{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:44:14Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 24.2, "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: 01a094c8-ac4d-7e43-a48d-18991ee28e31\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: claudins\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 regist", "usd": 0.0, "recall": true }, "codex": { "seconds": 80.6, "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: 01a094c8-ac5d-7151-a0f3-396adee56f39\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: claudins\nRegistry id: vr.tr.claudins\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContex" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:45:59+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:30+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q420863", "registryId": "vr.tr.claudins", "name": "claudins", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q420863/", "model": { "registry_id": "vr.tr.claudins", "name": "claudins", "purpose": "Enable an agent to identify claudin family members, assess their membrane and barrier states in a specified biological context, and judge which measurements or interventions are supported by evidence.", "definition": "Claudins are a family of small, four-pass transmembrane proteins that assemble into tight-junction strands and help determine the permeability and ion selectivity of the paracellular pathway between epithelial or endothelial cells.", "scope_statement": "This model owns claudins as a family of membrane proteins, including member identity, molecular forms, junctional organisation, context-dependent permeability functions and evidence for their detection or perturbation; it does not treat the family as one chemically uniform substance.", "in_scope": [ "Claudin family membership, species, paralogues and molecular forms", "Membrane topology, extracellular regions and intracellular interaction features", "Cellular localisation, junctional assembly and compatibility between claudin members", "Context-dependent paracellular barrier and selective permeability functions", "Expression, trafficking, turnover and experimentally supported perturbations", "Claudin-specific reagents, preparations and measurement limitations" ], "out_of_scope": [ "Complete tight-junction composition and tissue architecture", "Whole-organ physiology and organism-level homeostasis", "Other junctional protein families such as occludin and junctional adhesion molecules", "Diseases, diagnoses and treatment protocols associated with claudin changes", "Antibodies, drugs, toxins and delivery platforms as independently modelled products", "Gene regulatory networks beyond their directly evidenced effects on claudins" ], "distinguishing_features": [ "Family assignment requires sequence or curated protein-family evidence; localisation at a tight junction alone does not establish that a protein is a claudin.", "The characteristic four-pass membrane architecture supports recognition, but topology alone does not distinguish claudins from unrelated membrane proteins.", "A claudin name must resolve to a species and family member; different members cannot be treated as interchangeable forms of one substance.", "Detection of claudin RNA or total protein does not establish incorporation into a functional junction.", "A permeability effect must specify the member, transported species and biological context; claudin presence alone does not imply a uniformly tighter barrier." ], "characteristics": [ { "name": "Family-member identity", "kind": "category", "unit_or_values": "Species, accepted protein name, gene symbol and versioned sequence accession", "why_it_matters": "Prevents conflating paralogues, orthologues and historically ambiguous names." }, { "name": "Molecular form", "kind": "category", "unit_or_values": "Sequence variant, isoform, truncation, fusion tag and modification state", "why_it_matters": "A construct or modified protein may differ from the endogenous form in localisation and function." }, { "name": "Membrane topology", "kind": "category", "unit_or_values": "Transmembrane-segment assignments, extracellular regions and cytoplasmic termini, with evidence status", "why_it_matters": "Supports interpretation of assembly interfaces, accessible epitopes and intracellular interactions." }, { "name": "Cellular distribution", "kind": "state", "unit_or_values": "Junctional, nonjunctional plasma membrane, intracellular, mixed or unresolved", "why_it_matters": "Distinguishes protein abundance from placement where a proposed function can occur." }, { "name": "Protein abundance", "kind": "measurement", "unit_or_values": "Molecules per cell, amount per sample or explicitly normalised assay units", "why_it_matters": "Supports comparison only when the sampled compartment and measurement method are known." }, { "name": "Assembly and partner compatibility", "kind": "relation", "unit_or_values": "Named claudin or scaffold partner, same-membrane or opposing-membrane relationship, and evidence", "why_it_matters": "Coexpression does not establish physical compatibility or functional assembly." }, { "name": "Paracellular permeability", "kind": "measurement", "unit_or_values": "Permeability coefficient in cm/s, permeability ratios or tracer flux with explicit units and assay conditions", "why_it_matters": "Identifies which ions or solutes cross and whether selectivity changes." }, { "name": "Transepithelial electrical resistance", "kind": "measurement", "unit_or_values": "Ω·cm², with blank correction, tissue or culture geometry and measurement conditions", "why_it_matters": "Provides a barrier readout whose attribution to a particular