylation", "name": "AICAR formylation", "description": "Human AICAR transformylase transfers a formyl group from 10-formyltetrahydrofolate to AICAR to form FAICAR. [Primary biochemical study](https://www.sciencedirect.com/science/article/pii/S002192581932109X)", "questions": [ { "text": "Which organism, enzyme and formyl donor account for FAICAR formation in this sample?", "kind": "provenance", "id": "aicar-formylation-q01" }, { "text": "What measurement distinguishes newly formed FAICAR from residual AICAR and other reaction components?", "kind": "measurement", "id": "aicar-formylation-q02" } ] } ] }, { "id": "faicar-consumption", "name": "FAICAR consumption", "description": "Connect FAICAR to its immediate IMP-forming reaction without absorbing the enzyme model.", "findings": [ { "id": "imp-ring-closure", "name": "IMP ring closure", "description": "IMP cyclohydrolase catalyses the reversible conversion of FAICAR to IMP and water. [Reactome reaction](https://reactome.org/content/detail/R-HSA-73797)", "questions": [ { "text": "Which IMP cyclohydrolase and experimental conditions apply to the proposed FAICAR conversion?", "kind": "provenance", "id": "imp-ring-closure-q01" }, { "text": "Which controls and measurements establish FAICAR consumption together with IMP formation?", "kind": "measurement", "id": "imp-ring-closure-q02" } ] } ] } ] }, { "id": "faicar-analytical-confidence", "name": "FAICAR analytical confidence", "description": "Determine whether a reported signal and quantity genuinely represent FAICAR.", "rationale": "Closely related pathway metabolites and preparation components can undermine substrate assignment and quantification.", "layers": [ { "id": "identity-evidence", "name": "Identity evidence", "description": "Evaluate measurements that resolve FAICAR from plausible alternatives.", "findings": [ { "id": "discriminating-identification", "name": "Discriminating identification", "description": "Identity evidence should document a method capable of distinguishing FAICAR from AICAR, IMP and relevant isomeric or dephosphorylated candidates.", "questions": [ { "text": "Which reference standard, chromatographic, mass-spectral or structural evidence supports the FAICAR assignment?", "kind": "measurement", "id": "discriminating-identification-q01" }, { "text": "Which plausible alternative compounds remain unresolved by the identification method?", "kind": "boundary", "id": "discriminating-identification-q02" } ] } ] }, { "id": "amount-and-impurities", "name": "Amount and impurities", "description": "Separate quantified FAICAR from the overall preparation.", "findings": [ { "id": "usable-faicar-amount", "name": "Usable FAICAR amount", "description": "Quantification must distinguish FAICAR content from total solids, detector area and nominal preparation concentration.", "questions": [ { "text": "What calibration, recovery and uncertainty support the reported FAICAR concentration?", "kind": "measurement", "id": "usable-faicar-amount-q01" }, { "text": "How much AICAR, IMP or other relevant impurity is present, and does it interfere with the intended assay?", "kind": "measurement", "id": "usable-faicar-amount-q02" } ] } ] } ] }, { "id": "faicar-sample-fitness", "name": "FAICAR sample fitness", "description": "Assess whether a particular preparation remains suitable for its intended use.", "rationale": "Identity alone cannot establish preservation, compatibility or handling requirements for a FAICAR preparation.", "layers": [ { "id": "preservation-and-integrity", "name": "Preservation and integrity", "description": "Tie storage and preparation conditions to measured retention of FAICAR.", "findings": [ { "id": "condition-dependent-integrity", "name": "Condition-dependent integrity", "description": "Acceptable storage and working conditions require evidence for FAICAR under the relevant solvent, pH, temperature and duration; this draft assigns no universal stability limit.", "questions": [ { "text": "What fraction of FAICAR remains after the actual storage and handling history?", "kind": "measurement", "id": "condition-dependent-integrity-q01" }, { "text": "What evidence establishes the maximum working time and conditions before reanalysis is required?", "kind": "action", "id": "condition-dependent-integrity-q02" } ] } ] }, { "id": "assay-and-handling-decisions", "name": "Assay and handling decisions", "description": "Link preparation-specific evidence to a concrete use decision.", "findings": [ { "id": "preparation-release", "name": "Preparation release", "description": "Use decisions should consider FAICAR identity and concentration alongside counterions, residual synthesis components, buffer compatibility and documented handling requirements.", "questions": [ { "text": "Do the preparation's composition and analytical results meet the stated requirements of the intended FAICAR assay?", "kind": "action", "id": "preparation-release-q01" }, { "text": "Which safety documentation applies to this exact FAICAR form or mixture, and what handling requirements does it establish?", "kind": "provenance", "id": "preparation-release-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 identification assumes the registered lowercase name 'faicar' denotes the biochemical intermediate FAICAR.", "Exact database identifiers, isolated chemical forms, physical constants and hazard classifications require verification." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of faicar 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": "FAICAR", "note": "Abbreviation for 5-formamidoimidazole-4-carboxamide ribonucleotide." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of faicar 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": [ "Serves as the intermediate between AICAR and inosine monophosphate in de novo purine biosynthesis.", "Serves as the substrate for IMP cyclohydrolase." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of faicar 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": "AICAR", "difference": "AICAR has an amino group where FAICAR has a formamido group; formyl transfer from 10-formyltetrahydrofolate converts AICAR to FAICAR." }, { "name": "Inosine monophosphate", "difference": "Inosine monophosphate has the completed bicyclic purine ring system produced by ring closure of FAICAR." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of faicar this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the originating registry identifier confirm that faicar denotes 5-formamidoimidazole-4-carboxamide ribonucleotide?", "Which CAS, ChEBI and EC identifiers, if any, apply to the intended parent structure and its separately identified salts?", "Which validated analytical methods and reference materials best distinguish and quantify FAICAR alongside AICAR and IMP?", "What experimental evidence establishes FAICAR solubility, acid-base behaviour and stability under relevant preparation, storage and assay conditions?", "Which preparation-specific safety classifications and handling requirements are supported by authoritative documentation?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 12, "questions": 20 } }