{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T09:41:00Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 21.0, "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: 01a094fc-9739-7022-95d1-086b896d50eb\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: FGF23\nSense to describe: (none recorded)\nDomain code: PHY.OBJ\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001 registere", "usd": 0.0, "recall": true }, "codex": { "seconds": 83.9, "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: 01a094fc-9749-72b3-8db4-a1b4bcb7db1b\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: FGF23\nRegistry id: vr.tr.fgf23\nPlane / domain: PHY / PHY.OBJ\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext for " } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:57:13+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "visual_identification" ] }, "revisions": [ { "at": "2026-10-07T11:11:27+00:00", "engine": "codex", "fields": [ "agent_conduct", "definition", "distinguishing_features", "failure_modes_and_hazards", "in_scope", "out_of_scope", "owners", "purpose", "scope_statement", "visual_identification" ], "answering_review": "05386045e7c972feaefa9ccb9ce0668c2461fbb7897a54f807e2919799701d96" } ], "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T12:16:28+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q14897899", "registryId": "vr.tr.fgf23", "name": "FGF23", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q14897899/", "model": { "registry_id": "vr.tr.fgf23", "name": "FGF23", "purpose": "Enable an agent to identify the human FGF23 gene, distinguish its variants and transcripts from the encoded hormone, and assess gene-related evidence in a specified context.", "definition": "FGF23 is a human protein-coding gene that encodes fibroblast growth factor 23, a secreted hormone produced predominantly by bone osteocytes that regulates phosphate and vitamin D metabolism.", "scope_statement": "This model owns FGF23 as a protein-coding gene in Homo sapiens, including genomic identity, variants, regulation, transcripts and gene expression, with hormone functions represented as relationships to its encoded product.", "in_scope": [ "Human FGF23 gene identity and reference genomic sequence are included.", "Genomic coordinates qualified by reference assembly are included.", "Gene variants and their evidence-supported annotations are included.", "Transcript models, transcriptional regulation and RNA expression are included.", "Relationships between the gene, its transcripts and its encoded hormone are included." ], "out_of_scope": [ "The FGF23 protein hormone, its processing and cleavage fragments as independent molecular entities are excluded.", "FGF receptors, alpha-Klotho and processing enzymes as independently modeled entities are excluded.", "Whole-organism phosphate homeostasis and bone remodeling are excluded.", "Diseases associated with altered FGF23 as complete clinical entities are excluded.", "Assay kits, therapeutic antibodies and treatment protocols as independent products or interventions are excluded." ], "distinguishing_features": [ "Human FGF23 gene identity is represented by NCBI Gene 8074 and must be distinguished from the encoded hormone.", "Genomic coordinates and variant descriptions require an explicit reference assembly or sequence accession.", "FGF23 is distinct from the human FGF19 and FGF21 genes.", "Transcript abundance describes RNA expression and does not directly establish circulating hormone abundance or activity.", "Intact and C-terminal hormone assays measure protein-related signals rather than gene identity or genotype." ], "characteristics": [ { "name": "Species and protein reference", "kind": "relation", "unit_or_values": "Taxon, protein accession and sequence version", "why_it_matters": "Prevents unsupported transfer of sequence numbering, reagent specificity and biological findings between species." }, { "name": "Molecular form", "kind": "category", "unit_or_values": "Precursor; mature intact hormone; N-terminal fragment; C-terminal fragment; engineered construct; unresolved mixture", "why_it_matters": "Forms can differ in receptor activity and assay detectability." }, { "name": "Sequence alteration", "kind": "category", "unit_or_values": "Reference sequence; substitution; truncation; fusion or tag; unknown, with residue numbering reference", "why_it_matters": "An alteration can affect cleavage, recognition or signaling." }, { "name": "Post-translational processing", "kind": "state", "unit_or_values": "Site-specific glycosylation, phosphorylation and cleavage status; measured or unresolved", "why_it_matters": "Processing must be considered when assessing intact-hormone