claudin requires additional evidence." }, { "name": "Perturbation response", "kind": "relation", "unit_or_values": "Specified genetic, biochemical or binding intervention linked to localisation, abundance or functional outcomes", "why_it_matters": "Separates observed responses from assumptions about causality or therapeutic usefulness." } ], "affordances": [ "Resolve a claudin label to a species-specific protein member and distinguish endogenous proteins from experimental constructs.", "Assess whether available measurements establish expression, junctional localisation, assembly or permeability function.", "Compare claudin states across matched tissues or experimental systems while retaining assay conditions.", "Select member-specific detection approaches and identify required specificity controls.", "Formulate testable perturbations of claudin expression, localisation or interactions with appropriate functional readouts.", "Identify where evidence supports a member-specific conclusion and where extrapolation across the family remains unresolved." ], "agent_conduct": { "may": [ "Describe claudins and their role in tight junctions from cell biology sources.", "Summarize published research on claudins, citing the studies." ], "must_not": [ "Overstate preliminary research on claudin-targeted therapies as proven treatments.", "Misreport experimental findings or attribute them to the wrong authors.", "Present gene variant findings as a diagnosis for a person.", "Use patient data from studies beyond the consent given." ], "requires_human": [ "Endorsing a claudin-targeted therapy for a patient." ] }, "ethics": { "considerations": [ "Patients with cancers that express claudins may hope for new treatments; honest reporting avoids false hope.", "Research credit matters to scientists." ], "affected_parties": [ "Patients", "Researchers" ] }, "owners": { "steward": "Nobody owns the protein family; it belongs to the scientific commons.", "master_systems": [] }, "failure_modes_and_hazards": [ "Inherited claudin defects can cause kidney, hearing or skin disorders." ], "what_it_is_for": [ "Claudins occur at tight junctions in epithelial and endothelial tissues, where their composition helps regulate movement between neighboring cells.", "They are studied in cell biology and biomedical research to investigate tissue barriers, selective ion transport and changes associated with disease." ], "standards_and_regulation": [ "The HUGO Gene Nomenclature Committee provides approved symbols and names for human claudin genes, supporting consistent identification of their encoded proteins." ], "facets_not_applicable": { "recognition": "Claudins have no directly visible identifying appearance, and their identification requires molecular evidence rather than visual cues alone." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q420863: claudins", "url": "https://www.wikidata.org/wiki/Q420863", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Claudin", "url": "https://en.wikipedia.org/wiki/Claudin", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "family-member-and-molecular-identity", "name": "Family member and molecular identity", "description": "Resolve what counts as a claudin and which biological or experimental form is being considered.", "rationale": "The registry entry denotes a protein family rather than a single molecule with one composition or chemical identifier.", "layers": [ { "id": "family-membership-and-naming", "name": "Family membership and naming", "description": "Separate family-level identity from member- and species-level assignments.", "findings": [ { "id": "member-assignment", "name": "Member assignment", "description": "Record the evidence needed to assign a protein to the claudin family and resolve its name.", "questions": [ { "text": "Which curated accession, species and sequence support the proposed claudin member assignment?", "kind": "provenance", "id": "member-assignment-q01" }, { "text": "Does the supplied name identify the whole family, one paralogue, an orthologue group or an unresolved historical label?", "kind": "definition", "id": "member-assignment-q02" } ] } ] }, { "id": "sequence-and-preparation", "name": "Sequence and preparation", "description": "Distinguish endogenous molecular forms from constructs and isolated preparations.", "findings": [ { "id": "form-specific-identity", "name": "Form-specific identity", "description": "Establish which sequence and preparation features constrain interpretation.", "questions": [ { "text": "Which isoform, substitutions, tags, truncations or post-translational modifications distinguish this form from the reference sequence?", "kind": "definition", "id": "form-specific-identity-q01" }, { "text": "For an isolated preparation, what evidence establishes identity, purity and the detergent, lipid or membrane environment?", "kind": "measurement", "id": "form-specific-identity-q02" } ] } ] } ] }, { "id": "membrane-architecture-and-junctional-assembly", "name": "Membrane architecture and junctional assembly", "description": "Represent claudin topology, interaction surfaces and incorporation into junctional structures.", "rationale": "Claudin behaviour depends on membrane placement and assembly, which cannot be inferred from a protein name or expression value.", "layers": [ { "id": "topology-and-accessible-regions", "name": "Topology and accessible regions", "description": "Locate regions relevant to extracellular recognition and intracellular interactions.", "findings": [ { "id": "structural-region-assignment", "name": "Structural region assignment", "description": "Distinguish experimentally established structure from sequence-based