{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:29:13Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 19.4, "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: 01a094bb-0c95-7bb0-9817-eacfc92632d4\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: CDH1\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 registered", "usd": 0.0, "recall": true }, "codex": { "seconds": 72.8, "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: 01a094bb-0ca5-74f0-8cb4-c1bfb48a0edf\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: CDH1\nRegistry id: vr.tr.cdh1\nPlane / domain: PHY / PHY.OBJ\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext for th" } }, "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": "2026-10-07T10:10:27+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q17859787", "registryId": "vr.tr.cdh1", "name": "CDH1", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q17859787/", "model": { "registry_id": "vr.tr.cdh1", "name": "CDH1", "purpose": "Enable an agent to identify CDH1, distinguish its gene identity from its molecular products, and assess evidence about its sequence, expression and functional state.", "definition": "CDH1 is the human gene encoding E-cadherin, a calcium-dependent transmembrane adhesion protein that supports epithelial cell-cell adhesion and adherens junctions.", "scope_statement": "Provisionally model vr.tr.cdh1 as the human protein-coding gene CDH1, cadherin 1, owning its locus identity and relationships to transcripts, E-cadherin products and observed alterations; the registry's intended organism and gene-versus-protein boundary remain unresolved.", "in_scope": [ "Organism-qualified CDH1 identity and authoritative identifiers", "Assembly-specific locus and versioned transcript references", "CDH1 sequence alterations and allele context", "Context-specific transcription and regulatory observations", "Relationships between CDH1 products and measured cell adhesion" ], "out_of_scope": [ "E-cadherin protein specimens and their complete biochemical characterization", "Other cadherin genes and nonhuman orthologs as independent entities", "Other biological entities named Cdh1", "Cancer syndromes, patient diagnoses and clinical management", "Laboratory instruments, assay protocols and specimen custody" ], "distinguishing_features": [ "Resolve the label against organism and identifier: the provisional human gene interpretation requires NCBI Gene 999 or HGNC:1748, rather than a symbol match alone.", "Distinguish the genomic locus from an RNA transcript or E-cadherin protein using the referenced sequence type and accession.", "Require identifier or sequence evidence to distinguish CDH1 from other cadherin-family members.", "Represent an altered allele as a state associated with CDH1, rather than treating the variant as the entire registered thing.", "Keep measured transcript abundance, protein localization and adhesion function separate; none alone identifies all the others." ], "characteristics": [ { "name": "Resolved biological identity", "kind": "relation", "unit_or_values": "Organism, nomenclature authority, stable identifier and entity type", "why_it_matters": "Prevents a short symbol from merging genes, proteins or organisms." }, { "name": "Genomic reference", "kind": "relation", "unit_or_values": "Assembly accession and version, sequence accession, interval, strand and coordinate convention", "why_it_matters": "Makes locus and variant positions interpretable." }, { "name": "Transcript reference", "kind": "relation", "unit_or_values": "Versioned transcript accession linked to a protein accession when applicable", "why_it_matters": "Sequence consequences depend on the transcript used." }, { "name": "Observed sequence alteration", "kind": "category", "unit_or_values": "Reference-qualified substitution, insertion, deletion, splice-region alteration, copy-number alteration or unresolved change", "why_it_matters": "Separates the observed change from predictions about its effects." }, { "name": "Allele context", "kind": "state", "unit_or_values": "Zygosity, phase, allele fraction and germline, somatic or unknown origin", "why_it_matters": "An alteration's interpretation depends on which copies and cells carry it." }, { "name": "CDH1 transcript abundance", "kind": "measurement", "unit_or_values": "Assay-specific units such as TPM or normalized counts, with specimen and normalization method", "why_it_matters": "Supports comparison only when biological and assay contexts are compatible." }, { "name": "Regulatory-region methylation", "kind": "measurement", "unit_or_values": "Fraction or percent methylation at explicitly identified sites or intervals", "why_it_matters": "Records a candidate regulatory observation without equating methylation with demonstrated silencing." }, { "name": "Linked E-cadherin localization", "kind": "state", "unit_or_values": "Junctional membrane, other membrane, intracellular, mixed, undetected or unresolved", "why_it_matters": "Connects gene-level observations to spatially resolved product evidence." }, { "name": "Functional evidence status", "kind": "category", "unit_or_values": "Directly measured, indirectly supported, predicted, conflicting or untested", "why_it_matters": "Prevents sequence predictions from