{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T10:25:43Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 19.0, "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: 01a09525-3136-7081-bf61-6fe0eeefe77a\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: IGF1R\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": 106.0, "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: 01a09525-313f-7c02-a936-26c1b7dd994c\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: IGF1R\nRegistry id: vr.tr.igf1r\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": [ "definition", "distinguishing_features", "in_scope", "out_of_scope", "purpose", "scope_statement", "visual_identification" ], "answering_review": "b1b1ce508b1fe60e52c705ca2d80ff2b6f0ba22bc1c13f32f240a323109dca5d" } ], "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-Q14901457", "registryId": "vr.tr.igf1r", "name": "IGF1R", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q14901457/", "model": { "registry_id": "vr.tr.igf1r", "name": "IGF1R", "purpose": "Enable an agent to identify the human IGF1R gene, assess evidence about its variants and expression, and distinguish genomic and transcript observations from receptor measurements.", "definition": "IGF1R is a human protein-coding gene that encodes the insulin-like growth factor 1 receptor, a cell-surface receptor tyrosine kinase that binds IGF-1 and IGF-2 and regulates cellular growth, survival and proliferation.", "scope_statement": "This model owns IGF1R as a protein-coding gene in Homo sapiens, including genomic identity, variants, inheritance, regulation, transcripts and gene expression, with receptor functions represented as relationships to its encoded product.", "in_scope": [ "Human IGF1R gene identity and reference genomic sequence are included.", "Genomic coordinates qualified by reference assembly are included.", "Gene variants, inheritance and evidence-supported annotations are included.", "Transcript models, transcriptional regulation and RNA expression are included.", "Relationships between the gene, its transcripts and its encoded receptor are included." ], "out_of_scope": [ "The IGF1R protein's processing, assembly, ligand binding and kinase activity as an independent entity are excluded.", "IGF1, IGF2 and insulin as independently modeled ligands are excluded.", "INSR and IGF2R as independently modeled receptors are excluded.", "Complete downstream signaling networks and whole-organism endocrine regulation are excluded.", "Cancer, growth disorders and patient-specific diagnosis or treatment are excluded.", "Antibodies, inhibitors and assay instruments as independently modeled products are excluded." ], "distinguishing_features": [ "NCBI Gene 3480 identifies the human IGF1R gene, whereas UniProt P08069 identifies its encoded protein.", "Genomic coordinates and variants require an explicit reference assembly or sequence accession.", "IGF1R is distinct from the human INSR, IGF2R, IGF1 and IGF2 genes.", "Transcript abundance does not directly establish receptor abundance, assembly or kinase activation.", "Receptor hybrid formation and ligand responsiveness describe protein behavior rather than gene identity." ], "characteristics": [ { "name": "Reference protein identity", "kind": "relation", "unit_or_values": "Protein accession with version, organism and linked encoding-gene identifier", "why_it_matters": "Prevents gene-protein conflation and unsupported transfer between species." }, { "name": "Sequence and construct coverage", "kind": "category", "unit_or_values": "Reference sequence; named variant; residue interval; tags; engineered substitutions", "why_it_matters": "Defines which receptor functions and residue coordinates can be interpreted." }, { "name": "Processing state", "kind": "state", "unit_or_values": "Precursor; processed alpha/beta chains; fragment; unresolved", "why_it_matters": "Separates receptor maturation from simple detection of IGF1R-derived material." }, { "name": "Receptor assembly", "kind": "relation", "unit_or_values": "IGF1R-only complex; IGF1R-INSR hybrid; isolated subunit or domain; unresolved", "why_it_matters": "Determines whether binding and signaling observations belong to IGF1R alone or a mixed receptor." }, { "name": "Cell-surface abundance", "kind": "measurement", "unit_or_values": "Receptors per cell when calibrated; otherwise explicitly named assay-relative units", "why_it_matters": "Distinguishes accessible receptor abundance from total cellular protein." }, { "name": "Ligand-binding affinity", "kind": "measurement", "unit_or_values": "Kd in nM, with ligand, receptor assembly, preparation and assay conditions", "why_it_matters": "Supports comparisons without confusing affinity with downstream potency." }, { "name": "Site-specific phosphorylation", "kind": "measurement", "unit_or_values": "Site occupancy (%) or normalized phospho/total signal, with sequence coordinates and time point", "why_it_matters": "Makes activation evidence interpretable and flags ambiguous phospho-receptor assays." }, { "name": "Kinase activity", "kind": "measurement", "unit_or_values": "Specified