{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:17:11Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 15.4, "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: 01a09554-e533-74f2-a380-e86e19f028ea\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: methanofuran\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 044: 1001 re", "usd": 0.0, "recall": true }, "codex": { "seconds": 67.4, "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: 01a09554-e537-7692-8350-e5c22ff75f19\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: methanofuran\nRegistry id: vr.tr.methanofuran\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:54:52+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:30+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q410734", "registryId": "vr.tr.methanofuran", "name": "methanofuran", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q410734/", "model": { "registry_id": "vr.tr.methanofuran", "name": "methanofuran", "purpose": "Enable an AI agent to identify methanofuran, distinguish its molecular variants and carrier states, and judge whether a preparation is suitable for a specified biochemical use.", "definition": "Methanofuran is a family of aminomethylfuran-containing coenzymes that carry formyl groups during the initial reduction of carbon dioxide in methanogenic archaea.", "scope_statement": "This model owns vr.tr.methanofuran as a family-level biochemical cofactor identity, including variant composition, preparation quality and functional state; whether the registry intends one specific molecular species remains unresolved.", "in_scope": [ "Methanofuran core identity and structurally resolved side-chain variants", "Unsubstituted, N-formylated and other experimentally identified carrier states", "Biological or synthetic provenance of a methanofuran preparation", "Analytical identity, concentration, purity and variant distribution", "Compatibility with specified methanofuran-dependent biochemical assays", "Evidence-based storage, handling and substance identifiers" ], "out_of_scope": [ "Complete methanogenesis pathways and methane production systems", "Structures and catalytic mechanisms of methanofuran-dependent enzymes", "Taxonomy, cultivation and physiology of source organisms", "Methylofuran as a separately characterized neighboring cofactor", "Tetrahydromethanopterin and other downstream one-carbon carriers", "Commercial reagent formulations beyond their methanofuran content" ], "distinguishing_features": [ "Require structural evidence for the substituted aminomethylfuran-containing methanofuran core; the presence of a furan ring alone does not establish identity.", "Resolve the side chain before assigning a variant-specific formula, molecular mass or identifier: methanofuran is structurally diverse across organisms.", "Distinguish the free carrier from N-formylmethanofuran by identifying substitution at the carrier amine.", "Distinguish methanofuran from methylofuran through the resolved core and side-chain structure, rather than treating similar names or shared formyl transfer activity as identity.", "Distinguish the cofactor from formylmethanofuran dehydrogenase and formyltransferase: enzyme activity is supporting functional evidence, not proof of molecular identity." ], "characteristics": [ { "name": "Identity resolution", "kind": "state", "unit_or_values": "family assigned | variant assigned | complete structure resolved | unresolved", "why_it_matters": "Controls whether a preparation can receive a specific formula, mass and chemical identifier." }, { "name": "Side-chain composition", "kind": "category", "unit_or_values": "Glutamate residue count, linkage positions, stereochemistry and additional resolved moieties", "why_it_matters": "Separates methanofuran variants and reveals heterogeneous preparations." }, { "name": "Carrier amine substitution", "kind": "state", "unit_or_values": "unsubstituted | N-formylated | N-acetylated | mixed | unresolved", "why_it_matters": "Determines whether the measured material represents available carrier, formyl-bearing carrier or another derivative." }, { "name": "Molecular formula and exact mass", "kind": "measurement", "unit_or_values": "Formula and Da, with variant, protonation and ion/adduct assignment", "why_it_matters": "Supports mass-spectrometric identification without assigning one mass to the entire family." }, { "name": "Methanofuran concentration", "kind": "measurement", "unit_or_values": "µmol/L or nmol per preparation, with calibration method and species measured", "why_it_matters": "Allows reproducible cofactor dosing and interpretation of biochemical activity." }, { "name": "Preparation composition", "kind": "measurement", "unit_or_values": "Mass fraction, molar fraction or chromatographic area %, explicitly distinguished", "why_it_matters": "Separates chemical purity from variant distribution and carrier-state distribution." }, { "name": "Source and preparation lineage", "kind": "relation", "unit_or_values": "Source organism and strain or synthetic route, extraction