{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:25:14Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 16.8, "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: 01a094b7-5711-79f1-a9fc-cccbf52b1ee8\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: CASP6\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": 76.5, "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: 01a094b7-5708-7d71-a8bc-d2da70dea5c0\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: CASP6\nRegistry id: vr.tr.casp6\nPlane / domain: PHY / PHY.OBJ\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext for " } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:57:57+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:27+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q17855895", "registryId": "vr.tr.casp6", "name": "CASP6", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q17855895/", "model": { "registry_id": "vr.tr.casp6", "name": "CASP6", "purpose": "Enable an agent to recognise CASP6, distinguish its gene identity from its RNA and protein products, and assess evidence about its expression and functional consequences.", "definition": "CASP6 is the human protein-coding gene encoding caspase-6, a cysteine protease that cleaves substrates after aspartate residues and participates in apoptotic cellular dismantling.", "scope_statement": "This draft provisionally treats vr.tr.casp6 as the human CASP6 gene, which encodes caspase-6, following [NCBI Gene 839](https://www.ncbi.nlm.nih.gov/gene/839); it owns gene identity, sequence variation, expression and evidence-linked relationships to its products, pending confirmation of the registry's intended species and gene-versus-protein boundary.", "in_scope": [ "CASP6 gene identity, organism and reference genome placement", "CASP6 transcript relationships and alternative splicing", "Alleles and sequence variants with reference-specific coordinates", "Expression observations tied to tissue, cell type and experimental conditions", "Relationships between CASP6 perturbation, caspase-6 activity and observed cellular outcomes" ], "out_of_scope": [ "Independent molecular specifications for caspase-6 protein preparations", "Other caspase genes and their products", "Whole apoptosis pathways and cell-death classifications", "Diseases, patient diagnoses and treatment recommendations", "Assay instruments, reagent products and laboratory protocols", "Nonhuman orthologs as interchangeable instances of the human gene" ], "distinguishing_features": [ "Resolve CASP6 through an organism-qualified gene identifier; the human candidate is NCBI Gene 839.", "Distinguish a genomic CASP6 locus from a CASP6 transcript accession and from the encoded caspase-6 protein.", "Require sequence or identifier evidence that separates CASP6 from other caspase family members; a generic caspase assay is insufficient.", "Separate CASP6 RNA abundance from caspase-6 protein abundance, processing and catalytic activity.", "Treat matching gene symbols in different species as possible ortholog relationships, not proof of identical registry identity." ], "characteristics": [ { "name": "Organism-qualified gene identity", "kind": "category", "unit_or_values": "Taxonomy identifier, approved symbol and stable gene identifier", "why_it_matters": "Prevents conflation of human CASP6 with orthologs or similarly named entities." }, { "name": "Genomic placement", "kind": "relation", "unit_or_values": "Genome assembly, chromosome accession, interval in bp and strand", "why_it_matters": "Makes locus and variant references interpretable across genome releases." }, { "name": "Transcript repertoire", "kind": "relation", "unit_or_values": "Versioned transcript accessions, exon structures and annotation status", "why_it_matters": "Allows expression and variant observations to be assigned to the relevant transcript." }, { "name": "Sequence variation", "kind": "category", "unit_or_values": "Reference-qualified HGVS description, allele state and evidence status", "why_it_matters": "Distinguishes a specific CASP6 alteration from a claim about the entire gene." }, { "name": "RNA expression", "kind": "measurement", "unit_or_values": "TPM, counts or assay-specific relative expression, with normalization and biological context", "why_it_matters": "Supports expression comparisons without equating transcription with protease activity." }, { "name": "Encoded product identity", "kind": "relation", "unit_or_values": "Transcript-to-protein accession mapping, isoform and construct status", "why_it_matters": "Connects gene evidence to the particular caspase-6 product actually studied." }, { "name": "Linked product activity evidence", "kind": "state", "unit_or_values": "Unmeasured, detected, not detected or inconclusive, with assay conditions and