{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T10:23:21Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 20.2, "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: 01a09523-a0d0-7443-a6a1-854dcb814b7e\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: hypusine\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 regist", "usd": 0.0, "recall": true }, "codex": { "seconds": 66.7, "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: 01a09523-a0c9-7a43-b3c2-ea3271e376c1\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: hypusine\nRegistry id: vr.tr.hypusine\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContex" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:53:40+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:28+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q2067805", "registryId": "vr.tr.hypusine", "name": "hypusine", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q2067805/", "model": { "registry_id": "vr.tr.hypusine", "name": "hypusine", "purpose": "Enable an agent to identify hypusine, distinguish its free and protein-bound contexts, assess analytical evidence and material quality, and select justified research uses.", "definition": "Hypusine is a nonproteinogenic amino acid formed by post-translational modification of a specific lysine residue in eukaryotic translation factor eIF5A, whose activity depends on this modification.", "scope_statement": "This model owns the chemical identity, material state, detection criteria and biological-context relationships of hypusine under vr.tr.hypusine in PHY / PHY.MAT; proteins, enzymes and hypusination processes remain linked entities.", "in_scope": [ "Hypusine connectivity, stereochemistry and chemical identifiers", "Free hypusine, supplied chemical forms and relationships to protein-bound hypusine residues", "Sample purity, concentration, storage conditions and stability evidence", "Analytical discrimination from lysine, deoxyhypusine and stereoisomers", "Evidence connecting detected hypusine to a specified protein modification" ], "out_of_scope": [ "Complete models of eIF5A proteins and their translation functions", "Deoxyhypusine synthase and deoxyhypusine hydroxylase as enzymes", "Hypusination reaction protocols and pathway regulation", "Spermidine metabolism beyond its relationship to hypusine formation", "Disease mechanisms, therapeutic efficacy and clinical interventions" ], "distinguishing_features": [ "Hypusine is an L-lysine derivative bearing a (2R)-4-amino-2-hydroxybutyl substituent on its side-chain nitrogen; both attachment position and stereochemistry distinguish it from other modified lysines. [ChEBI](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI_21858)", "The hydroxylated side chain distinguishes hypusine from deoxyhypusine; an identification method must resolve these modification states.", "A free amino-acid assignment and a hypusine residue within a peptide describe different molecular contexts and require different mass calculations.", "Hypusine detected after protein hydrolysis does not by itself establish a freely available cellular pool or identify the original protein and modification site." ], "characteristics": [ { "name": "Chemical identity", "kind": "category", "unit_or_values": "ChEBI:21858; CAS 34994-11-1; free-compound formula C10H23N3O3", "why_it_matters": "Anchors the registry entry to a defined chemical entity; supplied salts and derivatives require separate form records." }, { "name": "Stereochemical assignment", "kind": "category", "unit_or_values": "L-lysine configuration and 2R side-chain hydroxyl configuration; confirmed, mixed or unresolved", "why_it_matters": "Connectivity or nominal mass alone cannot establish the intended stereoisomer." }, { "name": "Molecular context", "kind": "category", "unit_or_values": "Free amino acid; salt; peptide-bound residue; protein-bound residue; hydrolysate analyte", "why_it_matters": "Controls interpretation of abundance, identity and suitability for an assay." }, { "name": "Hypusine content", "kind": "measurement", "unit_or_values": "mol/L, nmol/sample or mol/mol protein, with preparation and normalization basis", "why_it_matters": "Makes measurements comparable without conflating total recovered hypusine with site occupancy." }, { "name": "Chemical and stereochemical purity", "kind": "measurement", "unit_or_values": "Percent, with assay basis and separately reported deoxyhypusine, lysine and stereoisomer impurities", "why_it_matters": "Determines whether material can support calibration or discriminate modification states." }, { "name": "Protein-site association", "kind": "relation", "unit_or_values": "Protein accession, organism, isoform, residue position and supporting peptide evidence", "why_it_matters": "Links the modification to a specific host without making the protein part of the substance identity." }, { "name": "Preparation