method, batch and reference", "why_it_matters": "Connects a preparation to evidence about its expected composition without substituting provenance for analysis." }, { "name": "Assay-supported cofactor activity", "kind": "measurement", "unit_or_values": "Reaction rate or relative activity with enzyme identity, normalization and assay conditions", "why_it_matters": "Determines suitability for a particular enzyme system." }, { "name": "Storage stability", "kind": "measurement", "unit_or_values": "Chemical recovery and retained activity % versus time at stated temperature, pH and atmosphere", "why_it_matters": "Supports storage and reuse decisions from observations rather than assumed cofactor stability." }, { "name": "Identifier and hazard evidence", "kind": "relation", "unit_or_values": "Structure-matched database records and applicable safety documents, or explicitly unresolved", "why_it_matters": "Prevents transferring identifiers or hazard classifications between a family, a derivative and a formulated reagent." } ], "affordances": [ "Classify a candidate preparation as methanofuran at the level supported by structural evidence.", "Compare side-chain variants and carrier-state mixtures between preparations.", "Calculate assay additions using a concentration specific to the measured molecular species.", "Select or reject a preparation for a specified enzyme assay using compatibility and purity evidence.", "Track experimentally observed formyl loading, unloading and loss of usable cofactor.", "Determine whether storage, reanalysis or disposal is appropriate using preparation-specific stability and handling evidence." ], "agent_conduct": { "may": [ "Identify methanofuran as a coenzyme family of methanogenic archaea and describe its role, citing sources.", "Report which methanofuran variant a sample or dataset refers to." ], "must_not": [ "Treat the different methanofuran variants as one compound when reporting structures or data.", "Present laboratory findings on methanogens as proven climate solutions.", "Report a measurement without stating method and limits.", "Label an unverified biological extract as a methanofuran standard." ], "requires_human": [ "Publishing conclusions that depend on an unverified reference.", "Releasing engineered methanogen cultures outside containment." ] }, "ethics": { "considerations": [ "Methanogen research bears on climate and agriculture, so overstated claims mislead policy.", "Research errors waste effort and mislead later studies." ], "affected_parties": [ "Researchers", "Policy makers relying on findings", "Laboratory staff" ] }, "owners": { "steward": "The laboratory that holds the sample.", "master_systems": [] }, "visual_identification": [ "Not identifiable by appearance; handled as small amounts in solution or as purified solids.", "Identity is settled by mass spectrometry and comparison with published structures." ], "failure_modes_and_hazards": [ "Degradation of samples on exposure to air.", "Confusion between variants in published data." ], "what_it_is_for": [ "Methanofuran occurs in methanogenic archaea as a carrier involved in converting carbon dioxide into methane.", "It is studied in biochemical research on carbon metabolism, enzyme activity and the differences between coenzyme variants." ], "facets_not_applicable": { "interfaces": "No specific standard or official classification is identified here for methanofuran as a coenzyme family." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q410734: methanofuran", "url": "https://www.wikidata.org/wiki/Q410734", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Methanofuran", "url": "https://en.wikipedia.org/wiki/Methanofuran", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "molecular-identity", "name": "Molecular identity and registry boundary", "description": "Establish what molecular material the methanofuran name denotes.", "rationale": "A family name cannot safely supply a universal formula or a single preparation identity.", "layers": [ { "id": "core-recognition", "name": "Core recognition", "description": "Separate methanofuran from related cofactors and partial structural matches.", "findings": [ { "id": "supported-core-assignment", "name": "Supported core assignment", "description": "Methanofurans share an aminomethylfuran-containing core while differing in attached side chains. Record the structural evidence supporting assignment. [Methanofuran biosynthesis study](https://pmc.ncbi.nlm.nih.gov/articles/PMC4524034/)", "questions": [ { "text": "Which experimentally resolved structural features establish the methanofuran core in this material?", "kind": "definition", "id": "supported-core-assignment-q01" }, { "text": "What evidence excludes methylofuran, a biosynthetic precursor or another furan-containing compound?", "kind": "boundary", "id": "supported-core-assignment-q02" } ] } ] }, { "id": "variant-resolution", "name": "Variant resolution", "description": "Describe side-chain identity and map identifiers at the supported level.", "findings": [ { "id": "side-chain-and-identifiers", "name": "Side