{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:25:08Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 16.4, "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: 01a094b7-4b4f-7191-bb7f-631d972633d2\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: CASP2\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": 74.0, "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: 01a094b7-4b59-7790-a135-fbacc49d1b5f\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: CASP2\nRegistry id: vr.tr.casp2\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": "2026-10-07T10:10:26+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q14913269", "registryId": "vr.tr.casp2", "name": "CASP2", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q14913269/", "model": { "registry_id": "vr.tr.casp2", "name": "CASP2", "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.", "definition": "CASP2 is the approved symbol for the human gene encoding caspase-2, a cysteine protease involved in cellular stress responses and regulated cell death.", "scope_statement": "This draft provisionally treats vr.tr.casp2 as the CASP2 gene concept, with explicit links to its transcripts and encoded caspase-2 proteins; human CASP2 is the reference anchor pending confirmation of the registry's intended species and molecular level.", "in_scope": [ "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_of_scope": [ "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" ], "distinguishing_features": [ "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." ], "characteristics": [ { "name": "Reference identity", "kind": "relation", "unit_or_values": "Organism-qualified gene identifier; provisional human anchor NCBI Gene 835", "why_it_matters": "Prevents symbol collisions and unsupported merging across species." }, { "name": "Molecular representation", "kind": "category", "unit_or_values": "Genomic locus | transcript | protein precursor | processed protein | engineered construct", "why_it_matters": "Determines whether a claim concerns the gene, its expression or its product." }, { "name": "Reference sequence", "kind": "relation", "unit_or_values": "Accession with version; genome assembly when coordinates are used", "why_it_matters": "Makes sequence comparisons and variant positions interpretable." }, { "name": "Isoform assignment", "kind": "state", "unit_or_values": "Resolved to accession | multiple compatible isoforms | unresolved", "why_it_matters": "Prevents measurements shared by several isoforms from being assigned to one." }, { "name": "Expression abundance", "kind": "measurement", "unit_or_values": "RNA or protein abundance in explicitly reported assay units, with normalization and biological context", "why_it_matters": "Separates transcript abundance from protein abundance and functional activity." }, { "name": "Protein processing state", "kind": "state", "unit_or_values": "Precursor detected | specified fragments detected | mixed | unresolved", "why_it_matters": "Records observed molecular forms without assuming that processing proves activity." }, { "name": "Attributed proteolytic activity", "kind": "measurement", "unit_or_values": "Substrate conversion rate in reported units, with substrate, conditions and specificity controls", "why_it_matters": "Supports evaluation of whether measured cleavage is attributable to caspase-2." }, { "name": "Perturbation relationship", "kind": "relation", "unit_or_values": "Targeted allele, transcript or protein linked to intervention and matched controls", "why_it_matters": "Connects observed effects to the molecular entity actually altered." } ], "affordances": [ "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." ], "agent_conduct": { "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." ], "must_not": [ "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." ], "requires_human": [ "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." ], "affected_parties": [ "People with genetic test results", "Patients", "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": [ "Confusion between caspase family members in reports.", "Overinterpretation of variant associations." ], "standards_and_regulation": [ "Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol." ], "what_it_is_for": [ "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": [ { "id": "wikidata", "title": "Wikidata item Q14913269: CASP2", "url": "https://www.wikidata.org/wiki/Q14913269", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Caspase 2", "url": "https://en.wikipedia.org/wiki/Caspase_2", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "casp2-identity-and-boundary", "name": "CASP2 identity and boundary", "description": "Establish what the registry name denotes before attaching molecular observations.", "rationale": "The registry supplies neither a definition nor a species, and CASP2 naming can blur gene and protein identity.", "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?", "kind": "definition", "id": "human-gene-anchor-q01" }, { "text": "Which original identifier and source support mapping vr.tr.casp2 