becoming asserted adhesion defects." } ], "affordances": [ "Resolve a CDH1-labelled record to a species-qualified gene identity.", "Attach sequence observations to a versioned genomic and transcript reference.", "Compare CDH1 expression across specimens with compatible assay contexts.", "Link an alteration to measured RNA, protein and adhesion outcomes while preserving uncertainty.", "Identify missing evidence before assigning a functional interpretation.", "Route unresolved identity or clinical interpretation to the appropriate neighbouring model." ], "agent_conduct": { "may": [ "Describe CDH1 and E-cadherin's role in cell adhesion, citing sources.", "Explain in general terms that inherited variants can raise cancer risk and that genetic counselling is available." ], "must_not": [ "Tell a person they have a hereditary cancer syndrome from a variant without clinical review.", "Share a person's genetic result with relatives, employers or insurers without consent.", "Recommend preventive surgery or screening for a person.", "Classify a variant of uncertain significance without evidence." ], "requires_human": [ "Returning genetic results to a person or family.", "Any decision on screening or preventive surgery." ] }, "ethics": { "considerations": [ "Hereditary cancer results lead to life-changing decisions for whole families.", "Genetic information can be used to discriminate." ], "affected_parties": [ "People with tested variants", "Relatives", "Clinicians and counsellors" ] }, "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 or tumour staining for E-cadherin.", "Loss of E-cadherin staining is reported by pathologists." ], "failure_modes_and_hazards": [ "Misclassification of variants.", "Genetic discrimination after disclosure." ], "standards_and_regulation": [ "Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol." ], "what_it_is_for": [ "CDH1 is encountered in human genome annotations and studies of epithelial organization, cell adhesion and cancer biology.", "Researchers examine its sequence and expression together with E-cadherin abundance and localization to investigate effects on cell junctions and tissue structure." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q17859787: CDH1", "url": "https://www.wikidata.org/wiki/Q17859787", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Cadherin-1", "url": "https://en.wikipedia.org/wiki/Cadherin-1", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "cdh1-identity", "name": "CDH1 identity", "description": "Establish which biological entity the registry label denotes.", "rationale": "Without a recorded definition, gene identity and organism must be resolved before downstream observations can be attached.", "layers": [ { "id": "organism-and-symbol", "name": "Organism and symbol", "description": "Anchor the provisional interpretation to an authoritative gene record.", "findings": [ { "id": "human-cadherin-1-anchor", "name": "Human cadherin 1 anchor", "description": "NCBI identifies human CDH1 as the protein-coding cadherin 1 gene, Gene ID 999, with HGNC:1748. This supports a provisional interpretation but does not establish the registry's intention. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/999)", "questions": [ { "text": "Does the registry's originating record resolve to human NCBI Gene 999 or HGNC:1748?", "kind": "provenance", "id": "human-cadherin-1-anchor-q01" }, { "text": "Which organism and biological entity type does the original registration explicitly identify?", "kind": "definition", "id": "human-cadherin-1-anchor-q02" } ] } ] }, { "id": "gene-product-boundary", "name": "Gene and product boundary", "description": "Keep the gene, its transcripts and its protein products distinguishable.", "findings": [ { "id": "cdh1-encodes-ecadherin", "name": "CDH1 encodes E-cadherin", "description": "CDH1 encodes epithelial cadherin, or E-cadherin; the gene and encoded protein require distinct observation targets. [MedlinePlus Genetics](https://medlineplus.gov/genetics/gene/cdh1/)", "questions": [ { "text": "Does each attached observation concern genomic CDH1, a transcript or an E-cadherin product?", "kind": "boundary", "id": "cdh1-encodes-ecadherin-q01" }, { "text": "Does the catalogue already own either entity in another publication that this entry should reference?", "kind": "boundary", "id": "cdh1-encodes-ecadherin-q02" } ] } ] } ] }, { "id": "cdh1-sequence-context", "name": "CDH1 sequence context", "description": "Make locus, transcript and alteration descriptions reproducible.", "rationale": "A CDH1 coordinate or consequence is ambiguous without its reference sequence and transcript context.", "layers": [ { "id": "locus-reference", "name": "Locus reference", "description": "Resolve genomic positions against an explicit assembly.", "findings": [ { "id": "assembly-bound-locus", "name": "Assembly-bound locus", "description": "Require a versioned genomic reference and coordinate convention for every CDH1 interval or genomic change.", "questions": [ { "text": "Which assembly, chromosome accession and coordinate convention locate the CDH1 observation?", "kind": "provenance", "id": "assembly-bound-locus-q01" }, { "text": "Does the reported reference allele agree with the sequence at that position?", "kind": "measurement", "id": "assembly-bound-locus-q02" } ] } ] }, { "id": "transcript-consequences", "name": "Transcript consequences", "description": "Relate sequence changes to explicitly selected RNA and protein products.", "findings": [ { "id": "versioned-transcript-mapping", "name": "Versioned transcript mapping", "description": "NCBI lists multiple CDH1 transcript variants. Record the selected accession and version before describing coding or splice consequences. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/999)", "questions": [ { "text": "Which CDH1 transcript accession and version underlie the reported consequence?", "kind": "provenance", "id": "versioned-transcript-mapping-q01" }, { "text": "Is the proposed RNA consequence measured in a relevant sample or inferred from sequence?", "kind": "measurement", "id": "versioned-transcript-mapping-q02" } ] } ] } ] }, { "id": "cdh1-expression-regulation", "name": "CDH1 expression and regulation", "description": "Describe when, where and how strongly CDH1 is transcribed.", "rationale": "The model must distinguish low expression from an altered sequence and from inadequate detection.", "layers": [ { "id": "transcription-context", "name": "Transcription context", "description": "Attach expression observations to cell composition and assay conditions.", "findings": [ { "id": "contextual-rna-abundance", "name": "Contextual RNA abundance", "description": "Treat CDH1 RNA abundance as a specimen-specific measurement, preserving cell type, sampling conditions, transcript coverage and normalization.", "questions": [ { "text": "Which cells or tissue contributed to the CDH1 RNA measurement, and could mixed cell populations explain the result?", "kind": "measurement", "id": "contextual-rna-abundance-q01" }, { "text": "What assay, normalization and detection limit distinguish low abundance from failure to detect CDH1?", "kind": "measurement", "id": "contextual-rna-abundance-q02" } ] } ] }, { "id": "regulatory-evidence", "name": "Regulatory evidence", "description": "Separate proposed regulation from demonstrated effects on transcription.", "findings": [ { "id": "site-specific-regulatory-observations", "name": "Site-specific regulatory observations", "description": "When methylation or another regulatory mechanism is proposed, retain the assayed CDH1 region and supporting expression evidence rather than assigning a global silenced state.", "questions": [ { "text": "Which CDH1 regulatory sites were assayed, and what measurement supports the proposed regulatory state?", "kind": "measurement", "id": "site-specific-regulatory-observations-q01" }, { "text": "What matched expression or perturbation evidence links that observation to reduced CDH1 transcription?", "kind": "provenance", "id": "site-specific-regulatory-observations-q02" } ] } ] } ] }, { "id": "ecadherin-functional-link", "name": "E-cadherin functional link", "description": "Connect CDH1 to product-level evidence without collapsing gene and protein states.", "rationale": "Gene sequence and RNA abundance alone do not establish whether the encoded product supports cell adhesion.", "layers": [ { "id": "product-architecture-localization", "name": "Product architecture and localization", "description": "Locate product observations along the encoded protein and within cells.", "findings": [ { "id": "adhesion-product-regions", "name": "Adhesion product regions", "description": "The encoded adhesion protein has extracellular cadherin repeats, a transmembrane region and a cytoplasmic tail. Use product-specific references when mapping observations to these regions. [NCBI PubChem](https://pubchem.ncbi.nlm.nih.gov/gene/CDH1/human)", "questions": [ { "text": "Which encoded isoform and protein region does the CDH1 alteration or detection reagent concern?", "kind": "boundary", "id": "adhesion-product-regions-q01" }, { "text": "Was E-cadherin detected at cell junctions, elsewhere in the cell or below the assay's detection limit?", "kind": "measurement", "id": "adhesion-product-regions-q02" } ] } ] }, { "id": "adhesion-function", "name": "Adhesion function", "description": "Require functional observations with defined experimental conditions.", "findings": [ { "id": "calcium-dependent-adhesion-evidence", "name": "Calcium-dependent adhesion evidence", "description": "E-cadherin participates in calcium-dependent cell-cell adhesion. A CDH1 functional interpretation should specify the assay, calcium conditions and controls. [NCBI PubChem](https://pubchem.ncbi.nlm.nih.gov/gene/CDH1/human)", "questions": [ { "text": "What adhesion endpoint was measured, under which calcium conditions and against which reference cells?", "kind": "measurement", "id": "calcium-dependent-adhesion-evidence-q01" }, { "text": "What perturbation, rescue or independent evidence supports attributing the result to CDH1?", "kind": "provenance", "id": "calcium-dependent-adhesion-evidence-q02" } ] } ] } ] }, { "id": "cdh1-alteration-interpretation", "name": "CDH1 alteration interpretation", "description": "Separate observed alleles, functional consequences and external clinical interpretations.", "rationale": "An agent needs to distinguish what changed in CDH1 from what has actually been demonstrated about that change.", "layers": [ { "id": "allele-and-sample-context", "name": "Allele and sample context", "description": "Describe which CDH1 copies and sampled cells carry an alteration.", "findings": [ { "id": "alteration-origin-and-dosage", "name": "Alteration origin and dosage", "description": "Record sequence or copy-number findings with allele fraction, zygosity, phase and evidence for origin when available; preserve unknown states.", "questions": [ { "text": "What evidence establishes whether the CDH1 alteration is germline, somatic or unresolved?", "kind": "provenance", "id": "alteration-origin-and-dosage-q01" }, { "text": "What allele fraction, copy-number and phase observations describe the affected CDH1 copies?", "kind": "measurement", "id": "alteration-origin-and-dosage-q02" } ] } ] }, { "id": "interpretation-and-actions", "name": "Interpretation and actions", "description": "Make the strength and permitted use of conclusions explicit.", "findings": [ { "id": "evidence-bounded-conclusions", "name": "Evidence-bounded conclusions", "description": "Keep measured molecular effects, computational predictions and externally supplied clinical classifications separate, with their sources and dates.", "questions": [ { "text": "Which CDH1 conclusions have direct experimental support, and which depend on predictions or conflicting interpretations?", "kind": "provenance", "id": "evidence-bounded-conclusions-q01" }, { "text": "Does the available evidence support annotation or comparison, or must the proposed clinical use be referred to a clinical interpretation model?", "kind": "action", "id": "evidence-bounded-conclusions-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "The registry supplies neither a sense nor an organism; this description assumes the human CDH1 gene.", "Confirm whether the registry intends the gene, its protein product, or the cell-cycle regulator also called Cdh1.", "These statements are recalled knowledge, not findings verified against sources during this response." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of CDH1 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": "CDH1", "note": "Human gene symbol; the approved name is cadherin 1." }, { "scheme": "HGNC ID", "value_or_pattern": "HGNC:1748", "note": "Identifies the human gene." }, { "scheme": "NCBI Gene", "value_or_pattern": "999", "note": "Identifies the human CDH1 gene." }, { "scheme": "UniProtKB accession", "value_or_pattern": "P12830", "note": "Identifies the human E-cadherin protein, rather than the gene." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of CDH1 this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-standards-and-regulation", "name": "Standards and regulation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "HUGO Gene Nomenclature Committee (HGNC) guidelines govern approved human gene symbols and names.", "Human Genome Variation Society (HGVS) recommendations provide notation for sequence variants; descriptions require an appropriate reference sequence." ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of CDH1 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 epithelial adhesion, tissue organisation and tumour invasion.", "Clinical genetic testing for inherited cancer predisposition associated with pathogenic CDH1 variants.", "Pathological assessment of E-cadherin protein expression, including evaluation of breast tumour differentiation." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of CDH1 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": [ "Pathogenic germline variants can confer predisposition to diffuse gastric cancer and lobular breast cancer.", "Somatic inactivation or reduced expression can impair epithelial adhesion and contribute to tumour progression.", "Some pathogenic variants are associated with blepharocheilodontic syndrome.", "Treating every CDH1 variant as pathogenic can produce incorrect biological or clinical interpretations." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of CDH1 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": "E-cadherin", "difference": "E-cadherin is the protein encoded by CDH1; CDH1 denotes the gene." }, { "name": "CDH2", "difference": "CDH2 is a separate gene encoding N-cadherin." }, { "name": "CDH3", "difference": "CDH3 is a separate gene encoding P-cadherin." }, { "name": "FZR1 / Cdh1", "difference": "Cdh1 also names an anaphase-promoting complex coactivator; in humans that protein is encoded by FZR1 and is unrelated to E-cadherin." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of CDH1 this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does vr.tr.cdh1 originally denote the human cadherin 1 gene, its protein product or a different entity sharing the label?", "Does an existing Vercy publication already cover this entity and therefore require a link instead of a separate model?", "Which genome assembly and transcript selection policy should govern CDH1 reference mappings?", "Which tissue contexts and validated assays are necessary to distinguish reduced CDH1 transcription, altered E-cadherin localization and impaired adhesion?", "Which evidence standards should govern importing variant interpretations and handling disagreement or subsequent reclassification?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 16, "questions": 26 } }