{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:41:32Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 18.2, "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: 01a0956b-1b41-7c53-82a8-1d9508229175\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: NR1H4\nSense to describe: (none recorded)\nDomain code: PHY.OBJ\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 044: 1001 registere", "usd": 0.0, "recall": true }, "codex": { "seconds": 72.5, "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: 01a0956b-1b31-7983-8f8d-4c7ad6d4a788\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: NR1H4\nRegistry id: vr.tr.nr1h4\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" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:26+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q14905041", "registryId": "vr.tr.nr1h4", "name": "NR1H4", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q14905041/", "model": { "registry_id": "vr.tr.nr1h4", "name": "NR1H4", "purpose": "Enable an agent to identify NR1H4, distinguish its gene and receptor forms, and interpret evidence about its expression, molecular state and experimental manipulation.", "definition": "NR1H4 is a gene encoding the farnesoid X receptor (FXR), a bile-acid-activated nuclear receptor that regulates transcription involved in bile acid homeostasis and lipid and glucose metabolism.", "scope_statement": "This draft provisionally models the NR1H4 molecular entity represented by vr.tr.nr1h4, keeping gene, transcript and protein records explicitly distinct within one entry until registry provenance resolves the intended referent and species. Human NR1H4 encodes a bile-acid-responsive transcription factor called FXR; this biological identity supersedes the batch's device framing. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/9971/)", "in_scope": [ "NR1H4 identity, species and gene-to-protein relationships", "Reference sequences, transcript variants and receptor isoforms", "Expression and receptor localization in specified biological contexts", "Ligand response and transcriptional activity", "Sequence alterations and experimentally supported functional effects" ], "out_of_scope": [ "Complete bile acid synthesis and transport pathways", "Independent models of NR1H4 ligands or medicinal products", "Whole-organ liver and intestinal physiology", "Diagnosis and treatment of diseases associated with NR1H4", "Other nuclear receptors and their independent molecular identities" ], "distinguishing_features": [ "Resolve the symbol through a species-specific identifier: human NR1H4 maps to NCBI Gene 9971, rather than treating the name alone as sufficient identification. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/9971/)", "Distinguish the coding locus from its protein product: UniProt Q96RI1 identifies the human bile acid receptor protein. [UniProt](https://www.uniprot.org/uniprotkb/Q96RI1/entry)", "Require sequence or accession evidence when separating NR1H4 from similarly named nuclear receptors.", "Distinguish receptor identification from a functional bile acid response; a response alone does not establish which receptor mediated it.", "Separate an endogenous NR1H4 isoform from a tagged, truncated or otherwise engineered experimental construct." ], "characteristics": [ { "name": "Molecular referent", "kind": "category", "unit_or_values": "gene locus | transcript | protein isoform | engineered construct", "why_it_matters": "Determines which identity, state and measurements can meaningfully be recorded." }, { "name": "Taxonomic identity", "kind": "relation", "unit_or_values": "Organism name and taxonomy identifier", "why_it_matters": "Prevents transferring sequence and functional evidence between species without justification." }, { "name": "Reference identity", "kind": "relation", "unit_or_values": "Versioned gene, transcript and protein accessions; assembly for genomic coordinates", "why_it_matters": "Anchors variants, isoforms and assay targets to reproducible references." }, { "name": "Sequence alteration", "kind": "category", "unit_or_values": "Reference sequence | accession-relative variant | documented construct modification", "why_it_matters": "Separates native receptor observations from altered experimental materials." }, { "name": "Expression abundance", "kind": "measurement", "unit_or_values": "RNA abundance in a declared normalization system; protein abundance in assay-specific units", "why_it_matters": "Supports context-specific comparisons without equating RNA abundance with protein activity." }, { "name": "Subcellular distribution", "kind": "state", "unit_or_values": "Observed compartment distribution, method and observation time", "why_it_matters": "Locates the measured receptor pool and constrains interpretation of transcriptional activity." }, { "name": "Ligand