substrate conversion per time and receptor amount, with ATP conditions", "why_it_matters": "Separates catalytic activity from abundance, binding and phosphorylation proxies." }, { "name": "Subcellular distribution", "kind": "state", "unit_or_values": "Plasma membrane; intracellular compartment specified by evidence; mixed; unresolved", "why_it_matters": "Conditions receptor accessibility and interpretation of trafficking observations." }, { "name": "Perturbation selectivity", "kind": "relation", "unit_or_values": "Intervention linked to IGF1R, INSR and other tested targets, with exposure and evidence", "why_it_matters": "Limits causal attribution to what the intervention actually distinguishes." } ], "affordances": [ "Resolve an IGF1R observation to a species, protein sequence and receptor preparation.", "Classify a sample as precursor, mature receptor, fragment or hybrid-containing preparation.", "Compare receptor binding or activation measurements under explicitly matched conditions.", "Assess whether an assay distinguishes IGF1R from INSR and hybrid receptors.", "Select an experimental readout or perturbation appropriate to the receptor property being investigated.", "Flag conclusions that require additional assembly, localization or selectivity evidence." ], "agent_conduct": { "may": [ "Describe IGF1R and its role in growth signalling, citing sources.", "Report what a variant or expression result shows, with source and limits." ], "must_not": [ "Interpret a person's IGF1R result as a diagnosis or cancer prognosis.", "Share genetic data without consent.", "Recommend growth factor products or drugs to a person.", "Present doping or anti-ageing uses of growth signalling as safe." ], "requires_human": [ "Using results in treatment decisions.", "Research on patient samples without documented consent." ] }, "ethics": { "considerations": [ "Growth signalling is linked to cancer, so overstated claims can frighten or mislead.", "Genetic results about growth disorders affect families." ], "affected_parties": [ "Patients and families", "Athletes", "Researchers" ] }, "owners": { "steward": "The person whose genome carries it; laboratories and biobanks hold records.", "master_systems": [ "Gene and variant databases" ] }, "visual_identification": [ "The gene is identified through human genomic sequence records and reference identifiers.", "Its approved gene symbol supports identification when paired with species and reference context.", "Antibody staining and receptor assays measure the protein product rather than the gene." ], "failure_modes_and_hazards": [ "Overinterpretation of expression data.", "Misuse of growth signalling products in sport." ], "standards_and_regulation": [ "Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol." ], "what_it_is_for": [ "The human IGF1R gene is encountered in studies of growth, development and cellular responses to insulin-like growth factors.", "Researchers examine its sequence and expression to investigate the production and regulation of its encoded receptor, including in cancer biology." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q14901457: IGF1R", "url": "https://www.wikidata.org/wiki/Q14901457", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Insulin-like growth factor 1 receptor", "url": "https://en.wikipedia.org/wiki/Insulin-like_growth_factor_1_receptor", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "igf1r-identity", "name": "IGF1R identity and reference boundary", "description": "Resolve what the IGF1R label denotes before attaching molecular observations.", "rationale": "The registry lacks a definition, and a gene symbol can also label its protein product.", "layers": [ { "id": "gene-protein-resolution", "name": "Gene and protein resolution", "description": "Separate the registered referent from linked genetic identifiers.", "findings": [ { "id": "registered-referent", "name": "Registered referent", "description": "Record whether the entry denotes a protein, gene or broader concept, retaining unresolved mapping explicitly.", "questions": [ { "text": "Does the originating registry record identify the IGF1R protein or its encoding gene?", "kind": "boundary", "id": "registered-referent-q01" }, { "text": "Which originating identifier and definition establish that interpretation?", "kind": "provenance", "id": "registered-referent-q02" } ] } ] }, { "id": "sequence-context", "name": "Species and sequence context", "description": "Anchor variants, constructs and residue numbers to a reference.", "findings": [ { "id": "reference-and-construct", "name": "Reference and construct identity", "description": "Capture organism, accession version, sequence changes and experimental coverage.", "questions": [ { "text": "Which organism and protein sequence version define this IGF1R observation?", "kind": "definition", "id": "reference-and-construct-q01" }, { "text": "Which substitutions, truncations or tags distinguish the observed material from that reference?", "kind": "boundary", "id": "reference-and-construct-q02" } ] } ] } ] }, { "id": "receptor-maturation-assembly", "name": "Receptor maturation