{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:29:04Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 24.3, "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: 01a094ba-bb84-72d1-ac53-8f61633d793e\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: caveolins\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001 regis", "usd": 0.0, "recall": true }, "codex": { "seconds": 84.6, "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: 01a094ba-bb94-7240-bc07-ce92196907d1\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: caveolins\nRegistry id: vr.tr.caveolins\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nCont" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:41:57+00:00", "fields": [ "agent_conduct", "ethics", "owners" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:29+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q24724230", "registryId": "vr.tr.caveolins", "name": "caveolins", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q24724230/", "model": { "registry_id": "vr.tr.caveolins", "name": "caveolins", "purpose": "Enable an agent to identify caveolin proteins, assess their molecular and cellular state, and select justified measurements or perturbations of their membrane-associated functions.", "definition": "Caveolins are a family of small, oligomer-forming integral membrane proteins that participate in caveola formation and membrane lipid organization, with distinct family members differing in tissue distribution and function.", "scope_statement": "This model owns vr.tr.caveolins as a protein-family entry within PHY / PHY.MAT, recording member-specific identity, molecular forms, membrane assembly, cellular context and experimentally supported functions while keeping genes, caveolae and diseases as related entities.", "in_scope": [ "Caveolin family membership, organism, paralog, isoform and sequence identity", "Native and engineered caveolin proteoforms, modifications and preparation quality", "Membrane association, oligomer composition and assembly state", "Cellular abundance, localization, trafficking and turnover", "Context-dependent interactions, functional evidence and responses to perturbation" ], "out_of_scope": [ "CAV gene loci and transcriptional regulation as independently modeled genetic entities", "Caveolae as complete membrane structures with their own morphology and dynamics", "Cavin proteins, other membrane scaffolds and lipid constituents as independent entities", "Whole-cell signaling networks and endocytic pathways beyond demonstrated caveolin contributions", "Disease diagnosis, patient management and therapeutic products", "Commercial antibodies, expression vectors and assay kits as products" ], "distinguishing_features": [ "Require sequence-supported caveolin family membership; caveolar localization alone does not establish protein identity.", "Resolve caveolin-1, caveolin-2 and caveolin-3 separately when applicable, recording organism and isoform instead of treating a family-level label as an exact molecular identity.", "Distinguish caveolin proteins from cavin coat proteins through sequence identity and family annotation, even when both occur in the same membrane structure.", "Distinguish a caveolin molecule or oligomer from a caveola: detecting the protein does not establish a complete membrane invagination.", "Use membrane topology and assembly evidence as supporting identifiers; the human caveolin-1 8S structure is a member-specific reference, not a universal structure for every caveolin. Reference: [RCSB PDB 7SC0](https://www.rcsb.org/structure/7SC0)." ], "characteristics": [ { "name": "Family member and biological origin", "kind": "category", "unit_or_values": "Organism and taxonomy identifier; caveolin member; sequence accession and version; isoform", "why_it_matters": "Prevents transfer of identity and functional claims across paralogs, species or isoforms." }, { "name": "Sequence and construct identity", "kind": "state", "unit_or_values": "Full-length or fragment; residue boundaries; substitutions; tags; reference sequence", "why_it_matters": "Truncations, variants and tags may alter membrane association or oligomerization." }, { "name": "Molecular mass", "kind": "measurement", "unit_or_values": "Da or kDa; calculated, intact-mass measured or electrophoretically apparent", "why_it_matters": "Supports identity checks while distinguishing sequence-derived mass from assay-dependent migration." }, { "name": "Modification state", "kind": "state", "unit_or_values": "Modification type, residue, occupancy percentage if measured, and unknown status", "why_it_matters": "Allows modification-dependent behavior to be assessed without assuming every family member shares the same sites." }, { "name": "Membrane topology