state", "kind": "state", "unit_or_values": "Solid or solution; counterion, solvent, pH, temperature and storage history", "why_it_matters": "Supports concentration calculations and condition-specific stability judgments." }, { "name": "Handling evidence", "kind": "category", "unit_or_values": "Form-specific safety documentation, jurisdiction and date; unresolved when unavailable", "why_it_matters": "Prevents an agent from treating missing hazard information as evidence of safety." } ], "affordances": [ "Match a candidate structure or material record to hypusine and flag unresolved stereochemistry.", "Select an analytical approach that distinguishes hypusine from deoxyhypusine and lysine.", "Calculate hypusine-equivalent concentration using the documented salt, hydration and purity basis.", "Link a measured residue to a protein and site when localization evidence supports the assignment.", "Assess whether a lot is suitable as a calibration standard, hydrolysate control or other specified research reagent.", "Identify missing evidence that prevents a handling, storage or biological interpretation decision." ], "agent_conduct": { "may": [ "Explain hypusine's formation on eIF5A and its role in cell biology, citing research.", "Report research on hypusination as a drug target with its stage of evidence." ], "must_not": [ "Present hypusine or hypusination inhibitors as approved treatments when they are not.", "Sell or promote hypusine as a supplement with health claims.", "Overstate preliminary research findings to patients." ], "requires_human": [ "Using research findings in a treatment decision for a patient." ] }, "ethics": { "considerations": [ "Overstated biomedical claims can mislead patients seeking treatment.", "Research integrity depends on accurate reporting." ], "affected_parties": [ "Patients", "Researchers", "Readers of science news" ] }, "owners": { "steward": "Nobody owns the molecule; researchers answer for samples and claims.", "master_systems": [] }, "visual_identification": [ "Identified by container label, chemical name and identifier, and certificate of analysis rather than by appearance alone." ], "failure_modes_and_hazards": [ "Misrepresentation of research as treatment.", "Errors in assays measuring hypusination." ], "what_it_is_for": [ "Hypusine is encountered in biochemical research on the post-translational modification and activity of eukaryotic translation factor eIF5A.", "Analytical studies distinguish free hypusine from the modified residue within proteins or peptides.", "It supports investigations of protein modification and translation when identity and sample context are established." ], "standards_and_regulation": [ "The REACH Regulation, Regulation (EC) No 1907/2006 issued by the European Parliament and the Council of the European Union, applies to manufacture, import and supply subject to its scope and exemptions.", "The CLP Regulation, Regulation (EC) No 1272/2008 issued by the European Parliament and the Council of the European Union, governs applicable classification, labelling and packaging obligations without itself establishing that hypusine is hazardous." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q2067805: hypusine", "url": "https://www.wikidata.org/wiki/Q2067805", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Hypusine", "url": "https://en.wikipedia.org/wiki/Hypusine", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "chemical-identity-and-boundaries", "name": "Chemical identity and boundaries", "description": "Defines which molecular structures and representations belong to hypusine.", "rationale": "Modified lysines can share similar names and analytical behavior while differing in hydroxylation, stereochemistry or molecular context.", "layers": [ { "id": "structure-and-stereochemistry", "name": "Structure and stereochemistry", "description": "Anchors recognition to connectivity and configuration.", "findings": [ { "id": "reference-structure", "name": "Reference structure", "description": "ChEBI records hypusine as N6-[(2R)-4-amino-2-hydroxybutyl]-L-lysine, with formula C10H23N3O3 and CAS 34994-11-1. [ChEBI](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI_21858)", "questions": [ { "text": "Does the candidate structure match the side-chain attachment and both specified stereochemical configurations?", "kind": "definition", "id": "reference-structure-q01" }, { "text": "Which authoritative record or structural analysis supports the supplied identifier and stereochemical assignment?", "kind": "provenance", "id": "reference-structure-q02" } ] } ] }, { "id": "free-compound-and-residue", "name": "Free compound and residue", "description": "Separates substance identity from incorporation into larger molecules.", "findings": [ { "id": "context-specific-identity", "name": "Context-specific identity", "description": "ChEBI distinguishes hypusine from hypusinate