response", "kind": "measurement", "unit_or_values": "Concentration in mol/L; response and baseline; EC50 or IC50 only when fitted appropriately", "why_it_matters": "Makes receptor response conditional on ligand, exposure and assay context." }, { "name": "Transcriptional effect", "kind": "measurement", "unit_or_values": "Target-specific expression change or reporter activity relative to a stated control", "why_it_matters": "Records functional output separately from receptor presence or ligand binding." } ], "affordances": [ "Resolve an NR1H4 label to a species, molecular form and reference accession.", "Check whether a sequence, reagent or construct actually targets the intended NR1H4 form.", "Compare expression or activity observations under compatible biological and assay conditions.", "Assess whether a ligand-response experiment supports NR1H4-specific activity.", "Identify the controls and additional evidence needed before attributing a phenotype to NR1H4." ], "agent_conduct": { "may": [ "Describe NR1H4 and the bile-acid receptor it encodes, citing sources.", "Report what a variant or expression result shows, with source and limits." ], "must_not": [ "Interpret a person's NR1H4 variant as a diagnosis of liver disease.", "Share genetic data without consent.", "Recommend drugs acting on this receptor to a person.", "Present supplement claims linked to it as proven." ], "requires_human": [ "Using results in treatment decisions.", "Research on patient samples without documented consent." ] }, "ethics": { "considerations": [ "Genetic findings about liver disease affect patients and their families.", "Health claims about bile acid signalling can mislead consumers." ], "affected_parties": [ "Patients and families", "Consumers", "Researchers" ] }, "owners": { "steward": "The person whose genome carries it; laboratories and biobanks hold records.", "master_systems": [ "Gene and variant databases" ] }, "visual_identification": [ "Not visible; known from sequence data and receptor assays.", "Identified by its approved gene symbol; the receptor is often called by another name." ], "failure_modes_and_hazards": [ "Confusion between the gene symbol and the receptor name in reports.", "Overinterpretation of variant associations." ], "standards_and_regulation": [ "Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol." ], "what_it_is_for": [ "The human NR1H4 gene is encountered in studies of bile acid regulation and metabolism, particularly in liver and intestinal tissues.", "Its sequence and transcript expression support investigation of the encoded farnesoid X receptor and its role in controlling gene transcription." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q14905041: NR1H4", "url": "https://www.wikidata.org/wiki/Q14905041", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Farnesoid X receptor", "url": "https://en.wikipedia.org/wiki/Farnesoid_X_receptor", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "nr1h4-identity", "name": "NR1H4 identity and registry boundary", "description": "Resolve what the registered name denotes before attaching biological observations.", "rationale": "NR1H4 can label a gene or its receptor product; merging those referents creates invalid state claims.", "layers": [ { "id": "registry-referent", "name": "Registry referent", "description": "Establish the molecular and taxonomic scope of this entry.", "findings": [ { "id": "gene-protein-boundary", "name": "Gene and receptor boundary", "description": "Require an explicit referent instead of inferring it from PHY.OBJ.", "questions": [ { "text": "Does the originating registry record denote the NR1H4 gene, its protein product or a deliberately combined molecular concept?", "kind": "boundary", "id": "gene-protein-boundary-q01" }, { "text": "Which original identifier and organism support that interpretation?", "kind": "provenance", "id": "gene-protein-boundary-q02" } ] } ] }, { "id": "identifier-resolution", "name": "Identifier resolution", "description": "Reconcile symbols, aliases and accessions without conflating related receptors.", "findings": [ { "id": "alias-disambiguation", "name": "Alias disambiguation", "description": "Treat names such as FXR as lookup aids that require accession confirmation.", "questions": [ { "text": "Which authoritative record connects the supplied NR1H4 or FXR label to the intended species and molecular form?", "kind": "provenance", "id": "alias-disambiguation-q01" }, { "text": "What accession or sequence check excludes a similarly named receptor or an ortholog from another species?", "kind": "boundary", "id": "alias-disambiguation-q02" } ] } ] } ] }, { "id": "nr1h4-sequence-forms", "name": "NR1H4 sequences and molecular forms", "description": "Connect locus, transcripts, receptor isoforms and experimental constructs.", "rationale": "An assay on one sequence form cannot automatically