specificity controls", "why_it_matters": "Keeps claims of caspase-6 activity distinct from gene presence and expression." } ], "affordances": [ "Resolve a CASP6 mention to a species-qualified gene, transcript or protein reference.", "Map a reported CASP6 variant to its genome assembly and affected transcripts.", "Compare CASP6 expression observations when biological contexts and normalization are compatible.", "Trace a caspase-6 functional claim back to the CASP6 allele, transcript or experimental construct studied.", "Assess whether a perturbation or assay supports CASP6-specific attribution.", "Flag unsupported transfers from gene expression or model-organism evidence to human disease claims." ], "agent_conduct": { "may": [ "Describe CASP6 and caspase-6, including research on its role in neurodegeneration, citing sources.", "Report what an experimental result shows, with source and limits." ], "must_not": [ "Present caspase-6 research as an available treatment for a neurological disease.", "Interpret a person's CASP6 variant as a diagnosis.", "Share genetic data without consent.", "Confuse caspase-6 with other caspases in reports." ], "requires_human": [ "Using results in clinical decisions.", "Research on patient samples without documented consent." ] }, "ethics": { "considerations": [ "People with neurodegenerative diseases are vulnerable to false hope.", "Genetic data is private and identifying." ], "affected_parties": [ "People with neurological diseases", "Families", "Researchers" ] }, "owners": { "steward": "The person whose genome carries it; laboratories and biobanks hold records.", "master_systems": [ "Gene and variant databases" ] }, "visual_identification": [ "Not visible; known from sequence data and enzyme activity assays.", "Identified by its approved gene symbol." ], "failure_modes_and_hazards": [ "Overstated research findings.", "Confusion between caspase family members." ], "standards_and_regulation": [ "Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol." ], "what_it_is_for": [ "CASP6 is encountered in human genome annotations and studies of apoptosis and cellular protein breakdown.", "Researchers examine its sequence and expression alongside separate measurements of caspase-6 processing and activity to investigate its biological function." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q17855895: CASP6", "url": "https://www.wikidata.org/wiki/Q17855895", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Caspase 6", "url": "https://en.wikipedia.org/wiki/Caspase_6", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "casp6-identity-boundary", "name": "CASP6 identity and registry boundary", "description": "Resolve what biological entity the registry label CASP6 identifies.", "rationale": "The registry provides neither a definition nor a species, and the gene symbol can be used informally for its protein product.", "layers": [ { "id": "species-and-locus", "name": "Species and locus", "description": "Anchor CASP6 to a stable gene record and organism.", "findings": [ { "id": "human-gene-candidate", "name": "Human gene candidate", "description": "NCBI identifies human CASP6 as Gene 839, but this does not by itself establish the registry's intended referent. Source: [NCBI CASP6](https://www.ncbi.nlm.nih.gov/gene/839).", "questions": [ { "text": "Which original registry identifier establishes whether CASP6 means the human gene?", "kind": "provenance", "id": "human-gene-candidate-q01" }, { "text": "What taxonomy identifier and stable gene accession define this entry?", "kind": "definition", "id": "human-gene-candidate-q02" } ] } ] }, { "id": "gene-product-separation", "name": "Gene and product separation", "description": "Distinguish the genomic entity from its expressed molecules.", "findings": [ { "id": "casp6-versus-caspase6", "name": "CASP6 versus caspase-6", "description": "Record explicit relationships between the gene, its transcripts and caspase-6 protein; route protein-state observations to the linked product.", "questions": [ { "text": "Does the registry source describe a gene locus, a protein or a combined gene-product concept?", "kind": "boundary", "id": "casp6-versus-caspase6-q01" }, { "text": "Does an existing Vercy model already own the resolved CASP6 concept or its caspase-6 product?", "kind": "boundary", "id": "casp6-versus-caspase6-q02" } ] } ] } ] }, { "id": "casp6-sequence-and-transcripts", "name": "CASP6 sequence and transcripts", "description": "Make CASP6 sequence references, splice forms and product mappings explicit.", "rationale": "A variant or expression result can mean different things depending on the genome assembly and transcript used.", "layers": [ { "id": "reference-sequence-placement", "name": "Reference sequence placement", "description": "Define the coordinate system