{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T10:25:16Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 17.6, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09525-4e9e-72a0-af5e-cebac3eed715\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: IL1RN\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": 72.3, "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: 01a09525-4ea6-72d2-821d-90e597bd2a8f\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: IL1RN\nRegistry id: vr.tr.il1rn\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": "2026-10-06T08:57:57+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-Q14914156", "registryId": "vr.tr.il1rn", "name": "IL1RN", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q14914156/", "model": { "registry_id": "vr.tr.il1rn", "name": "IL1RN", "purpose": "Enable an agent to identify IL1RN, interpret observations of its sequence and expression, and judge which functional conclusions or follow-up analyses the evidence supports.", "definition": "IL1RN is the human gene encoding interleukin-1 receptor antagonist, a protein that inhibits interleukin-1 signalling by competing with IL-1α and IL-1β for binding to the type I interleukin-1 receptor.", "scope_statement": "This model provisionally treats vr.tr.il1rn as the human IL1RN gene, owning its identity, sequence variation, transcript relationships, expression context and evidence linking its products to interleukin-1 antagonism; the registry's intended species and gene-versus-protein boundary remain unresolved.", "in_scope": [ "Species-qualified IL1RN gene identity and reference-sequence mapping", "Alleles, sequence variants and their transcript-specific consequences", "Transcript and encoded protein-isoform relationships", "Expression observations qualified by tissue, cell type and experimental condition", "Evidence connecting IL1RN alterations to antagonist activity and phenotypes" ], "out_of_scope": [ "Standalone physical and biochemical characterization of isolated IL-1 receptor antagonist protein", "IL1R1 receptor identity and receptor-specific signaling machinery", "Independent models of IL1A, IL1B and other interleukin-family genes", "Nonhuman orthologs as interchangeable instances of the human gene", "Recombinant medicines, their manufacturing specifications and dosing", "Patient diagnosis and treatment decisions" ], "distinguishing_features": [ "Resolve the symbol with species and stable identifier: the human IL1RN record is NCBI Gene 3557. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/3557/)", "Distinguish an IL1RN DNA locus from its RNA transcripts and encoded IL-1 receptor antagonist protein; these require different identifiers and assays.", "Distinguish the antagonist-encoding gene from receptor genes: a record describing the IL-1 receptor itself does not identify IL1RN.", "Check whether a sequence maps specifically to IL1RN rather than another interleukin-family locus.", "Require product and preparation metadata when a reagent catalog uses IL1RN as a protein label; the label alone does not identify a genomic entity." ], "characteristics": [ { "name": "Species-qualified gene identity", "kind": "relation", "unit_or_values": "Taxonomy identifier plus stable gene identifier", "why_it_matters": "Prevents human IL1RN and ortholog observations from being merged without qualification." }, { "name": "Reference locus", "kind": "relation", "unit_or_values": "Genome assembly, chromosome or contig accession, interval in bp, strand and coordinate convention", "why_it_matters": "Makes sequence mappings and variant positions reproducible." }, { "name": "Transcript-product mapping", "kind": "relation", "unit_or_values": "Versioned transcript accession linked to versioned protein accession", "why_it_matters": "Separates consequences and measurements that apply to different IL1RN products." }, { "name": "Allelic configuration", "kind": "state", "unit_or_values": "Reference-qualified variants, zygosity, copy number and phase; unknown where unresolved", "why_it_matters": "A sample's functional interpretation can depend on both copies and their configuration." }, { "name": "IL1RN RNA abundance", "kind": "measurement", "unit_or_values": "TPM, normalized counts or relative qPCR expression with method and normalization", "why_it_matters": "Supports expression comparisons without equating RNA abundance with antagonist activity." }, { "name": "Product compartment", "kind": "category", "unit_or_values": "Secreted, intracellular, mixed or unresolved, qualified by isoform and evidence", "why_it_matters": "Prevents measurements from different compartments from being treated as equivalent." }, { "name": "Product-mediated antagonism", "kind": "measurement", "unit_or_values": "Assay-specific inhibition percentage or concentration-response parameter with units and conditions", "why_it_matters": "Connects gene-associated changes to measured function through an explicitly identified product." }, { "name": "Variant