chain and identifiers", "description": "Resolve glutamate content, connectivity and additional side-chain moieties before assigning a variant-specific identity. Structurally distinct methanofurans have been isolated from different methanogens. [Structural diversity study](https://pmc.ncbi.nlm.nih.gov/articles/PMC211496/)", "questions": [ { "text": "Which side-chain residues, linkages and stereochemical assignments are established, and which remain unresolved?", "kind": "definition", "id": "side-chain-and-identifiers-q01" }, { "text": "Do the proposed ChEBI, PubChem, CAS or EC records describe this exact variant and chemical form or only a broader name?", "kind": "boundary", "id": "side-chain-and-identifiers-q02" } ] } ] } ] }, { "id": "carrier-state-and-function", "name": "Carrier state and biochemical function", "description": "Represent the chemical state of the carrier and evidence for its use in a particular reaction.", "rationale": "Methanofuran identity alone does not establish formyl occupancy or functional compatibility.", "layers": [ { "id": "amine-occupancy", "name": "Carrier amine occupancy", "description": "Distinguish available carrier from chemically substituted derivatives.", "findings": [ { "id": "resolved-acylation-state", "name": "Resolved acylation state", "description": "Formyl groups bind to a primary amine of methanofuran; N-acetyl derivatives have also been reported and should not be silently counted as free carrier. [Formyl carrier study](https://pubmed.ncbi.nlm.nih.gov/3922409/), [Acylated methanofuran study](https://pubmed.ncbi.nlm.nih.gov/25203397/)", "questions": [ { "text": "What fractions are unsubstituted, N-formylated, N-acetylated or unidentified?", "kind": "measurement", "id": "resolved-acylation-state-q01" }, { "text": "Was this distribution measured directly or inferred after extraction or treatment that could alter substitution?", "kind": "provenance", "id": "resolved-acylation-state-q02" } ] } ] }, { "id": "reaction-compatibility", "name": "Reaction compatibility", "description": "Attach functional conclusions to a specified enzyme and assay context.", "findings": [ { "id": "demonstrated-formyl-transfer", "name": "Demonstrated formyl transfer", "description": "Record supported participation in formyl loading or transfer, including the enzyme and partner carrier. Formylmethanofuran:tetrahydromethanopterin formyltransferase provides one established interaction context. [Coenzyme complex study](https://pubmed.ncbi.nlm.nih.gov/16466742/)", "questions": [ { "text": "Which enzyme preparation and reaction direction demonstrate activity with this methanofuran variant?", "kind": "measurement", "id": "demonstrated-formyl-transfer-q01" }, { "text": "What controls distinguish cofactor-dependent activity from endogenous carrier contamination or background turnover?", "kind": "measurement", "id": "demonstrated-formyl-transfer-q02" }, { "text": "Does the evidence support substituting this preparation into the intended assay?", "kind": "action", "id": "demonstrated-formyl-transfer-q03" } ] } ] } ] }, { "id": "preparation-and-analysis", "name": "Preparation provenance and analytical quality", "description": "Connect an actual preparation to its origin, measured composition and usable amount.", "rationale": "A biological extract or purified fraction can contain several variants and carrier states.", "layers": [ { "id": "preparation-lineage", "name": "Preparation lineage", "description": "Track how the material was obtained and processed.", "findings": [ { "id": "traceable-isolation", "name": "Traceable isolation", "description": "Record organism or synthesis provenance and processing steps that might select variants or change the recovered carrier state.", "questions": [ { "text": "Which organism, strain and culture batch, or which synthetic route, produced this preparation?", "kind": "provenance", "id": "traceable-isolation-q01" }, { "text": "Which extraction, purification or chemical treatment steps could have changed its variant distribution or acylation state?", "kind": "provenance", "id": "traceable-isolation-q02" } ] } ] }, { "id": "analytical-composition", "name": "Analytical composition", "description": "Resolve methanofuran amount, identity confidence and preparation heterogeneity.", "findings": [ { "id": "quantified-species-distribution", "name": "Quantified species distribution", "description": "Keep concentration, chemical purity, variant abundance and carrier-state abundance distinct; document calibration and unresolved signals.", "questions": [ { "text": "Which LC-MS, fragmentation, NMR or other observations support the assigned methanofuran species?", "kind": "measurement", "id": "quantified-species-distribution-q01" }, { "text": "How was concentration calibrated, and does the result measure one variant, free carrier or total methanofuran equivalents?", "kind": "measurement", "id": "quantified-species-distribution-q02" }, { "text": "Which co-purified substances or unresolved methanofuran species could affect the planned