{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.casp6","code":"thing-q17855895","url":"https://ver.cy/models/thing/q17855895/","name":"CASP6","alternateNames":[],"kind":"thing","status":"published","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.OBJ"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"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.","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.","scope":{"in":["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":["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"],"boundaries":[]},"distinguishingFeatures":["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."],"structure":{"bundles":[{"id":"casp6-identity-boundary","name":"CASP6 identity and registry boundary","description":"Resolve what biological entity the registry label CASP6 identifies.","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?","id":"human-gene-candidate-q01","kind":"provenance"},{"text":"What taxonomy identifier and stable gene accession define this entry?","id":"human-gene-candidate-q02","kind":"definition"}]}]},{"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?","id":"casp6-versus-caspase6-q01","kind":"boundary"},{"text":"Does an existing Vercy model already own the resolved CASP6 concept or its caspase-6 product?","id":"casp6-versus-caspase6-q02","kind":"boundary"}]}]}]},{"id":"casp6-sequence-and-transcripts","name":"CASP6 sequence and transcripts","description":"Make CASP6 sequence references, splice forms and product mappings explicit.","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?","id":"assembly-qualified-locus-q01","kind":"definition"},{"text":"Were reported CASP6 coordinates measured directly or converted from another assembly?","id":"assembly-qualified-locus-q02","kind":"provenance"}]}]},{"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?","id":"transcript-specific-interpretation-q01","kind":"provenance"},{"text":"Which exons or splice junctions distinguish the transcript measured or altered in this observation?","id":"transcript-specific-interpretation-q02","kind":"measurement"}]}]}]},{"id":"casp6-variation-and-perturbation","name":"CASP6 variation and perturbation","description":"Represent endogenous alleles and experimental alterations without merging them.","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?","id":"variant-to-product-consequence-q01","kind":"definition"},{"text":"Which reported effects were measured, and which were inferred from sequence annotation?","id":"variant-to-product-consequence-q02","kind":"provenance"}]}]},{"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?","id":"perturbation-specificity-q01","kind":"boundary"},{"text":"What target validation, independent intervention or rescue evidence is needed before attributing the outcome to CASP6?","id":"perturbation-specificity-q02","kind":"action"}]}]}]},{"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.","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?","id":"casp6-expression-observation-q01","kind":"measurement"},{"text":"Can the assay distinguish CASP6 transcripts, and what normalization makes the reported values comparable?","id":"casp6-expression-observation-q02","kind":"measurement"}]}]},{"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?","id":"activity-attribution-q01","kind":"boundary"},{"text":"Which controls distinguish caspase-6-dependent cleavage from activity of other caspases?","id":"activity-attribution-q02","kind":"measurement"}]}]}]},{"id":"casp6-functional-evidence","name":"CASP6 functional evidence","description":"Connect CASP6 to cellular outcomes while preserving experimental and causal limits.","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?","id":"apoptosis-linked-evidence-q01","kind":"measurement"},{"text":"What evidence distinguishes a causal CASP6 contribution from expression correlated with cell death?","id":"apoptosis-linked-evidence-q02","kind":"provenance"}]}]},{"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?","id":"context-qualified-functional-claim-q01","kind":"provenance"},{"text":"What additional evidence is required before transferring this result to another species, tissue or disease context?","id":"context-qualified-functional-claim-q02","kind":"action"}]}]}]},{"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.","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.","questions":[{"text":"Which of these check these first hold for the sense of CASP6 this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of CASP6 this model covers, and on what evidence?","id":"evidence-identifiers-q01","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.","questions":[{"text":"Which of these real-world use hold for the sense of CASP6 this model covers, and on what evidence?","id":"evidence-real-world-use-q01","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.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of CASP6 this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","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.","questions":[{"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?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"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."],"mustNot":["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."],"requiresHuman":["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."],"affectedParties":["People with neurological diseases","Families","Researchers"]},"owners":{"steward":"The person whose genome carries it; laboratories and biobanks hold records.","roles":[],"masterSystems":["Gene and variant databases"]},"relations":[{"target":"Q20747295","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.casp6","Wikidata: Q17855895 (https://www.wikidata.org/wiki/Q17855895)"]},"properties":{"applicability":"required","items":["Organism-qualified gene identity: Taxonomy identifier, approved symbol and stable gene identifier","Genomic placement: Genome assembly, chromosome accession, interval in bp and strand","Transcript repertoire: Versioned transcript accessions, exon structures and annotation status","Sequence variation: Reference-qualified HGVS description, allele state and evidence status","RNA expression: TPM, counts or assay-specific relative expression, with normalization and biological context","Encoded product identity: Transcript-to-protein accession mapping, isoform and construct status","Linked product activity evidence: Unmeasured, detected, not detected or inconclusive, with assay conditions and specificity controls"]},"recognition":{"applicability":"required","items":["Not visible; known from sequence data and enzyme activity assays.","Identified by its approved gene symbol."]},"capabilities":{"applicability":"required","items":["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."]},"hazards":{"applicability":"required","items":["Overstated research findings.","Confusion between caspase family members."]},"interfaces":{"applicability":"required","items":["Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol."]},"context":{"applicability":"required","items":["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":[{"title":"Wikidata item Q17855895: CASP6","url":"https://www.wikidata.org/wiki/Q17855895","note":"identity and sense of the item"},{"title":"Wikipedia: Caspase 6","url":"https://en.wikipedia.org/wiki/Caspase_6","note":"general description of the item"}],"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?"],"resources":{"spec":"/models/things/publications/thing-q17855895/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q17855895/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T08:25:14Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"filled","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T10:10:27+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}