interpretation", "kind": "state", "unit_or_values": "Unassessed, uncertain or evidence-supported interpretation, with assertion source and date", "why_it_matters": "Separates observed sequence differences from claims about their effects." } ], "affordances": [ "Resolve an IL1RN label to a species-qualified gene and reference sequence.", "Map a reported variant to affected IL1RN transcripts and candidate product consequences.", "Assess whether an assay distinguishes IL1RN from related loci and individual transcripts from total expression.", "Compare expression observations with compatible sample context and normalization.", "Trace a functional or phenotype claim to the specific allele, product and experiment supporting it.", "Recommend additional sequence, expression or functional analysis when competing interpretations remain unresolved." ], "agent_conduct": { "may": [ "Describe IL1RN and the interleukin-1 receptor antagonist it encodes, citing sources.", "Explain in general terms that rare inherited loss of this gene causes severe inflammation needing specialist care." ], "must_not": [ "Diagnose an autoinflammatory disease in a person from a variant or symptoms.", "Share genetic data without consent.", "Recommend biological medicines that block interleukin-1 to a person.", "Classify a variant of uncertain significance as harmful without evidence." ], "requires_human": [ "Returning genetic results to a family.", "Any treatment decision for a person." ] }, "ethics": { "considerations": [ "Severe inherited inflammatory disease often affects newborns, so results reach worried families.", "Genetic data about children needs particular care." ], "affected_parties": [ "Children and families", "Patients", "Clinicians" ] }, "owners": { "steward": "The person whose genome carries it; laboratories and clinical variant databases hold records.", "master_systems": [ "Clinical variant databases", "Gene and variant databases" ] }, "visual_identification": [ "Not visible; known from sequence data and protein assays.", "Identified by its approved gene symbol." ], "failure_modes_and_hazards": [ "Misclassification of variants.", "Delayed diagnosis of severe neonatal inflammation." ], "standards_and_regulation": [ "Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol." ], "what_it_is_for": [ "IL1RN is encountered in human genomic sequencing, gene expression studies and research on inflammatory regulation.", "Its sequence and expression are examined to assess evidence about interleukin-1 antagonism, while distinguishing the gene from its protein products.", "Interpretation depends on the sampled tissue, transcript and experimental conditions." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q14914156: IL1RN", "url": "https://www.wikidata.org/wiki/Q14914156", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Interleukin-1 receptor antagonist", "url": "https://en.wikipedia.org/wiki/Interleukin-1_receptor_antagonist", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "il1rn-identity", "name": "IL1RN identity and entity boundary", "description": "Resolve what biological entity the registry name denotes.", "rationale": "IL1RN can appear as a gene symbol or a product label, while the registry supplies no definition.", "layers": [ { "id": "gene-and-species", "name": "Gene and species", "description": "Anchor the entry to an organism and stable gene record.", "findings": [ { "id": "species-qualified-anchor", "name": "Species-qualified anchor", "description": "Record the evidence supporting the provisional human-gene interpretation.", "questions": [ { "text": "Does the registry's originating identifier resolve to human IL1RN or to a different species or entity?", "kind": "provenance", "id": "species-qualified-anchor-q01" }, { "text": "Which stable gene identifier and approved symbol establish the intended identity?", "kind": "definition", "id": "species-qualified-anchor-q02" } ] } ] }, { "id": "gene-product-separation", "name": "Gene and product separation", "description": "Keep locus, transcript, protein and reagent references distinguishable.", "findings": [ { "id": "label-resolution", "name": "Ambiguous IL1RN labels", "description": "Require molecular-entity evidence before attaching a reported observation to the gene.", "questions": [ { "text": "Does this IL1RN record describe genomic DNA, RNA, endogenous protein or a recombinant preparation?", "kind": "boundary", "id": "label-resolution-q01" }, { "text": "Which accession or preparation identifier resolves the label, and which neighboring model should own product-specific properties?", "kind": "action", "id": "label-resolution-q02" } ] } ] } ] }, { "id": "locus-and-alleles", "name": "Reference locus and allelic state", "description": "Represent sequence observations against explicit IL1RN references.", "rationale": "Variant meaning depends on reference sequence, transcript choice and allelic configuration.", "layers": [ { "id": "reference-mapping", "name": "Reference mapping", "description": "Make