{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.casp2","code":"thing-q14913269","url":"https://ver.cy/models/thing/q14913269/","name":"CASP2","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":"CASP2 is the approved symbol for the human gene encoding caspase-2, a cysteine protease involved in cellular stress responses and regulated cell death.","purpose":"Enable an agent to identify CASP2, distinguish its gene, transcript and protein representations, and judge which experimental observations support claims about its expression or function.","scope":{"in":["CASP2 identity, organism and reference identifiers","Gene-to-transcript-to-protein relationships","Sequence variants and experimental constructs attributed to CASP2","CASP2 expression and caspase-2 molecular state","Evidence connecting CASP2 perturbation to observed cellular effects"],"out":["Other caspase genes and their independent models","Complete models of apoptosis or cellular stress responses","Diseases associated with CASP2 as independent clinical entities","Antibody, inhibitor and assay-kit products as commercial objects","Whole genomes, organisms and cell lines beyond their relationship to CASP2"],"boundaries":[]},"distinguishingFeatures":["For the provisional human interpretation, require agreement with NCBI Gene 835 or HGNC:1503, rather than accepting the symbol alone.","Distinguish the CASP2 DNA locus from an RNA transcript or caspase-2 protein by molecule type and accession.","Require organism identification before treating similarly named genes as the same entity rather than orthologs.","Resolve transcript or protein isoforms by sequence accession and version; a shared CASP2 label does not establish sequence identity.","Do not treat a general caspase activity signal as identification of caspase-2 without evidence that distinguishes other caspases."],"structure":{"bundles":[{"id":"casp2-identity-and-boundary","name":"CASP2 identity and boundary","description":"Establish what the registry name denotes before attaching molecular observations.","layers":[{"id":"reference-anchor","name":"Reference anchor","description":"Resolve the symbol against an organism-qualified authority record.","findings":[{"id":"human-gene-anchor","name":"Human gene anchor","description":"NCBI identifies human CASP2 as a protein-coding gene, Gene ID 835, linked to HGNC:1503; this establishes a candidate interpretation, not the registry's intended referent. [NCBI CASP2](https://www.ncbi.nlm.nih.gov/gene/835)","questions":[{"text":"Does the originating registry record identify human CASP2, another organism's ortholog or the protein?","id":"human-gene-anchor-q01","kind":"definition"},{"text":"Which original identifier and source support mapping vr.tr.casp2 to this reference?","id":"human-gene-anchor-q02","kind":"provenance"}]}]},{"id":"molecular-and-species-boundaries","name":"Molecular and species boundaries","description":"Keep related biological entities connected without making them interchangeable.","findings":[{"id":"gene-product-and-ortholog-separation","name":"Gene, product and ortholog separation","description":"Require explicit relationships between the CASP2 gene, its RNA products, caspase-2 proteins and orthologous genes.","questions":[{"text":"Is this observation about CASP2 DNA, RNA or caspase-2 protein?","id":"gene-product-and-ortholog-separation-q01","kind":"boundary"},{"text":"Does the catalogue already contain the same molecular concept under caspase-2 or another identifier?","id":"gene-product-and-ortholog-separation-q02","kind":"boundary"}]}]}]},{"id":"casp2-sequences-and-products","name":"CASP2 sequences and products","description":"Represent the sequence distinctions needed to interpret CASP2 observations.","layers":[{"id":"transcript-product-mapping","name":"Transcript-product mapping","description":"Connect each measured or manipulated transcript to its supported protein product.","findings":[{"id":"isoform-resolution","name":"Isoform resolution","description":"Human CASP2 has alternatively spliced transcripts encoding multiple isoforms; measurements should retain their actual resolution. [NCBI CASP2](https://www.ncbi.nlm.nih.gov/gene/835)","questions":[{"text":"Which versioned transcript and protein accessions describe the isoform under study?","id":"isoform-resolution-q01","kind":"definition"},{"text":"Can the primers, reads or detected peptides distinguish that isoform from other CASP2 products?","id":"isoform-resolution-q02","kind":"measurement"}]}]},{"id":"variants-and-constructs","name":"Variants and constructs","description":"Record departures from the chosen CASP2 reference sequence.","findings":[{"id":"sequence-change-attribution","name":"Sequence change attribution","description":"Separate natural alleles from engineered mutations, truncations and tags before generalizing observations to endogenous CASP2.","questions":[{"text":"Which substitutions, deletions, tags or domain boundaries distinguish this construct from its CASP2 reference?","id":"sequence-change-attribution-q01","kind":"definition"},{"text":"What sequence verification supports the reported allele or construct identity?","id":"sequence-change-attribution-q02","kind":"provenance"}]}]}]},{"id":"casp2-expression-and-protein-state","name":"CASP2 expression and protein state","description":"Distinguish how much CASP2 product is present from its processing and activity.","layers":[{"id":"expression-context","name":"Expression context","description":"Interpret CASP2 abundance in its sampled biological setting.","findings":[{"id":"contextual-abundance","name":"Contextual abundance","description":"Require the molecular target, sample context and normalization for every CASP2 abundance observation.","questions":[{"text":"Which organism, tissue or cell system, treatment and time point produced the CASP2 measurement?","id":"contextual-abundance-q01","kind":"provenance"},{"text":"Does the result quantify total CASP2 RNA, a particular transcript or a defined protein form, and in what units?","id":"contextual-abundance-q02","kind":"measurement"}]}]},{"id":"processing-and-catalysis","name":"Processing and catalysis","description":"Keep evidence of protein cleavage separate from evidence of catalytic function.","findings":[{"id":"activity-attribution","name":"Activity attribution","description":"Assess caspase-2 processing and substrate cleavage as separately supported observations.","questions":[{"text":"Which caspase-2 molecular forms or cleavage products were directly detected?","id":"activity-attribution-q01","kind":"measurement"},{"text":"Which substrate, assay conditions and controls establish that the activity signal depends on