and from a hypusine residue; these relationships should be explicit when interpreting material records or molecular masses. [ChEBI](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI_21858)", "questions": [ { "text": "Does this record represent free hypusine, an ionic form or a covalently incorporated residue?", "kind": "boundary", "id": "context-specific-identity-q01" }, { "text": "Was the reported free analyte present before preparation or released from a peptide or protein?", "kind": "provenance", "id": "context-specific-identity-q02" } ] } ] } ] }, { "id": "hypusination-context", "name": "Hypusination context", "description": "Connects hypusine to the biological modification in which it is observed.", "rationale": "A hypusine signal becomes biologically interpretable only when its host, site and modification state are distinguished.", "layers": [ { "id": "modification-state", "name": "Modification state", "description": "Distinguishes the hydroxylated product from its precursor state.", "findings": [ { "id": "deoxyhypusine-hydroxylation", "name": "Deoxyhypusine hydroxylation", "description": "Deoxyhypusine hydroxylase catalyzes stereospecific hydroxylation of the deoxyhypusine residue in the eIF5A intermediate. This relationship does not establish that free hypusine is an equivalent enzyme substrate. [Assay of deoxyhypusine hydroxylase activity](https://pubmed.ncbi.nlm.nih.gov/21318876/)", "questions": [ { "text": "Does the evidence distinguish hypusine-bearing material from deoxyhypusine-bearing material?", "kind": "measurement", "id": "deoxyhypusine-hydroxylation-q01" }, { "text": "Does a proposed enzyme experiment require a modified eIF5A substrate rather than the isolated amino acid?", "kind": "action", "id": "deoxyhypusine-hydroxylation-q02" } ] } ] }, { "id": "host-and-site", "name": "Host and site", "description": "Records the context required for protein-modification claims.", "findings": [ { "id": "localized-residue-evidence", "name": "Localized residue evidence", "description": "The model requires a protein identity and localization evidence before attributing a hypusine measurement to a particular protein site.", "questions": [ { "text": "Which organism, protein accession, isoform and residue-numbering convention identify the proposed host site?", "kind": "provenance", "id": "localized-residue-evidence-q01" }, { "text": "Is the assignment supported by a localized modified peptide or only by bulk hydrolysate measurement?", "kind": "measurement", "id": "localized-residue-evidence-q02" } ] } ] } ] }, { "id": "analytical-recognition-and-quantity", "name": "Analytical recognition and quantity", "description": "Defines what evidence supports identifying and quantifying hypusine.", "rationale": "Preparation artifacts, precursor overlap and loss of protein context can change what a measurement means.", "layers": [ { "id": "specificity-of-identification", "name": "Specificity of identification", "description": "Evaluates whether an assay uniquely supports the claimed analyte.", "findings": [ { "id": "orthogonal-identity-evidence", "name": "Orthogonal identity evidence", "description": "The model records the evidence used to distinguish hypusine from lysine, deoxyhypusine, isomers and matrix interference rather than treating a nominal-mass match as conclusive.", "questions": [ { "text": "Which retention, fragmentation, structural or stereochemical measurements support the assignment?", "kind": "measurement", "id": "orthogonal-identity-evidence-q01" }, { "text": "Were authentic hypusine and relevant competing analytes tested under the same analytical conditions?", "kind": "provenance", "id": "orthogonal-identity-evidence-q02" } ] } ] }, { "id": "recovery-and-normalization", "name": "Recovery and normalization", "description": "Preserves the preparation and denominator behind an abundance value.", "findings": [ { "id": "interpretable-abundance", "name": "Interpretable abundance", "description": "Free-pool concentration, total hypusine recovered after hydrolysis and protein-site occupancy are separate quantities requiring distinct preparation and normalization evidence.", "questions": [ { "text": "What extraction, hydrolysis or derivatization steps were used, and how were recovery and analyte integrity checked?", "kind": "measurement", "id": "interpretable-abundance-q01" }, { "text": "Does the reported value describe free concentration, total recovered amount or occupancy of a defined protein site?", "kind": "boundary", "id": "interpretable-abundance-q02" } ] } ] } ] }, { "id": "material-fitness-and-handling", "name": "Material fitness and handling", "description": "Supports decisions about a specific hypusine preparation.", "rationale": "A chemical name alone cannot establish standard quality, solution concentration, storage suitability or handling requirements.", "layers": [ { "id": "lot-composition", "name": "Lot