genomic and transcript coordinates reproducible.", "findings": [ { "id": "coordinate-anchoring", "name": "Coordinate anchoring", "description": "Retain the reference and mapping assumptions behind each IL1RN sequence assertion.", "questions": [ { "text": "Which assembly, accession version, strand and coordinate convention locate the reported IL1RN interval?", "kind": "provenance", "id": "coordinate-anchoring-q01" }, { "text": "Does the reported sequence map uniquely to IL1RN, and what alignment evidence excludes related loci?", "kind": "measurement", "id": "coordinate-anchoring-q02" } ] } ] }, { "id": "variant-configuration", "name": "Variant configuration", "description": "Separate individual variants from the genotype carried by a sample.", "findings": [ { "id": "alleles-and-consequences", "name": "Alleles and transcript consequences", "description": "Capture sequence changes, copy-number findings and unresolved phase without presuming functional loss.", "questions": [ { "text": "What IL1RN variants, copy-number changes, zygosity and phase were measured, and which regions were inadequately covered?", "kind": "measurement", "id": "alleles-and-consequences-q01" }, { "text": "Which transcript-specific effects are predicted, and which have direct experimental support?", "kind": "provenance", "id": "alleles-and-consequences-q02" } ] } ] } ] }, { "id": "transcripts-and-expression", "name": "Transcripts, products and expression", "description": "Connect gene-level observations to identifiable molecular products and biological contexts.", "rationale": "IL1RN has multiple transcript-product records; pooled measurements can obscure the relevant product. [NCBI RefSeq records](https://www.ncbi.nlm.nih.gov/gene/3557/)", "layers": [ { "id": "transcript-product-resolution", "name": "Transcript and product resolution", "description": "Track isoforms without assuming that numbering is consistent across resources.", "findings": [ { "id": "isoform-compartment-link", "name": "Isoform and compartment linkage", "description": "Establish which transcript encodes the observed product and how its compartment was determined.", "questions": [ { "text": "Which versioned IL1RN transcript and protein accessions correspond to the isoform named in this source?", "kind": "definition", "id": "isoform-compartment-link-q01" }, { "text": "What evidence assigns the product to a secreted or intracellular form in the observed system?", "kind": "provenance", "id": "isoform-compartment-link-q02" } ] } ] }, { "id": "expression-context", "name": "Expression context", "description": "Qualify abundance by sample composition, condition and time.", "findings": [ { "id": "contextual-abundance", "name": "Contextual abundance", "description": "Keep total IL1RN expression, transcript-specific expression and product abundance as distinct observations.", "questions": [ { "text": "In which tissue, cell population, stimulation condition and time point was IL1RN expression measured?", "kind": "measurement", "id": "contextual-abundance-q01" }, { "text": "Does the assay measure total IL1RN RNA, a specific transcript or protein, and what normalization supports comparison?", "kind": "measurement", "id": "contextual-abundance-q02" } ] } ] } ] }, { "id": "antagonist-function", "name": "Product-mediated IL-1 antagonism", "description": "Connect IL1RN observations to tested antagonist function through identified products.", "rationale": "The encoded antagonist inhibits IL-1 binding to receptors, so functional interpretation must distinguish the gene from the molecule acting at the receptor. [Original receptor-antagonist gene study](https://pubmed.ncbi.nlm.nih.gov/1386337/)", "layers": [ { "id": "functional-readout", "name": "Functional readout", "description": "Specify the receptor system, agonist and endpoint used to assess antagonism.", "findings": [ { "id": "antagonism-assay", "name": "Antagonism assay interpretation", "description": "Separate receptor binding from demonstrated suppression of an IL-1 response.", "questions": [ { "text": "Which IL1RN product, IL-1 agonist, receptor context and concentration range were tested?", "kind": "measurement", "id": "antagonism-assay-q01" }, { "text": "Does the endpoint establish binding, inhibition of signaling or a downstream response, and what controls distinguish these?", "kind": "boundary", "id": "antagonism-assay-q02" } ] } ] }, { "id": "gene-to-function", "name": "Gene-to-function attribution", "description": "Evaluate whether a gene alteration explains the observed functional change.", "findings": [ { "id": "causal-functional-link", "name": "Causal functional link", "description": "Track the steps between IL1RN sequence or expression changes and product activity.", "questions": [ { "text": "Were altered transcription, splicing, product abundance, localization or antagonist activity directly measured?", "kind": "provenance", "id": "causal-functional-link-q01" }, { "text": "Would a matched control, rescue experiment or