assay?", "kind": "boundary", "id": "quantified-species-distribution-q03" } ] } ] } ] }, { "id": "condition-and-handling", "name": "Condition, stability and handling", "description": "Determine whether a particular methanofuran preparation remains usable under its actual conditions.", "rationale": "Storage requirements and safety conclusions require evidence for the specific chemical form and preparation.", "layers": [ { "id": "physical-and-storage-state", "name": "Physical and storage state", "description": "Record the preparation form and experimentally supported stability envelope.", "findings": [ { "id": "retained-identity-and-activity", "name": "Retained identity and activity", "description": "Describe solution or dry form, counterions, buffer, temperature and storage history; evaluate chemical integrity and activity separately.", "questions": [ { "text": "In what solvent, buffer, pH, counterion form and temperature is the methanofuran held?", "kind": "measurement", "id": "retained-identity-and-activity-q01" }, { "text": "How do storage duration, atmosphere and freeze-thaw history affect variant composition, carrier occupancy and retained activity?", "kind": "measurement", "id": "retained-identity-and-activity-q02" }, { "text": "What observed acceptance limits determine whether this preparation can be reused?", "kind": "action", "id": "retained-identity-and-activity-q03" } ] } ] }, { "id": "handling-evidence", "name": "Handling evidence", "description": "Tie handling decisions to documented properties of the actual material.", "findings": [ { "id": "form-specific-handling", "name": "Form-specific handling", "description": "Record applicable safety documentation and measured physical properties without treating absent hazard data as evidence of harmlessness or assigning generic constants to all variants.", "questions": [ { "text": "Which safety or regulatory records apply to this exact methanofuran form and preparation?", "kind": "provenance", "id": "form-specific-handling-q01" }, { "text": "Are reported solubility or thermal properties measured for this material, and do thermal observations represent decomposition rather than a phase transition?", "kind": "measurement", "id": "form-specific-handling-q02" }, { "text": "Which documented controls govern handling and disposal of the cofactor preparation, including its solvent and contaminants?", "kind": "action", "id": "form-specific-handling-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": [ "Methanofuran denotes related coenzyme structures; a molecular formula, molecular mass or chemical registry identifier should be assigned only after specifying the variant.", "Variant names, organism-specific distributions and physical-property values require verification.", "No substance-specific hazard classification or regulatory status is confidently recalled; empty fields do not establish safety or exemption." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of methanofuran 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 the carbon carrier on which carbon dioxide is reduced to a formyl group by formylmethanofuran dehydrogenase during carbon dioxide-dependent methanogenesis.", "Transfers its formyl group to tetrahydromethanopterin in the next stage of the methanogenic pathway.", "Serves as a substrate or cofactor in biochemical studies of archaeal one-carbon metabolism." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of methanofuran 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": "Formylmethanofuran", "difference": "Formylmethanofuran is the formyl-loaded derivative of methanofuran." }, { "name": "Tetrahydromethanopterin", "difference": "A structurally distinct one-carbon carrier that accepts the formyl group from formylmethanofuran and carries intermediates through subsequent reduction steps." }, { "name": "Coenzyme M", "difference": "A thiol coenzyme that carries the methyl group used in the terminal methane-forming reaction, rather than the initial formyl group." }, { "name": "Coenzyme F420", "difference": "An electron-transfer coenzyme rather than a carrier of covalently bound one-carbon groups." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of methanofuran this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does vr.tr.methanofuran intend the cofactor family or a particular reference structure, and which chemical identifiers match that intended scope?", "Which methanofuran variants should be explicitly recognized, and what structural evidence reliably separates them from methylofuran and incompletely characterized analogues?", "What functional significance and assay consequences do N-acetylated methanofurans have, beyond their experimentally reported occurrence?", "Which validated reference materials and quantitative methods permit comparison of variant abundance and carrier occupancy across laboratories?", "What variant-specific storage, solubility, thermal behavior and safety data exist, and which handling limits remain unestablished?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 11, "questions": 23 } }