for CASP6 observations.", "findings": [ { "id": "assembly-qualified-locus", "name": "Assembly-qualified locus", "description": "Require assembly and accession versions before interpreting CASP6 genomic coordinates.", "questions": [ { "text": "Which genome assembly, chromosome accession, strand and interval locate CASP6?", "kind": "definition", "id": "assembly-qualified-locus-q01" }, { "text": "Were reported CASP6 coordinates measured directly or converted from another assembly?", "kind": "provenance", "id": "assembly-qualified-locus-q02" } ] } ] }, { "id": "splice-product-mapping", "name": "Splice and product mapping", "description": "Connect CASP6 transcript structures to their annotated products.", "findings": [ { "id": "transcript-specific-interpretation", "name": "Transcript-specific interpretation", "description": "Record which CASP6 transcript an observation concerns instead of assuming all transcripts share the same coding consequences.", "questions": [ { "text": "Which versioned CASP6 transcripts are supported, and which have experimentally supported protein products?", "kind": "provenance", "id": "transcript-specific-interpretation-q01" }, { "text": "Which exons or splice junctions distinguish the transcript measured or altered in this observation?", "kind": "measurement", "id": "transcript-specific-interpretation-q02" } ] } ] } ] }, { "id": "casp6-variation-and-perturbation", "name": "CASP6 variation and perturbation", "description": "Represent endogenous alleles and experimental alterations without merging them.", "rationale": "A CASP6 sequence change, gene depletion and altered caspase-6 activity provide different kinds of evidence.", "layers": [ { "id": "allele-consequences", "name": "Allele consequences", "description": "Describe CASP6 variants relative to explicit reference sequences.", "findings": [ { "id": "variant-to-product-consequence", "name": "Variant-to-product consequence", "description": "Separate predicted CASP6 consequences from measured effects on RNA, protein abundance or enzymatic function.", "questions": [ { "text": "What reference-qualified variant and allele state were observed, and which CASP6 transcripts are affected?", "kind": "definition", "id": "variant-to-product-consequence-q01" }, { "text": "Which reported effects were measured, and which were inferred from sequence annotation?", "kind": "provenance", "id": "variant-to-product-consequence-q02" } ] } ] }, { "id": "experimental-casp6-alteration", "name": "Experimental CASP6 alteration", "description": "Track the target and validation of interventions used to study CASP6.", "findings": [ { "id": "perturbation-specificity", "name": "Perturbation specificity", "description": "Distinguish locus editing, RNA depletion, overexpression and product inhibition, with evidence of the intended effect.", "questions": [ { "text": "Does the intervention alter the CASP6 locus, a particular transcript or the caspase-6 protein?", "kind": "boundary", "id": "perturbation-specificity-q01" }, { "text": "What target validation, independent intervention or rescue evidence is needed before attributing the outcome to CASP6?", "kind": "action", "id": "perturbation-specificity-q02" } ] } ] } ] }, { "id": "casp6-expression-and-activity", "name": "CASP6 expression and linked activity", "description": "Keep CASP6 transcription separate from the abundance and functional state of its protein product.", "rationale": "Expression measurements alone cannot establish that caspase-6 is catalytically active.", "layers": [ { "id": "contextual-rna-expression", "name": "Contextual RNA expression", "description": "Attach CASP6 expression to biological samples and assay resolution.", "findings": [ { "id": "casp6-expression-observation", "name": "CASP6 expression observation", "description": "Record tissue, cell type, condition, time point and whether the assay measures total CASP6 RNA or a specific transcript.", "questions": [ { "text": "In which species, tissue, cell type and condition was CASP6 RNA measured?", "kind": "measurement", "id": "casp6-expression-observation-q01" }, { "text": "Can the assay distinguish CASP6 transcripts, and what normalization makes the reported values comparable?", "kind": "measurement", "id": "casp6-expression-observation-q02" } ] } ] }, { "id": "linked-protease-state", "name": "Linked protease state", "description": "Associate protein-state evidence with the appropriate CASP6 product.", "findings": [ { "id": "activity-attribution", "name": "Caspase-6 activity attribution", "description": "Capture separate evidence for protein detection, processing and substrate cleavage, including whether other proteases could explain the signal.", "questions": [ { "text": "Does the observation demonstrate caspase-6 abundance, proteolytic processing or catalytic