and environment", "kind": "relation", "unit_or_values": "Membrane compartment, lipid composition, insertion model and supporting method", "why_it_matters": "Connects caveolin structure and behavior to the membrane or experimental mimic in which they were observed." }, { "name": "Oligomeric state", "kind": "measurement", "unit_or_values": "Subunits per complex; member composition; sedimentation coefficient in S when measured", "why_it_matters": "Separates measured assembly properties from labels inferred from migration or fractionation." }, { "name": "Cellular abundance and distribution", "kind": "measurement", "unit_or_values": "Molecules per cell, calibrated concentration or normalized assay signal; fraction per compartment", "why_it_matters": "Distinguishes changes in protein quantity from redistribution between cellular locations." }, { "name": "Caveolar association", "kind": "state", "unit_or_values": "Demonstrated caveolar association; non-caveolar pool; mixed; unresolved", "why_it_matters": "Prevents caveolin positivity from being used as sufficient evidence of caveola formation." }, { "name": "Partner relationship", "kind": "relation", "unit_or_values": "Partner identity; direct binding, co-complex association, colocalization or functional dependence", "why_it_matters": "Keeps different strengths and types of interaction evidence distinct." }, { "name": "Preparation integrity", "kind": "state", "unit_or_values": "Purity percentage with method; detergent or lipid carrier; aggregation and degradation status", "why_it_matters": "Determines whether an isolated preparation can support conclusions about caveolin behavior." } ], "affordances": [ "Resolve a caveolin label to a documented member, organism, sequence and molecular form.", "Compare caveolin abundance, localization and assembly across matched cellular conditions.", "Assess whether a preparation or structural model represents the caveolin state relevant to an intended experiment.", "Select member-specific detection and assembly assays with appropriate identity controls.", "Design and interpret caveolin perturbation and rescue comparisons while recording effects on partner proteins and caveolae.", "Flag claims that extend beyond the tested paralog, construct, membrane environment or evidence type." ], "agent_conduct": { "may": [ "Describe the caveolin family and their roles in cell membranes, citing biology sources.", "Distinguish the family members and the tissues they occur in." ], "must_not": [ "Present preliminary links between caveolins and diseases as established.", "Give medical advice based on caveolin research.", "Invent experimental results or citations.", "Mix up caveolins with cavins or other related proteins." ], "requires_human": [ "Using research findings in clinical decisions." ] }, "ethics": { "considerations": [ "Overstating early research raises false hopes for patients.", "Correct credit matters in science." ], "affected_parties": [ "Patients with related rare disorders", "Researchers" ] }, "owners": { "steward": "Nobody owns the proteins; protein databases keep authoritative records.", "master_systems": [ "Protein sequence databases" ] }, "what_it_is_for": [ "Caveolins are studied in cell biology to understand caveolae, membrane lipid organization and membrane-associated signalling.", "Their family members are characterized in tissue samples, cultured cells and protein preparations to relate molecular identity to cellular function." ], "standards_and_regulation": [ "The InterPro protein family classification, maintained by the European Bioinformatics Institute of the European Molecular Biology Laboratory with its partner databases, applies to caveolin family annotation." ], "failure_modes_and_hazards": [ "Confusing caveolin family members can lead to incorrect conclusions about tissue distribution or cellular function.", "Protein aggregation or loss of membrane context can make experimental measurements unrepresentative of the native state.", "Poorly specific detection reagents can produce misleading localization or abundance results." ], "facets_not_applicable": { "recognition": "Caveolin identity has no directly visible distinguishing appearance and requires molecular characterization." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q24724230: caveolins", "url": "https://www.wikidata.org/wiki/Q24724230", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Caveolin", "url": "https://en.wikipedia.org/wiki/Caveolin", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "family-and-proteoform-identity", "name": "Family and proteoform identity", "description": "Resolve what the caveolin label denotes at family, member and molecular-form levels.", "rationale": "A family-level registry entry must preserve biologically consequential differences without creating separate registry things.", "layers": [ { "id": "member-resolution", "name": "Member resolution", "description": "Establish the organism and sequence-supported identity of the caveolin being described.", "findings": [ { "id": "sequence-anchored-membership", "name": "Sequence-anchored membership", "description": "Require an accession or explicit sequence to support an exact caveolin identity.", "questions": [ { "text": "Which organism, caveolin member and isoform does this observation concern?", "kind": "definition", "id": "sequence-anchored-membership-q01" }, { "text": "Which sequence record and evidence establish caveolin family membership?", "kind": "provenance", "id": "sequence-anchored-membership-q02" } ] } ] }, { "id": "molecular-form-resolution", "name": "Molecular form resolution", "description": "Capture differences between endogenous proteins and the molecular forms actually tested.", "findings": [ { "id": "construct-and-modification-state", "name": "Construct and modification state", "description": "Record sequence alterations, tags and measured modifications with member-specific residue numbering.", "questions": [ { "text": "Is the tested caveolin endogenous, recombinant, tagged, truncated or sequence-altered?", "kind": "definition", "id": "construct-and-modification-state-q01" }, { "text": "Which modifications and occupancies were measured, and which remain uncharacterized?", "kind": "measurement", "id": "construct-and-modification-state-q02" }, { "text": "Which conclusions require confirmation using the corresponding native proteoform?", "kind": "boundary", "id": "construct-and-modification-state-q03" } ] } ] } ] }, { "id": "membrane-structure-and-assembly", "name": "Membrane structure and assembly", "description": "Describe caveolin insertion, membrane environment and oligomer organization.", "rationale": "Membrane-associated assembly is central to caveolin interpretation, but structural results depend on member and experimental context.", "layers": [ { "id": "membrane-insertion", "name": "Membrane insertion", "description": "Connect topology observations to the membrane system examined.", "findings": [ { "id": "topology-in-context", "name": "Topology in context", "description": "Record experimentally supported topology rather than treating a hydrophobic sequence segment as sufficient proof of insertion geometry.", "questions": [ { "text": "What evidence establishes the membrane-facing regions and accessibility of the caveolin termini?", "kind": "measurement", "id": "topology-in-context-q01" }, { "text": "Was topology assessed in a native membrane, reconstituted bilayer or detergent preparation?", "kind": "provenance", "id": "topology-in-context-q02" } ] } ] }, { "id": "oligomer-architecture", "name": "Oligomer architecture", "description": "Resolve subunit composition and assembly state without conflating oligomers with complete caveolae.", "findings": [ { "id": "member-specific-assembly", "name": "Member-specific assembly", "description": "Use the human caveolin-1 8S complex as a bounded structural reference for evaluating assembly claims. Reference: [RCSB PDB 7SC0](https://www.rcsb.org/structure/7SC0).", "questions": [ { "text": "What subunit number and caveolin-member composition are directly supported for this complex?", "kind": "measurement", "id": "member-specific-assembly-q01" }, { "text": "How were discrete oligomers distinguished from aggregates or detergent-associated particles?", "kind": "measurement", "id": "member-specific-assembly-q02" }, { "text": "What evidence permits extending this assembly model to another member or membrane environment?", "kind": "boundary", "id": "member-specific-assembly-q03" } ] } ] } ] }, { "id": "cellular-location-and-lifecycle", "name": "Cellular location and lifecycle", "description": "Track caveolin abundance, compartment occupancy and movement through cellular states.", "rationale": "The same caveolin identity can occur in different pools whose localization and persistence affect interpretation.", "layers": [ { "id": "cellular-pools", "name": "Cellular pools", "description": "Place caveolin observations in a specified cell type and membrane compartment.", "findings": [ { "id": "abundance-versus-localization", "name": "Abundance versus localization", "description": "Separate total protein abundance from the distribution of caveolin among caveolar and other cellular pools.", "questions": [ { "text": "Which cell type, tissue and physiological or experimental condition define this caveolin pool?", "kind": "provenance", "id": "abundance-versus-localization-q01" }, { "text": "What proportion occupies each measured compartment, and how was that proportion