availability." }, { "name": "FGF23 assay result", "kind": "measurement", "unit_or_values": "Assay-reported units, commonly pg/mL or RU/mL, with method and analyte definition", "why_it_matters": "Results from different assay formats or calibrations cannot be treated as interchangeable." }, { "name": "Production source", "kind": "relation", "unit_or_values": "Organism, tissue, cell population or recombinant expression system", "why_it_matters": "Connects the detected material to evidence of synthesis and secretion." }, { "name": "Signaling context", "kind": "relation", "unit_or_values": "Target cell, FGFR identity, alpha-Klotho status and experimental conditions", "why_it_matters": "Activity depends on the responding system as well as the ligand." }, { "name": "Functional potency", "kind": "measurement", "unit_or_values": "Assay-defined response, relative potency or EC50 with concentration units and endpoint", "why_it_matters": "Separates a functional measurement from protein abundance." }, { "name": "Specimen condition", "kind": "state", "unit_or_values": "Matrix, collection conditions, processing delay, storage temperature and freeze-thaw history", "why_it_matters": "Determines whether the result is supported by the assay's validated specimen conditions." } ], "affordances": [ "Resolve whether an FGF23 record describes a protein, fragment, construct or gene-related observation.", "Select an assay whose detected molecular forms match the question being asked.", "Compare serial FGF23 results after checking method, units, specimen conditions and physiological context.", "Assess a recombinant FGF23 preparation for a specified binding or signaling experiment.", "Link FGF23 observations to phosphate and vitamin D measurements without inferring diagnosis from FGF23 alone.", "Identify missing evidence that prevents claims about production, cleavage, clearance or biological activity." ], "agent_conduct": { "may": [ "Describe the human FGF23 gene and its encoded hormone's role in phosphate and vitamin D regulation, citing sources.", "Report gene variant and RNA expression evidence with its reference context and limits." ], "must_not": [ "Diagnose a person's phosphate or kidney disorder from an FGF23 result.", "Share a person's test results without consent.", "Recommend phosphate or vitamin D dosing to a person.", "Present research findings as established treatment." ], "requires_human": [ "Any clinical decision using FGF23 results.", "Research on patient samples without documented consent." ] }, "ethics": { "considerations": [ "Patients with kidney disease and rare bone disorders depend on accurate information.", "Lab results are private health data." ], "affected_parties": [ "Patients with kidney or bone disorders", "Clinicians", "Researchers" ] }, "owners": { "steward": "The person whose genome carries it has interests in associated samples and data; laboratories and biobanks steward the records.", "master_systems": [ "Gene and variant databases hold relevant reference records." ] }, "visual_identification": [ "The gene is identified through human genomic sequence records and reference identifiers.", "Blood hormone immunoassays measure the encoded product rather than identify the gene." ], "failure_modes_and_hazards": [ "Confusing genomic variants, RNA expression and hormone measurements can produce misleading comparisons.", "Misinterpretation of results by non-specialists can cause harm.", "Reference sequence or assembly mismatches can produce incorrect variant annotations." ], "standards_and_regulation": [ "Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol." ], "what_it_is_for": [ "The human FGF23 gene is studied in bone biology and research on phosphate and vitamin D regulation.", "Its sequence and expression help relate genetic variation and hormone production to mineral metabolism, while circulating protein forms require separate characterization." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q14897899: FGF23", "url": "https://www.wikidata.org/wiki/Q14897899", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Fibroblast growth factor 23", "url": "https://en.wikipedia.org/wiki/Fibroblast_growth_factor_23", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "fgf23-identity", "name": "FGF23 identity", "description": "Establish what biological entity the FGF23 name denotes in each record.", "rationale": "The shared gene and protein name and the existence of orthologs and constructs make name matching insufficient.", "layers": [ { "id": "protein-boundary", "name": "Protein boundary", "description": "Separate the hormone from its encoding locus and neighbouring FGF family members.", "findings": [ { "id": "entity-resolution", "name": "Entity resolution", "description": "Record the evidence identifying the entity as FGF23 protein rather than DNA, RNA or another FGF.", "questions": [ { "text": "Does this record concern FGF23 protein, its encoding gene or its transcript?", "kind": "boundary", "id": "entity-resolution-q01" }, { "text": "Which accession or sequence evidence establishes FGF23 protein identity?", "kind": "definition", "id": "entity-resolution-q02" } ] } ] }, { "id": "ortholog-and-construct", "name": "Ortholog and construct", "description": "Resolve species, sequence reference and modifications introduced during production.", "findings": [ { "id": "sequence-provenance", "name": "Sequence provenance", "description": "Attach species and construct boundaries to molecular and experimental claims.", "questions": [ { "text": "Which species and versioned protein sequence define the residue numbering?", "kind": "provenance", "id": "sequence-provenance-q01" }, { "text": "Which substitutions, truncations or tags distinguish this material from endogenous FGF23?", "kind": "definition", "id": "sequence-provenance-q02" } ] } ] } ] }, { "id": "fgf23-processing", "name": "FGF23 processing", "description": "Represent conversion between precursor, intact hormone and cleavage fragments.", "rationale": "FGF23 abundance is not interpretable without knowing which molecular forms are present.", "layers": [ { "id": "maturation-and-cleavage", "name": "Maturation and cleavage", "description": "Track signal-peptide removal separately from cleavage of the hormone.", "findings": [ { "id": "form-assignment", "name": "Form assignment", "description": "Record experimentally supported residue boundaries and distinguish secretory maturation from subsequent fragmentation.", "questions": [ { "text": "Does the material retain its signal peptide, represent mature intact FGF23 or contain cleavage fragments?", "kind": "definition", "id": "form-assignment-q01" }, { "text": "Which sequence, mass-spectrometric or immunoblot evidence establishes the assigned form?", "kind": "measurement", "id": "form-assignment-q02" } ] } ] }, { "id": "processing-control", "name": "Processing control", "description": "Capture modifications and sequence changes relevant to proteolytic susceptibility.", "findings": [ { "id": "cleavage-susceptibility", "name": "Cleavage susceptibility", "description": "Distinguish measured modification states and cleavage behavior from predictions based on enzyme expression. [Primary processing study](https://pubmed.ncbi.nlm.nih.gov/26746780/)", "questions": [ { "text": "Which glycosylation or phosphorylation sites were measured on this FGF23 preparation?", "kind": "measurement", "id": "cleavage-susceptibility-q01" }, { "text": "What evidence connects its sequence or modifications to cleavage under the stated conditions?", "kind": "provenance", "id": "cleavage-susceptibility-q02" } ] } ] } ] }, { "id": "fgf23-production-and-disposition", "name": "FGF23 production and disposition", "description": "Connect FGF23 synthesis and secretion to circulating abundance and removal.", "rationale": "An elevated concentration alone cannot distinguish increased production from altered processing or clearance.", "layers": [ { "id": "source-and-secretion", "name": "Source and secretion", "description": "Identify the producing cells and evidence that their product enters the measured compartment.", "findings": [ { "id": "production-evidence", "name": "Production evidence", "description": "Keep transcript expression, intracellular protein and released FGF23 as distinct observations.", "questions": [ { "text": "Which cells or tissues are evidenced to produce FGF23 in this organism and condition?", "kind": "provenance", "id": "production-evidence-q01" }, { "text": "Was production inferred from RNA, measured as intracellular protein or demonstrated by secretion?", "kind": "measurement", "id": "production-evidence-q02" } ] } ] }, { "id": "circulation-and-removal", "name": "Circulation and removal", "description": "Assess compartment, timing and clearance when interpreting abundance.", "findings": [ { "id": "concentration-drivers", "name": "Concentration drivers", "description": "Separate evidence for synthesis, cleavage and removal; human renal sampling provides one approach to studying clearance. [Primary renal clearance study](https://pmc.ncbi.nlm.nih.gov/articles/PMC9177785/)", "questions": [ { "text": "Which compartment and sampling time does the FGF23 concentration describe?", "kind": "measurement", "id": "concentration-drivers-q01" }, { "text": "What evidence distinguishes increased secretion from changed cleavage or reduced