activity?", "kind": "boundary", "id": "activity-attribution-q01" }, { "text": "Which controls distinguish caspase-6-dependent cleavage from activity of other caspases?", "kind": "measurement", "id": "activity-attribution-q02" } ] } ] } ] }, { "id": "casp6-functional-evidence", "name": "CASP6 functional evidence", "description": "Connect CASP6 to cellular outcomes while preserving experimental and causal limits.", "rationale": "A role assigned to caspase-6 does not automatically explain every phenotype associated with CASP6 expression or variation.", "layers": [ { "id": "cellular-outcome-attribution", "name": "Cellular outcome attribution", "description": "Evaluate whether observed cellular changes depend on CASP6.", "findings": [ { "id": "apoptosis-linked-evidence", "name": "Apoptosis-linked evidence", "description": "Caspase-6 has an annotated role in apoptosis; individual gene-level causal claims still require contextual evidence. Source: [UniProt caspase-6](https://www.uniprot.org/uniprotkb/P55212/entry).", "questions": [ { "text": "Which measured cellular outcome connects the CASP6 perturbation to apoptosis in this experimental system?", "kind": "measurement", "id": "apoptosis-linked-evidence-q01" }, { "text": "What evidence distinguishes a causal CASP6 contribution from expression correlated with cell death?", "kind": "provenance", "id": "apoptosis-linked-evidence-q02" } ] } ] }, { "id": "evidence-transfer-limits", "name": "Evidence transfer limits", "description": "Set boundaries on generalization across assays, organisms and disease contexts.", "findings": [ { "id": "context-qualified-functional-claim", "name": "Context-qualified functional claim", "description": "Keep purified-protein, cell-culture, animal and human observations distinguishable when interpreting CASP6.", "questions": [ { "text": "Was the CASP6 claim established in purified protein, cultured cells, an animal model or human material?", "kind": "provenance", "id": "context-qualified-functional-claim-q01" }, { "text": "What additional evidence is required before transferring this result to another species, tissue or disease context?", "kind": "action", "id": "context-qualified-functional-claim-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": [ "No sense or organism was supplied; the gene interpretation is provisional, and the registry should distinguish the human gene, its protein product, and the protein-structure prediction event.", "The batch's device framing does not fit the biological interpretation.", "This description is recalled knowledge; no sources were consulted." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of CASP6 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": "CASP6", "note": "Identifies the human gene; caspase-6 is its encoded protein." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of CASP6 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": [ "Studying execution mechanisms of apoptosis.", "Investigating caspase-mediated protein cleavage in neurodegeneration.", "Developing and evaluating experimental caspase-6 inhibitors." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of CASP6 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": [ "Experimental substrate cleavage or inhibitor effects may be misattributed to caspase-6 because related caspases can share substrate preferences or inhibitor sensitivity." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of CASP6 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": "Caspase-6", "difference": "The protein enzyme encoded by CASP6, rather than the gene itself." }, { "name": "CASP3", "difference": "A distinct gene encoding caspase-3, another executioner caspase with different substrate preferences." }, { "name": "CASP7", "difference": "A distinct gene encoding caspase-7, another executioner caspase." }, { "name": "CASP6 protein-structure prediction assessment", "difference": "CASP6 can also denote the sixth Critical Assessment of protein Structure Prediction exercise, an event rather than a biological entity." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of CASP6 this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the original registry record identify the human CASP6 gene, caspase-6 protein or another referent?", "Does an existing world model already cover the resolved concept and therefore require linking instead of a new publication?", "Which reference assembly, transcripts and protein products should anchor this entry?", "Which CASP6-specific expression and activity assays have sufficient validation for the intended agent decisions?", "Which proposed functional or disease associations have causal evidence, and which remain context-limited correlations?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 15, "questions": 25 } }