topology predictions.", "questions": [ { "text": "Which transmembrane, extracellular and cytoplasmic regions are established for this member, and by what method?", "kind": "provenance", "id": "structural-region-assignment-q01" }, { "text": "Which proposed binding epitopes or interaction motifs are accessible in the membrane state under consideration?", "kind": "boundary", "id": "structural-region-assignment-q02" } ] } ] }, { "id": "claudin-assembly-and-scaffold-coupling", "name": "Claudin assembly and scaffold coupling", "description": "Assess interactions within one membrane, across adjacent cells and with junctional scaffolds.", "findings": [ { "id": "assembly-compatibility", "name": "Assembly compatibility", "description": "Require direct evidence for partner compatibility and functional junctional incorporation.", "questions": [ { "text": "Which same-membrane and opposing-membrane claudin interactions are demonstrated rather than inferred from coexpression?", "kind": "provenance", "id": "assembly-compatibility-q01" }, { "text": "What imaging, interaction or structural evidence establishes junctional assembly and scaffold association for this molecular form?", "kind": "measurement", "id": "assembly-compatibility-q02" } ] } ] } ] }, { "id": "paracellular-barrier-and-selectivity", "name": "Paracellular barrier and selectivity", "description": "Characterise claudin-associated permeability using explicit transported species and experimental conditions.", "rationale": "Barrier effects differ by member and context, and electrical resistance alone cannot specify the permeability mechanism.", "layers": [ { "id": "ion-and-solute-permeation", "name": "Ion and solute permeation", "description": "Distinguish ion selectivity, molecular passage and broader barrier disruption.", "findings": [ { "id": "permeation-profile", "name": "Permeation profile", "description": "Frame permeability as a measured profile rather than a binary barrier label.", "questions": [ { "text": "Which ions or solutes were tested, and what permeability coefficients, selectivity ratios or fluxes were measured?", "kind": "measurement", "id": "permeation-profile-q01" }, { "text": "Under which ionic gradients, pH, temperature and epithelial or endothelial conditions does the reported profile hold?", "kind": "boundary", "id": "permeation-profile-q02" } ] } ] }, { "id": "functional-attribution", "name": "Functional attribution", "description": "Assess whether a barrier phenotype can be assigned to a particular claudin.", "findings": [ { "id": "member-specific-barrier-contribution", "name": "Member-specific barrier contribution", "description": "Separate claudin-dependent effects from changes in cell viability, junction integrity or other transport routes.", "questions": [ { "text": "Which matched controls, loss-of-function comparisons or rescue experiments support attribution to this claudin?", "kind": "provenance", "id": "member-specific-barrier-contribution-q01" }, { "text": "Do resistance, tracer and ion-selectivity measurements distinguish selective permeation from nonspecific leakage or transcellular transport?", "kind": "measurement", "id": "member-specific-barrier-contribution-q02" } ] } ] } ] }, { "id": "biological-context-and-state-transitions", "name": "Biological context and state transitions", "description": "Track where claudins occur and how their abundance, localisation and molecular state change.", "rationale": "The same family member may occupy different compartments and contribute differently across cell types and conditions.", "layers": [ { "id": "tissue-expression-and-localisation", "name": "Tissue expression and localisation", "description": "Anchor observations to species, tissue, cell type and cellular compartment.", "findings": [ { "id": "context-resolved-presence", "name": "Context-resolved presence", "description": "Keep transcript detection, protein abundance and junctional localisation distinct.", "questions": [ { "text": "In which species, tissue, cell type and developmental or experimental state was this claudin detected?", "kind": "boundary", "id": "context-resolved-presence-q01" }, { "text": "Does the evidence measure RNA, total protein, surface protein or junctional protein, and at what resolution?", "kind": "measurement", "id": "context-resolved-presence-q02" } ] } ] }, { "id": "trafficking-modification-and-turnover", "name": "Trafficking, modification and turnover", "description": "Capture transitions affecting delivery to, retention at and removal from junctions.", "findings": [ { "id": "state-change-mechanisms", "name": "State-change mechanisms", "description": "Connect observed claudin transitions to evidenced triggers and downstream readouts.", "questions": [ { "text": "Which stimulus or modification is associated with altered claudin trafficking, junctional retention or degradation?", "kind": "provenance", "id": "state-change-mechanisms-q01" }, { "text": "What time course and reversibility measurements connect the molecular transition to a change in localisation or permeability?", "kind": "measurement", "id": "state-change-mechanisms-q02" } ] } ] } ] }, { "id": "detection-and-perturbation-evidence", "name": "Detection and perturbation evidence", "description": "Judge the specificity of claudin measurements and the interpretability of interventions.", "rationale": "Related family members, shared epitopes and indirect junctional effects can produce misleading assignments of identity or function.", "layers": [ { "id": "member-specific-detection", "name": "Member-specific detection", "description": "Evaluate whether reagents and assays distinguish the intended claudin and molecular