orthogonal assay resolve the remaining attribution uncertainty?", "kind": "action", "id": "causal-functional-link-q02" } ] } ] } ] }, { "id": "phenotype-evidence", "name": "Phenotype evidence and interpretation limits", "description": "Evaluate claims linking IL1RN variation to biological or disease phenotypes.", "rationale": "A gene-level association cannot establish the consequence of every allele or the status of an individual sample.", "layers": [ { "id": "variant-phenotype-links", "name": "Variant-to-phenotype links", "description": "Keep causal assertions separate from statistical associations.", "findings": [ { "id": "assertion-strength", "name": "Assertion strength", "description": "Require allele-specific evidence and an explicit phenotype definition.", "questions": [ { "text": "Which exact IL1RN allele or genotype is linked to which phenotype, and is the claim causal, associative or unresolved?", "kind": "definition", "id": "assertion-strength-q01" }, { "text": "What segregation, functional, population or replication evidence supports that claim?", "kind": "provenance", "id": "assertion-strength-q02" } ] } ] }, { "id": "interpretation-and-next-actions", "name": "Interpretation and next actions", "description": "Translate evidence gaps into bounded analytical follow-up.", "findings": [ { "id": "evidence-limited-action", "name": "Evidence-limited action", "description": "Preserve uncertainty when applying published IL1RN findings to a new sample.", "questions": [ { "text": "Do conflicting assertions, unresolved phase or assay limitations prevent a supported interpretation of this IL1RN observation?", "kind": "boundary", "id": "evidence-limited-action-q01" }, { "text": "Which additional reference check, sequence confirmation or functional measurement would most directly resolve the uncertainty?", "kind": "action", "id": "evidence-limited-action-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 label is interpreted as the human gene; the registry supplies neither a species nor an explicit gene-versus-protein sense.", "Alternative transcripts encode secreted and intracellular protein forms; their exact classification and accession identifiers require checking.", "This description is based on recall, without source consultation." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of IL1RN 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": "IL1RN", "note": "The human gene symbol; the encoded protein is commonly called IL-1Ra." }, { "scheme": "NCBI Gene", "value_or_pattern": "3557", "note": "Identifier for the human IL1RN gene." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of IL1RN 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 regulation of inflammation and interleukin-1 signalling.", "Genetic investigation of deficiency of interleukin-1 receptor antagonist, an inherited autoinflammatory disorder.", "Study of associations between IL1RN variants and inflammatory disease." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of IL1RN 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": [ "Biallelic pathogenic loss-of-function variants can cause deficiency of interleukin-1 receptor antagonist, with severe early-onset inflammation involving skin and bone.", "Gene expression measurements do not directly establish the abundance or biological activity of the encoded protein.", "Reported associations between common variants and disease do not by themselves establish causation." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of IL1RN 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": "Interleukin-1 receptor antagonist", "difference": "The protein product; IL1RN denotes the gene encoding it." }, { "name": "IL1R1", "difference": "Encodes the type I interleukin-1 receptor, rather than its antagonist." }, { "name": "IL1A", "difference": "Encodes the signalling agonist IL-1α, rather than the receptor antagonist." }, { "name": "IL1B", "difference": "Encodes the signalling agonist IL-1β, rather than the receptor antagonist." }, { "name": "Anakinra", "difference": "A recombinant therapeutic form of human interleukin-1 receptor antagonist, rather than the endogenous gene." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of IL1RN this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry's originating record identify the human IL1RN gene, its protein product or a species-unspecified concept?", "Which reference assembly and transcript set should govern the initial model, and how should subsequent annotation changes be reconciled?", "Which IL1RN transcripts and intracellular or secreted products have direct evidence in the biological contexts the catalogue must support?", "Which allele-specific functional and phenotype assertions are sufficiently supported, and where do sources disagree?", "Does an existing Vercy publication already own this gene concept or its protein product, requiring a link rather than another model?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 15, "questions": 25 } }