caspase-2?","id":"activity-attribution-q02","kind":"measurement"},{"text":"What additional evidence is needed before labelling this caspase-2 preparation active?","id":"activity-attribution-q03","kind":"action"}]}]}]},{"id":"casp2-function-and-causal-evidence","name":"CASP2 function and causal evidence","description":"Evaluate what CASP2 perturbations and molecular associations establish in a defined biological context.","layers":[{"id":"perturbation-interpretation","name":"Perturbation interpretation","description":"Connect an intervention to its verified molecular effect and measured outcome.","findings":[{"id":"casp2-dependent-phenotypes","name":"CASP2-dependent phenotypes","description":"Record the evidence needed to distinguish effects of CASP2 loss or alteration from assay artifacts and other intervention effects.","questions":[{"text":"How was CASP2 deletion, knockdown, overexpression or inhibition verified at the relevant molecular level?","id":"casp2-dependent-phenotypes-q01","kind":"measurement"},{"text":"Do independent perturbations or an appropriate CASP2 rescue support attribution of the phenotype?","id":"casp2-dependent-phenotypes-q02","kind":"provenance"},{"text":"Which organism, cell state and experimental conditions bound the functional conclusion?","id":"casp2-dependent-phenotypes-q03","kind":"boundary"}]}]},{"id":"mechanistic-relationships","name":"Mechanistic relationships","description":"Separate direct CASP2 product interactions from downstream pathway associations.","findings":[{"id":"interaction-and-substrate-evidence","name":"Interaction and substrate evidence","description":"Qualify proposed caspase-2 partners and substrates by the type and context of supporting evidence.","questions":[{"text":"Does the experiment establish direct binding, complex membership, direct cleavage or only a downstream association?","id":"interaction-and-substrate-evidence-q01","kind":"boundary"},{"text":"Which controls and independent observations support the proposed caspase-2 partner or substrate relationship?","id":"interaction-and-substrate-evidence-q02","kind":"provenance"},{"text":"What experiment would distinguish a catalytic caspase-2 effect from another consequence of CASP2 perturbation?","id":"interaction-and-substrate-evidence-q03","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 CASP2 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 CASP2 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 CASP2 this model covers, and on what evidence?","id":"evidence-real-world-use-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 CASP2 this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Describe CASP2 and the caspase-2 enzyme's role in stress responses and cell death, citing sources.","Report what an experimental or variant result shows, with source and limits."],"mustNot":["Interpret a person's CASP2 variant as a diagnosis.","Share genetic data without consent.","Present early research on caspase-2 as available treatment.","Confuse caspase-2 with other caspases when reporting findings."],"requiresHuman":["Using results in clinical decisions.","Research on patient samples without documented consent."]},"ethics":{"considerations":["Overstated links between genes and disease can cause needless fear.","Genetic data is private and identifying."],"affectedParties":["People with genetic test results","Patients","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.casp2","Wikidata: Q14913269 (https://www.wikidata.org/wiki/Q14913269)"]},"properties":{"applicability":"required","items":["Reference identity: Organism-qualified gene identifier; provisional human anchor NCBI Gene 835","Molecular representation: Genomic locus | transcript | protein precursor | processed protein | engineered construct","Reference sequence: Accession with version; genome assembly when coordinates are used","Isoform assignment: Resolved to accession | multiple compatible isoforms | unresolved","Expression abundance: RNA or protein abundance in explicitly reported assay units, with normalization and biological context","Protein processing state: Precursor detected | specified fragments detected | mixed | unresolved","Attributed proteolytic activity: Substrate conversion rate in reported units, with substrate, conditions and specificity controls","Perturbation relationship: Targeted allele, transcript or protein linked to intervention and matched 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 CASP2-labelled record to an organism and molecular reference.","Map a transcript, protein isoform or engineered construct to its CASP2 parent.","Compare expression observations while preserving assay and biological context.","Assess whether a detection or activity assay distinguishes caspase-2 from related proteins.","Evaluate CASP2 perturbation evidence before attributing a cellular phenotype.","Flag unresolved identity, isoform or functional claims for targeted research."]},"hazards":{"applicability":"required","items":["Confusion between caspase family members in reports.","Overinterpretation of variant associations."]},"interfaces":{"applicability":"required","items":["Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol."]},"context":{"applicability":"required","items":["The human CASP2 gene is encountered in studies of cellular stress responses and regulated cell death.","Its sequence and transcript expression provide a basis for investigating caspase-2 production, while protein processing and enzyme activity require separate evidence."]}},"sources":[{"title":"Wikidata item Q14913269: CASP2","url":"https://www.wikidata.org/wiki/Q14913269","note":"identity and sense of the item"},{"title":"Wikipedia: Caspase 2","url":"https://en.wikipedia.org/wiki/Caspase_2","note":"general description of the item"}],"openQuestions":["Does vr.tr.casp2 denote the human gene, an organism-independent gene concept or caspase-2 protein?","Does an existing world-model publication already own this concept under caspase-2 or a synonymous identifier?","Which reference sequences and isoform nomenclature should anchor the confirmed registry referent?","Which available assays discriminate caspase-2 activity and individual CASP2 products adequately for the intended decisions?","Which proposed activation mechanisms, substrates and cellular roles have direct evidence in the biological contexts this model must cover?"],"resources":{"spec":"/models/things/publications/thing-q14913269/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q14913269/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T08:25:08Z","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 2026-10-07T10:10:26+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}