determined?", "kind": "measurement", "id": "abundance-versus-localization-q02" }, { "text": "What evidence distinguishes caveolar localization from other plasma-membrane localization?", "kind": "boundary", "id": "abundance-versus-localization-q03" } ] } ] }, { "id": "trafficking-and-turnover", "name": "Trafficking and turnover", "description": "Describe time-dependent delivery, retention, redistribution and loss of caveolin.", "findings": [ { "id": "pool-transition-evidence", "name": "Pool transition evidence", "description": "Require temporal evidence to distinguish trafficking or degradation from changes in synthesis or detection.", "questions": [ { "text": "Which caveolin movements or turnover rates were measured over what interval?", "kind": "measurement", "id": "pool-transition-evidence-q01" }, { "text": "How does the experiment distinguish redistribution from altered synthesis, degradation or epitope accessibility?", "kind": "boundary", "id": "pool-transition-evidence-q02" } ] } ] } ] }, { "id": "partners-and-functional-contribution", "name": "Partners and functional contribution", "description": "Evaluate caveolin interactions and contributions to caveolar or other cellular behavior.", "rationale": "Caveolin association, structural participation and causal effects require different evidence and cannot be treated as interchangeable.", "layers": [ { "id": "assembly-dependencies", "name": "Assembly dependencies", "description": "Record member-specific dependence on other caveolins, cavins and membrane constituents.", "findings": [ { "id": "partner-dependent-behavior", "name": "Partner-dependent behavior", "description": "Preserve distinct member roles; human caveolin-2 is annotated as acting with caveolin-1 in caveolar targeting and formation. Reference: [UniProt CAV2](https://www.uniprot.org/uniprotkb/P51636/entry).", "questions": [ { "text": "Which caveolin members, cavins and lipid conditions accompany the observed assembly?", "kind": "measurement", "id": "partner-dependent-behavior-q01" }, { "text": "Which partners are required under the tested conditions, and what depletion or reconstitution evidence supports that requirement?", "kind": "provenance", "id": "partner-dependent-behavior-q02" } ] } ] }, { "id": "interaction-and-causality", "name": "Interaction and causality", "description": "Assess proposed signaling, transport or mechanical contributions at the level supported by experiments.", "findings": [ { "id": "bounded-functional-claim", "name": "Bounded functional claim", "description": "Separate direct binding, shared localization and causal functional effects, including effects mediated by changes in caveolae.", "questions": [ { "text": "Does the evidence demonstrate direct binding, co-complex association, colocalization or a downstream response?", "kind": "boundary", "id": "bounded-functional-claim-q01" }, { "text": "Which measured endpoint changes after caveolin perturbation and returns after a suitable rescue?", "kind": "measurement", "id": "bounded-functional-claim-q02" }, { "text": "Can the effect be assigned to caveolin itself or only to the altered caveolar system?", "kind": "boundary", "id": "bounded-functional-claim-q03" } ] } ] } ] }, { "id": "experimental-fitness-and-intervention", "name": "Experimental fitness and intervention", "description": "Determine whether caveolin reagents, preparations and perturbations support the intended inference.", "rationale": "Member cross-reactivity, extraction effects and engineered expression can change what a caveolin experiment actually measures.", "layers": [ { "id": "detection-and-preparation", "name": "Detection and preparation", "description": "Validate protein detection and preserve relevant caveolin states during preparation.", "findings": [ { "id": "assay-specific-identity-and-integrity", "name": "Assay-specific identity and integrity", "description": "Connect detection specificity and preparation quality to the exact caveolin member and assembly under study.", "questions": [ { "text": "What controls establish that the antibody or peptide readout distinguishes the intended caveolin member and isoform?", "kind": "measurement", "id": "assay-specific-identity-and-integrity-q01" }, { "text": "Which extraction, detergent, lipid and storage conditions could alter the assembly or localization being inferred?", "kind": "provenance", "id": "assay-specific-identity-and-integrity-q02" }, { "text": "What integrity and aggregation checks are needed before using this preparation for structural or functional work?", "kind": "action", "id": "assay-specific-identity-and-integrity-q03" } ] } ] }, { "id": "perturbation-and-rescue", "name": "Perturbation and rescue", "description": "Make interventions interpretable against member identity, expression