and assembly", "description": "Describe the molecular form carrying the IGF1R identity.", "rationale": "Processing and mixed receptor assembly change what a detected IGF1R component represents.", "layers": [ { "id": "precursor-processing", "name": "Precursor processing", "description": "Distinguish precursor, mature chains and partial preparations.", "findings": [ { "id": "molecular-form", "name": "Observed molecular form", "description": "Require evidence for processing and chain coverage rather than inferring intact receptor from one signal.", "questions": [ { "text": "What evidence distinguishes precursor IGF1R from processed alpha and beta chains in this preparation?", "kind": "measurement", "id": "molecular-form-q01" }, { "text": "Which chain regions and modifications account for the observed bands or molecular masses?", "kind": "measurement", "id": "molecular-form-q02" } ] } ] }, { "id": "hybrid-composition", "name": "IGF1R-only and hybrid composition", "description": "Determine which receptor components coexist in the measured complex.", "findings": [ { "id": "assembly-assignment", "name": "Assembly assignment", "description": "Separate demonstrated complex composition from inferred association or cellular coexpression.", "questions": [ { "text": "What evidence establishes an IGF1R-only receptor versus an IGF1R-INSR hybrid?", "kind": "measurement", "id": "assembly-assignment-q01" }, { "text": "Does the assay resolve individual assemblies or report an unresolved mixture?", "kind": "boundary", "id": "assembly-assignment-q02" } ] } ] } ] }, { "id": "ligand-kinase-coupling", "name": "Ligand recognition and kinase activation", "description": "Connect ligand exposure to binding and receptor-level activity.", "rationale": "Binding, phosphorylation and downstream response measure different aspects of IGF1R function.", "layers": [ { "id": "ligand-recognition", "name": "Ligand recognition", "description": "Qualify ligand-binding measurements by receptor composition and experimental conditions.", "findings": [ { "id": "binding-evidence", "name": "Ligand-specific binding evidence", "description": "IGF1R binds IGF1 and can also bind IGF2 and insulin; measurements must specify the ligand and receptor preparation. [UniProt](https://www.uniprot.org/uniprotkb/P08069)", "questions": [ { "text": "Which ligand, concentration range and receptor assembly were used to measure binding?", "kind": "measurement", "id": "binding-evidence-q01" }, { "text": "Is the reported value an equilibrium Kd, competition IC50 or functional EC50?", "kind": "definition", "id": "binding-evidence-q02" } ] } ] }, { "id": "catalytic-activation", "name": "Catalytic activation", "description": "Resolve receptor phosphorylation and catalytic output over time.", "findings": [ { "id": "activation-evidence", "name": "Activation evidence", "description": "Ligand binding can activate IGF1R kinase and receptor autophosphorylation; record direct activity and proxy readouts separately. [UniProt](https://www.uniprot.org/uniprotkb/P08069)", "questions": [ { "text": "Which IGF1R phosphosites or catalytic substrates were measured, using which reference coordinates?", "kind": "measurement", "id": "activation-evidence-q01" }, { "text": "What time course, baseline and total-receptor normalization support the activation assignment?", "kind": "measurement", "id": "activation-evidence-q02" } ] } ] } ] }, { "id": "cellular-receptor-state", "name": "Cellular receptor availability and signaling context", "description": "Place IGF1R observations within a defined cell population and time window.", "rationale": "Receptor abundance and location constrain interpretation of ligand access and signaling responses.", "layers": [ { "id": "availability-trafficking", "name": "Availability and trafficking", "description": "Separate surface-accessible receptor from total receptor and track changes.", "findings": [ { "id": "surface-pool", "name": "Accessible receptor pool", "description": "Record surface abundance and localization with methods that can distinguish them from total protein.", "questions": [ { "text": "How much IGF1R is surface-accessible versus intracellular in the specified cells?", "kind": "measurement", "id": "surface-pool-q01" }, { "text": "Which observations distinguish internalization, recycling, degradation and altered receptor production?", "kind": "measurement", "id": "surface-pool-q02" } ] } ] }, { "id": "proximal-signaling", "name": "Receptor-proximal signaling", "description": "Link receptor state to immediate signaling evidence without assuming an entire phenotype.", "findings": [ { "id": "signal-attribution", "name": "Signal attribution", "description": "Record measured proximal partners and responses, with competing receptor contributions made explicit.", "questions": [ { "text": "Which proximal signaling partners show measured association or phosphorylation following IGF1R activation?", "kind": "measurement", "id": "signal-attribution-q01" }, { "text": "What evidence separates IGF1R contribution from INSR, hybrids and other active