characterize every form represented by the symbol.", "layers": [ { "id": "transcript-isoform-mapping", "name": "Transcript and isoform mapping", "description": "Preserve the reference chain from coding sequence to receptor product.", "findings": [ { "id": "reference-sequence-chain", "name": "Reference sequence chain", "description": "Record versioned references and the evidence linking each transcript to its protein sequence.", "questions": [ { "text": "Which versioned transcript and protein accessions describe the NR1H4 form being observed?", "kind": "definition", "id": "reference-sequence-chain-q01" }, { "text": "Does the experiment distinguish that isoform from other NR1H4 transcripts or proteins?", "kind": "measurement", "id": "reference-sequence-chain-q02" } ] } ] }, { "id": "receptor-sequence-integrity", "name": "Receptor sequence integrity", "description": "Assess changes affecting the receptor regions required by a particular experiment.", "findings": [ { "id": "native-versus-engineered-receptor", "name": "Native versus engineered receptor", "description": "Document domain coverage, substitutions, deletions and tags before interpreting function.", "questions": [ { "text": "Which DNA-binding and ligand-binding regions are present in the tested NR1H4 sequence?", "kind": "definition", "id": "native-versus-engineered-receptor-q01" }, { "text": "Could a truncation, tag or substitution limit what this experiment establishes about endogenous NR1H4?", "kind": "boundary", "id": "native-versus-engineered-receptor-q02" } ] } ] } ] }, { "id": "nr1h4-cellular-context", "name": "NR1H4 expression and cellular context", "description": "Situate receptor observations in a defined tissue, cell population and cellular compartment.", "rationale": "Expression, localization and activity are different observations whose interpretation depends on biological context.", "layers": [ { "id": "expression-context", "name": "Expression context", "description": "Separate endogenous expression from experimentally introduced receptor abundance.", "findings": [ { "id": "measured-receptor-abundance", "name": "Measured receptor abundance", "description": "Require tissue, cell identity, molecular analyte and normalization for abundance claims.", "questions": [ { "text": "In which species, tissue and cell population was NR1H4 RNA or protein measured?", "kind": "measurement", "id": "measured-receptor-abundance-q01" }, { "text": "Does the abundance reflect endogenous expression or an introduced construct, and how was it normalized?", "kind": "provenance", "id": "measured-receptor-abundance-q02" } ] } ] }, { "id": "localization-context", "name": "Localization context", "description": "Record where the receptor was observed under the tested conditions.", "findings": [ { "id": "receptor-compartment-evidence", "name": "Receptor compartment evidence", "description": "Keep observed distribution separate from assumed activity.", "questions": [ { "text": "What method establishes NR1H4 compartment distribution, and at what time after treatment?", "kind": "measurement", "id": "receptor-compartment-evidence-q01" }, { "text": "What additional evidence is required before interpreting the observed localization as transcriptional activation?", "kind": "boundary", "id": "receptor-compartment-evidence-q02" } ] } ] } ] }, { "id": "nr1h4-ligand-transcription", "name": "NR1H4 ligand response and transcription", "description": "Connect ligand exposure to receptor engagement and separately measured transcriptional output.", "rationale": "Binding, activation and downstream expression changes require distinct evidence.", "layers": [ { "id": "ligand-engagement", "name": "Ligand engagement", "description": "Characterize a specified ligand against a specified NR1H4 form.", "findings": [ { "id": "binding-versus-response", "name": "Binding versus functional response", "description": "Preserve assay type, concentration and exposure when assessing ligand effects.", "questions": [ { "text": "Was direct NR1H4 binding measured, or was engagement inferred from a functional response?", "kind": "measurement", "id": "binding-versus-response-q01" }, { "text": "Which ligand identity, concentration range, exposure duration and controls support the reported response?", "kind": "provenance", "id": "binding-versus-response-q02" } ] } ] }, { "id": "transcriptional-output", "name": "Transcriptional output", "description": "Resolve DNA-associated receptor activity from indirect downstream effects.", "findings": [ { "id": "target-regulation-evidence", "name": "Target regulation evidence", "description": "Ask which target, regulatory sequence and molecular partners are supported in the tested context.", "questions": [ { "text": "Which endogenous target or reporter was measured, and what evidence distinguishes direct regulation from an indirect