level and partner dependence.", "findings": [ { "id": "interpretable-caveolin-intervention", "name": "Interpretable caveolin intervention", "description": "Specify a caveolin perturbation together with controls for expression, localization, assembly and effects on associated proteins.", "questions": [ { "text": "Which member-specific depletion, variant or expression change addresses the proposed mechanism?", "kind": "action", "id": "interpretable-caveolin-intervention-q01" }, { "text": "Does the rescue restore an appropriate expression level, localization and assembly state?", "kind": "measurement", "id": "interpretable-caveolin-intervention-q02" }, { "text": "Which partner changes or broader membrane effects limit attribution of the outcome to the targeted caveolin?", "kind": "boundary", "id": "interpretable-caveolin-intervention-q03" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "This describes the protein family, with the three human and mammalian members as its principal examples; it is not a single chemically uniform substance.", "Molecular mass depends on family member, isoform and modification; apparent electrophoretic mass may differ from sequence-derived mass.", "Caveolin-2 should not be assumed to form caveolae independently; signaling and disease claims require member-, tissue- and variant-specific checking." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of caveolins this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Caveolin-1", "Caveolin-2", "Caveolin-3" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of caveolins 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 symbols", "value_or_pattern": "CAV1, CAV2, CAV3", "note": "Approved symbols for the three human genes encoding caveolins; these identify genes rather than individual protein isoforms." }, { "scheme": "UniProtKB accession", "value_or_pattern": "Protein accessions distinguish species and family members; isoforms may carry accession suffixes.", "note": "Caveolins are a protein family, so no single accession identifies the entire registered thing." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of caveolins 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": [ "Caveolin detection helps characterize caveola-associated membrane organization in cell biology research.", "Caveolin manipulation is used to investigate cholesterol handling, membrane mechanics and cellular signaling.", "Caveolin-3 analysis is used in research and diagnostic investigation of inherited muscle disorders." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of caveolins 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": "Approximate molecular mass of an individual caveolin polypeptide", "typical_range": "18-24", "unit": "kDa" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of caveolins 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 dysfunction of caveolin-1 or caveolin-3 can disrupt caveola formation in relevant tissues.", "Pathogenic CAV3 variants can cause inherited muscle disorders.", "Some pathogenic CAV1 variants are associated with lipodystrophy or pulmonary arterial hypertension.", "Experimental overexpression, tagging or detergent extraction can alter caveolin localization or assembly and complicate interpretation." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of caveolins 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": "Caveolae", "difference": "Caveolae are membrane invaginations; caveolins are proteins that contribute to their formation." }, { "name": "Cavins", "difference": "Cavins are a distinct family of peripheral membrane coat proteins that cooperate with caveolins in caveola organization." }, { "name": "Lipid rafts", "difference": "Lipid rafts are membrane domains defined by lipid and protein organization; caveolins are specific proteins, and many raft-associated domains lack caveolins." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of caveolins this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which taxonomic coverage and sequence resources should define caveolin family membership beyond the commonly studied mammalian members?", "Which structural and oligomerization observations generalize across caveolin members, and which depend on recombinant constructs or membrane mimics?", "What minimum evidence should qualify a caveolin pool as caveolar rather than merely membrane-associated?", "Which proposed signaling interactions remain supported by direct binding and controlled causal experiments at appropriate expression levels?", "Which member-specific modifications and preparation conditions materially change assembly or function, and what acceptance criteria can research justify?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 17, "questions": 33 } }