composition", "description": "Records the actual composition of supplied or isolated material.", "findings": [ { "id": "hypusine-equivalent-content", "name": "Hypusine-equivalent content", "description": "The model separates hypusine identity from counterions, water, residual solvents and impurities so that weighed mass can be interpreted correctly.", "questions": [ { "text": "What salt stoichiometry, water content and assay basis determine the hypusine-equivalent content of this lot?", "kind": "measurement", "id": "hypusine-equivalent-content-q01" }, { "text": "Are lysine, deoxyhypusine and stereoisomer impurities controlled sufficiently for the intended assay?", "kind": "action", "id": "hypusine-equivalent-content-q02" } ] } ] }, { "id": "condition-dependent-use", "name": "Condition-dependent use", "description": "Connects storage and handling decisions to evidence for the actual preparation.", "findings": [ { "id": "supported-use-conditions", "name": "Supported use conditions", "description": "Solubility, stability, thermal properties and hazard classifications remain form- and condition-specific evidence requirements; missing values must remain unresolved.", "questions": [ { "text": "Which measurements establish usable concentration and stability in the intended solvent, pH, temperature and storage interval?", "kind": "measurement", "id": "supported-use-conditions-q01" }, { "text": "Which current safety documentation applies to this hypusine form and concentration, and what handling actions does it support?", "kind": "action", "id": "supported-use-conditions-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 is recalled knowledge, not source-verified research.", "Verify stereospecific chemical identifiers and distinguish free amino acid, salts, and protein-bound residue before assigning substance records.", "No confident substance-specific hazard classification, exposure limits, or phase-transition measurements are supplied." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of hypusine 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": "Chemical nomenclature", "value_or_pattern": "N6-(4-amino-2-hydroxybutyl)-L-lysine", "note": "Describes the substituted lysine structure; a fully stereospecific name must also specify the hydroxyl-bearing side-chain stereocenter." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of hypusine 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": [ "Measured as a marker of eIF5A hypusination in biochemical and cellular research.", "Studied in the relationship between spermidine metabolism and protein synthesis.", "Used to investigate the activities of deoxyhypusine synthase and deoxyhypusine hydroxylase." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of hypusine this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Molar mass of the neutral free amino acid, molecular formula C10H23N3O3", "typical_range": "233.31", "unit": "g/mol" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of hypusine 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": [ "Failure to form the hypusine residue impairs normal eIF5A function in translation.", "Analytical results can be misinterpreted if free hypusine, protein-bound hypusine, and its precursor deoxyhypusine are not distinguished." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of hypusine 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": "Lysine", "difference": "Hypusine carries an additional hydroxylated aminobutyl substituent on lysine's side-chain nitrogen." }, { "name": "Deoxyhypusine", "difference": "Deoxyhypusine lacks hypusine's side-chain hydroxyl group and is its immediate biosynthetic precursor." }, { "name": "Spermidine", "difference": "Spermidine is a polyamine that supplies the aminobutyl group during hypusine biosynthesis, rather than the resulting modified amino acid." }, { "name": "eIF5A", "difference": "eIF5A is the protein carrying the modified residue; hypusine is the amino acid modification within it." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of hypusine this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which PubChem CID and EC identifier, if any, map to the specified stereochemical entity rather than a salt, derivative or incompletely specified structure?", "What experimentally supported solubility, acid-base constants, thermal behavior and storage stability are available for each relevant hypusine form?", "Which analytical methods adequately separate hypusine from deoxyhypusine and stereoisomers in the intended sample matrices?", "What evidence establishes endogenous free hypusine pools independently of protein hydrolysis during sample preparation?", "What form-specific hazard classifications and exposure guidance are documented for research-grade hypusine, and where are data absent?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 14, "questions": 22 } }