form.", "findings": [ { "id": "assay-specificity", "name": "Assay specificity", "description": "Require validation appropriate to the member, species, specimen and assay format.", "questions": [ { "text": "What knockout, orthogonal assay or cross-reactivity evidence validates detection of the intended claudin?", "kind": "provenance", "id": "assay-specificity-q01" }, { "text": "Could fixation, permeabilisation, tagging or epitope masking change the apparent abundance or localisation?", "kind": "boundary", "id": "assay-specificity-q02" } ] } ] }, { "id": "targeted-functional-perturbation", "name": "Targeted functional perturbation", "description": "Assess genetic and binding interventions against specific claudin-dependent outcomes.", "findings": [ { "id": "interpretable-intervention", "name": "Interpretable intervention", "description": "Define the intended target state, measurable outcome and controls needed for a supported action.", "questions": [ { "text": "Which genetic alteration or binding reagent can test the proposed claudin function in this system, and what establishes target engagement?", "kind": "action", "id": "interpretable-intervention-q01" }, { "text": "Which controls distinguish direct claudin effects from compensatory family-member expression, cytotoxicity or general junction disruption?", "kind": "measurement", "id": "interpretable-intervention-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": [ "This is a protein family, not a single chemical substance with one formula, purity specification or set of physical constants.", "Barrier-forming and pore-forming behavior depends on the family member, tissue and interacting proteins; it should not be generalized across all claudins.", "The molecular-mass range is approximate; exact sequences, isoforms, identifiers and disease associations require member-specific verification." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of claudins 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": [ "Claudin-1", "Claudin-2", "Claudin-4", "Claudin-5", "Claudin-16", "Claudin-19" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of claudins 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": "CLDN followed by a number, such as CLDN1 or CLDN5", "note": "Names individual human genes; gene symbols are not identifiers for the entire protein family." }, { "scheme": "UniProtKB accession", "value_or_pattern": "An accession for a particular organism's claudin protein", "note": "Protein identity requires the family member, organism and, where relevant, isoform." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of claudins 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": [ "Experimental analysis of epithelial and endothelial barrier function.", "Immunostaining to examine tight-junction composition and localization.", "Investigation of selective paracellular ion transport.", "Research into inherited disorders associated with particular claudin genes.", "Biomarker and therapeutic-target research in cancers expressing particular claudins." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of claudins 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": "Protein molecular mass", "typical_range": "Approximately 20-30", "unit": "kDa" }, { "quantity": "Transmembrane helices per protein", "typical_range": "4", "unit": "helices" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of claudins 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, mislocalization or altered expression of particular claudins can disrupt tissue barriers.", "Changes in claudin composition can alter paracellular ion selectivity without simply opening or closing the barrier.", "Pathogenic variants in particular claudin genes can cause inherited disorders, including renal electrolyte-handling defects or hearing impairment.", "Certain claudins serve as receptors for Clostridium perfringens enterotoxin.", "Antibody cross-reactivity and failure to distinguish isoforms can produce misleading experimental results." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of claudins 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": "Occludin", "difference": "A distinct tight-junction transmembrane protein, rather than a member of the claudin family." }, { "name": "Tight junction", "difference": "The multicompartment cellular junction assembled from claudins and other proteins, rather than a protein family." }, { "name": "Connexins", "difference": "Form gap-junction channels connecting cell interiors; claudins regulate passage between adjacent cells." }, { "name": "Cadherins", "difference": "Primarily mediate calcium-dependent cell adhesion rather than forming claudin-based paracellular barriers and pores." }, { "name": "CLDN genes", "difference": "DNA sequences encoding claudin proteins, rather than the proteins themselves." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of claudins this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry intend claudins across all relevant taxa, and which curated authority should define family membership and naming?", "Which member-specific assembly compatibilities and permeability profiles have sufficient direct evidence to support reusable claims?", "Which reported nonjunctional roles belong within this family model, and which require separate neighbouring models?", "Which assays and reference conditions permit meaningful comparison of claudin function across tissues, culture systems and reconstituted membranes?", "Which detection or perturbation reagents have adequate validation for each member, species and molecular form?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 17, "questions": 27 } }