to this reference?", "kind": "provenance", "id": "human-gene-anchor-q02" } ] } ] }, { "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?", "kind": "boundary", "id": "gene-product-and-ortholog-separation-q01" }, { "text": "Does the catalogue already contain the same molecular concept under caspase-2 or another identifier?", "kind": "boundary", "id": "gene-product-and-ortholog-separation-q02" } ] } ] } ] }, { "id": "casp2-sequences-and-products", "name": "CASP2 sequences and products", "description": "Represent the sequence distinctions needed to interpret CASP2 observations.", "rationale": "Transcript variation and experimental sequence changes can alter what a CASP2-labelled result actually describes.", "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?", "kind": "definition", "id": "isoform-resolution-q01" }, { "text": "Can the primers, reads or detected peptides distinguish that isoform from other CASP2 products?", "kind": "measurement", "id": "isoform-resolution-q02" } ] } ] }, { "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?", "kind": "definition", "id": "sequence-change-attribution-q01" }, { "text": "What sequence verification supports the reported allele or construct identity?", "kind": "provenance", "id": "sequence-change-attribution-q02" } ] } ] } ] }, { "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.", "rationale": "RNA abundance, protein detection and proteolytic activity answer different questions about CASP2.", "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?", "kind": "provenance", "id": "contextual-abundance-q01" }, { "text": "Does the result quantify total CASP2 RNA, a particular transcript or a defined protein form, and in what units?", "kind": "measurement", "id": "contextual-abundance-q02" } ] } ] }, { "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?", "kind": "measurement", "id": "activity-attribution-q01" }, { "text": "Which substrate, assay conditions and controls establish that the activity signal depends on caspase-2?", "kind": "measurement", "id": "activity-attribution-q02" }, { "text": "What additional evidence is needed before labelling this caspase-2 preparation active?", "kind": "action", "id": "activity-attribution-q03" } ] } ] } ] }, { "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.", "rationale": "A CASP2-associated phenotype does not by itself establish a direct substrate, mechanism or transferable biological role.", "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?", "kind": "measurement", "id": "casp2-dependent-phenotypes-q01" }, { "text": "Do independent perturbations or an appropriate CASP2 rescue support attribution of the phenotype?", "kind": "provenance", "id": "casp2-dependent-phenotypes-q02" }, { "text": "Which organism, cell state and experimental conditions bound the functional conclusion?", "kind": "boundary", "id": "casp2-dependent-phenotypes-q03" } ] } ] }, { "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?", "kind": "boundary", "id": "interaction-and-substrate-evidence-q01" }, { "text": "Which controls and independent observations support the proposed caspase-2 partner or substrate relationship?", "kind": "provenance", "id": "interaction-and-substrate-evidence-q02" }, { "text": "What experiment would distinguish a catalytic caspase-2 effect from another consequence of CASP2 perturbation?", "kind": "action", "id": "interaction-and-substrate-evidence-q03" } ] } ] } ] }, { "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 was supplied; this answer assumes CASP2 denotes the human gene. The registry's original record should be checked before accepting that interpretation.", "The batch's device-oriented context does not fit this interpretation and provides insufficient evidence to identify an alternative referent.", "This is recalled knowledge, with no sources consulted; specific biological effects depend on experimental context." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of CASP2 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 symbol", "value_or_pattern": "CASP2", "note": "Identifies the human gene; its protein product is called caspase-2." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of CASP2 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 apoptosis and cellular stress responses.", "Research on caspase activation through the PIDDosome protein complex." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of CASP2 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-2", "difference": "The protein encoded by CASP2, rather than the gene itself." }, { "name": "CASP3", "difference": "A distinct gene encoding caspase-3, an executioner caspase." }, { "name": "PIDDosome", "difference": "A multiprotein complex that recruits and activates caspase-2, rather than the CASP2 gene or its isolated protein product." } ], "questions": [ { "id": "evidence-neighbours-q01", "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?", "kind": "provenance" } ] } ] } ] } ] }, "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?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 12, "questions": 23 } }