clearance?", "kind": "boundary", "id": "concentration-drivers-q02" } ] } ] } ] }, { "id": "fgf23-signaling-and-response", "name": "FGF23 signaling and response", "description": "Connect a specified FGF23 form to receptor engagement and measured physiological effects.", "rationale": "Ligand detection, receptor binding and biological response are different claims requiring different evidence.", "layers": [ { "id": "receptor-competence", "name": "Receptor competence", "description": "Describe the receptor and co-receptor conditions supporting the observed response.", "findings": [ { "id": "signaling-attribution", "name": "Signaling attribution", "description": "Require a defined responding system and controls before attributing activity to FGF23.", "questions": [ { "text": "Which FGFR and alpha-Klotho conditions were established in the responding cells?", "kind": "measurement", "id": "signaling-attribution-q01" }, { "text": "Which inhibition, depletion or rescue controls attribute the response specifically to FGF23?", "kind": "provenance", "id": "signaling-attribution-q02" } ] } ] }, { "id": "mineral-metabolism-response", "name": "Mineral metabolism response", "description": "Relate FGF23 exposure to phosphate handling and vitamin D endpoints.", "findings": [ { "id": "functional-endpoints", "name": "Functional endpoints", "description": "Record the measured endpoint and timing instead of treating circulating FGF23 as a direct measurement of physiological effect.", "questions": [ { "text": "Which renal phosphate-handling or vitamin D endpoint changed after the defined FGF23 exposure?", "kind": "measurement", "id": "functional-endpoints-q01" }, { "text": "What separates an FGF23-mediated effect from concurrent changes in kidney function, PTH or mineral intake?", "kind": "boundary", "id": "functional-endpoints-q02" } ] } ] } ] }, { "id": "fgf23-measurement", "name": "FGF23 measurement", "description": "Make each FGF23 result interpretable in terms of molecular targets, calibration and specimen quality.", "rationale": "Intact and C-terminal assay results can represent different mixtures of FGF23 forms.", "layers": [ { "id": "assay-target", "name": "Assay target", "description": "Specify what the method actually detects.", "findings": [ { "id": "detected-molecular-population", "name": "Detected molecular population", "description": "C-terminal immunoreactivity must not be labeled fragment-only concentration; intact assays and C-terminal assays recognize different molecular populations. [Primary assay study](https://link.springer.com/article/10.1007/s00198-012-2029-3)", "questions": [ { "text": "Does the assay detect intact FGF23, intact plus C-terminal fragments or another defined target?", "kind": "definition", "id": "detected-molecular-population-q01" }, { "text": "Which epitope and cross-reactivity evidence supports that analyte definition for this species?", "kind": "provenance", "id": "detected-molecular-population-q02" } ] } ] }, { "id": "result-comparability", "name": "Result comparability", "description": "Establish whether measurements can be compared or combined.", "findings": [ { "id": "calibration-and-specimen", "name": "Calibration and specimen", "description": "Keep units, calibrator, assay platform and specimen history attached to the result; do not subtract unlike assay values to estimate fragments.", "questions": [ { "text": "What units, calibrator, quantification limits and specimen conditions apply to this result?", "kind": "measurement", "id": "calibration-and-specimen-q01" }, { "text": "What validation permits comparison, conversion or combination with the other FGF23 measurements?", "kind": "action", "id": "calibration-and-specimen-q02" } ] } ] } ] }, { "id": "fgf23-use-and-interpretation", "name": "FGF23 use and interpretation", "description": "Determine what an observation or preparation supports an agent doing next.", "rationale": "FGF23 can be a measured biomarker or an experimental reagent, with different evidence needed for each use.", "layers": [ { "id": "biological-interpretation", "name": "Biological interpretation", "description": "Interpret results against contemporaneous physiology and the intended question.", "findings": [ { "id": "contextual-meaning", "name": "Contextual meaning", "description": "An assay reference interval and physiological appropriateness are separate assessments; neither alone establishes a disease or treatment indication.", "questions": [ { "text": "Which simultaneous phosphate, kidney function, vitamin D and PTH observations are needed for this interpretation?", "kind": "measurement", "id": "contextual-meaning-q01" }, { "text": "Does the evidence support association, a mechanistic explanation or