receptors?", "kind": "boundary", "id": "signal-attribution-q02" } ] } ] } ] }, { "id": "igf1r-experimental-interpretation", "name": "IGF1R assay and intervention interpretation", "description": "Define which claims can follow from detection or manipulation of IGF1R.", "rationale": "A signal labeled IGF1R or a response to an inhibitor does not by itself establish receptor-specific causality.", "layers": [ { "id": "assay-discrimination", "name": "Assay discrimination", "description": "Assess whether the measurement identifies the intended receptor form.", "findings": [ { "id": "reagent-specificity", "name": "Detection specificity", "description": "Tie detection claims to reagent validation, epitope coverage and controls for related receptors.", "questions": [ { "text": "Which validation demonstrates that the antibody, probe or peptide measurement discriminates IGF1R from INSR?", "kind": "provenance", "id": "reagent-specificity-q01" }, { "text": "Which orthogonal measurement is needed if the assay cannot resolve receptor identity or assembly?", "kind": "action", "id": "reagent-specificity-q02" } ] } ] }, { "id": "perturbation-causality", "name": "Perturbation and causality", "description": "Match interventions to the receptor property under investigation.", "findings": [ { "id": "intervention-interpretability", "name": "Intervention interpretability", "description": "Record whether a perturbation changes receptor abundance, ligand access or catalytic activity and how specifically it does so.", "questions": [ { "text": "Does the intervention alter IGF1R abundance, binding or kinase activity, and what exposure was tested?", "kind": "action", "id": "intervention-interpretability-q01" }, { "text": "Which selectivity, target-engagement and rescue controls support attributing the observed response to IGF1R?", "kind": "provenance", "id": "intervention-interpretability-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": [ "With no recorded sense, this entry interprets IGF1R as the receptor protein; the same symbol also denotes its gene.", "Identifiers and precursor length refer to humans; other species have their own records.", "This is recalled knowledge, not a source-verified account; therapeutic indications and variant-specific effects require checking." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of IGF1R 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": "IGF1R", "note": "Approved symbol for the human gene encoding the receptor." }, { "scheme": "NCBI Gene", "value_or_pattern": "3480", "note": "Human IGF1R gene." }, { "scheme": "UniProtKB accession", "value_or_pattern": "P08069", "note": "Human insulin-like growth factor 1 receptor protein." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of IGF1R 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 on growth-factor signalling, including PI3K-AKT and RAS-MAPK pathways.", "Investigation of genetic causes of impaired prenatal and postnatal growth.", "Target for therapeutic antibodies and small-molecule inhibitors.", "Investigation of tumour-cell survival and resistance to anticancer therapies." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of IGF1R 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": "Canonical human protein precursor length", "typical_range": "1367", "unit": "amino acid residues" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of IGF1R 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": [ "Reduced receptor function or gene dosage can impair prenatal and postnatal growth.", "Excessive or dysregulated signalling can support tumour-cell proliferation and survival.", "Therapeutic inhibition can disturb glucose regulation and cause hyperglycaemia." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of IGF1R 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": "IGF1", "difference": "IGF1 encodes a secreted ligand; IGF1R encodes the membrane receptor that receives its signal." }, { "name": "IGF2R", "difference": "IGF2R is the cation-independent mannose-6-phosphate receptor involved in protein trafficking and IGF-2 clearance; it is not a receptor tyrosine kinase." }, { "name": "INSR", "difference": "The insulin receptor is encoded by a separate gene and primarily mediates insulin responses; it can form hybrid receptors with IGF1R." }, { "name": "IGF1R gene", "difference": "The gene is a DNA locus; the physical receptor described here is its protein product." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of IGF1R this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does vr.tr.igf1r denote the human gene, the human receptor protein or a species-general receptor concept?", "Does an existing Vercy world model already own this concept and require this registry entry to link to it?", "Which reference sequences, variants and experimental constructs should receive explicit distinctions within this entry?", "Which validated methods can distinguish IGF1R-only receptors, INSR and hybrids in the intended sample types?", "Which context-specific evidence and thresholds are sufficient to call IGF1R active, inhibited or depleted?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 16, "questions": 26 } }