response?", "kind": "measurement", "id": "target-regulation-evidence-q01" }, { "text": "Were RXR participation and relevant coregulators tested, inferred or left unresolved in this NR1H4 experiment?", "kind": "provenance", "id": "target-regulation-evidence-q02" } ] } ] } ] }, { "id": "nr1h4-perturbation-evidence", "name": "NR1H4 perturbation and causal interpretation", "description": "Determine what receptor alterations and experimental interventions actually establish.", "rationale": "A phenotype after perturbation does not by itself establish an NR1H4-specific mechanism.", "layers": [ { "id": "variant-function", "name": "Variant function", "description": "Connect sequence alterations to measured molecular consequences.", "findings": [ { "id": "alteration-functional-consequence", "name": "Alteration and functional consequence", "description": "Distinguish predicted effects from observed changes in abundance, binding or transcription.", "questions": [ { "text": "Against which reference accession is the NR1H4 alteration described?", "kind": "definition", "id": "alteration-functional-consequence-q01" }, { "text": "Which functional consequences were directly measured, and which remain predictions?", "kind": "measurement", "id": "alteration-functional-consequence-q02" } ] } ] }, { "id": "perturbation-specificity", "name": "Perturbation specificity", "description": "Assess whether genetic or chemical interventions support attribution to NR1H4.", "findings": [ { "id": "causal-attribution-controls", "name": "Causal attribution controls", "description": "Use specificity and rescue evidence to bound claims about receptor-dependent phenotypes.", "questions": [ { "text": "What independent perturbation, rescue or receptor-deficient control supports attribution of the observed effect to NR1H4?", "kind": "provenance", "id": "causal-attribution-controls-q01" }, { "text": "Which additional control is needed before using this result to choose a subsequent NR1H4 experiment?", "kind": "action", "id": "causal-attribution-controls-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 registry provides no species or sense; verify whether this entry denotes the human gene, its protein product, or an orthologous gene in another species.", "Human identifiers are supplied from recall and have not been checked against a database.", "NR1H4 is a biological gene designation; the batch's device-oriented guidance does not apply." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of NR1H4 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 gene symbol", "value_or_pattern": "NR1H4", "note": "Approved human gene symbol; the expanded name is nuclear receptor subfamily 1 group H member 4." }, { "scheme": "NCBI Gene", "value_or_pattern": "9971", "note": "Identifier for the human NR1H4 gene." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of NR1H4 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": [ "Research into feedback control of bile acid synthesis and transport.", "Investigation of metabolic regulation in the liver and intestine.", "Drug discovery targeting FXR activation or inhibition." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of NR1H4 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": [ "Loss or disruption of receptor function can impair feedback regulation of bile acid synthesis and transport." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of NR1H4 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": "Farnesoid X receptor (FXR)", "difference": "FXR denotes the receptor protein encoded by NR1H4; distinguish the gene from its protein product if the registry represents them separately." }, { "name": "GPBAR1 (TGR5)", "difference": "GPBAR1 encodes a membrane G-protein-coupled bile acid receptor, whereas NR1H4 encodes a nuclear receptor that regulates transcription." }, { "name": "NR1H3 (liver X receptor alpha)", "difference": "NR1H3 encodes a related nuclear receptor associated with oxysterol sensing, whereas NR1H4 encodes FXR, associated with bile acid sensing." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of NR1H4 this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the originating registry identifier intend human NR1H4, another species or the receptor family across species?", "Should the entry primarily own the gene locus or receptor protein, and does an existing Vercy model already own that referent?", "Which transcript and protein isoforms require distinct treatment because their differences affect recognition or functional interpretation?", "Which ligand, partner and direct-target claims have sufficient primary evidence in each relevant tissue and species?", "Which NR1H4 alterations have reproducible functional evidence, and where do phenotype associations remain mechanistically unresolved?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 15, "questions": 25 } }