only a request for further investigation?", "kind": "boundary", "id": "contextual-meaning-q02" } ] } ] }, { "id": "experimental-fitness", "name": "Experimental fitness", "description": "Match FGF23 material to a defined experimental use.", "findings": [ { "id": "preparation-acceptance", "name": "Preparation acceptance", "description": "Assess identity, intactness and activity in relation to the proposed experiment rather than relying on the reagent label.", "questions": [ { "text": "Which identity, cleavage, purity and potency measurements qualify this lot for the intended experiment?", "kind": "measurement", "id": "preparation-acceptance-q01" }, { "text": "Which controls distinguish FGF23 activity from tag effects, contaminants or accompanying fragments?", "kind": "action", "id": "preparation-acceptance-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 intended sense is assumed to be the protein hormone; confirm whether the registry instead denotes the gene.", "The precursor length refers to human FGF23; species and processing state matter.", "This is recalled knowledge, not source-checked research; assay specifications and treatment indications require verification." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of FGF23 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": "HGNC approved gene symbol", "value_or_pattern": "FGF23", "note": "Identifies the human gene encoding the hormone; the gene and its protein product are distinct entities." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of FGF23 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 during investigation of phosphate-wasting disorders, including inherited hypophosphatemic disorders and tumor-induced osteomalacia.", "Studied as a marker of disturbed mineral metabolism in chronic kidney disease.", "Targeted by the monoclonal antibody burosumab in selected FGF23-mediated hypophosphatemic disorders." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of FGF23 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": "Human protein precursor length", "typical_range": "251", "unit": "amino acid residues" }, { "quantity": "Circulating intact FGF23 concentration", "typical_range": "Assay-dependent; no universal reference interval", "unit": "pg/mL" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of FGF23 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": [ "Excess biologically active FGF23 can cause renal phosphate wasting, hypophosphatemia, and impaired bone mineralization.", "Deficient FGF23 activity or resistance to its action can cause hyperphosphatemia and ectopic calcification.", "Altered proteolytic processing can change the abundance of intact, biologically active hormone.", "Intact and C-terminal FGF23 assays detect different molecular species; treating their results as interchangeable can mislead interpretation." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of FGF23 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": "FGF23 gene", "difference": "The gene is a DNA sequence encoding FGF23; the hormone is its secreted protein product." }, { "name": "FGF21", "difference": "A related endocrine fibroblast growth factor with principally metabolic functions and different coreceptor requirements." }, { "name": "Parathyroid hormone", "difference": "A distinct hormone secreted by the parathyroid glands that also promotes phosphate excretion but generally stimulates renal calcitriol production." }, { "name": "Alpha-Klotho", "difference": "A coreceptor supporting canonical FGF23 signaling, rather than the hormone ligand." }, { "name": "C-terminal FGF23 fragments", "difference": "Cleavage products of FGF23 that lack the intact hormone's canonical phosphaturic activity and can contribute to C-terminal assay measurements." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of FGF23 this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does vr.tr.fgf23 identify the protein hormone, the human gene or a cross-species concept in its originating registry record?", "Which species, sequence variants and recombinant constructs require explicit subordinate descriptions within this single model?", "Which assay-specific reference intervals, specimen stability limits and cross-platform comparisons are validated for the intended population and use?", "Under which endogenous conditions do FGF23 fragments have demonstrated biological effects, and how do those differ from experimental peptide administration?", "Which proposed extra-renal or alpha-Klotho-independent effects have sufficiently strong causal evidence to include as established FGF23 activities?" ], "statistics": { "bundles": 7, "layers": 13, "findings": 18, "questions": 30 } }