{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:25:25Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 17.3, "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-aa56-7af1-8005-b925ad313dc0\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: CASP7\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": 66.2, "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-aa64-72a0-adb6-b859c8a1ecfa\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: CASP7\nRegistry id: vr.tr.casp7\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-Q17855901", "registryId": "vr.tr.casp7", "name": "CASP7", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q17855901/", "model": { "registry_id": "vr.tr.casp7", "name": "CASP7", "purpose": "Enable an agent to identify CASP7, distinguish its gene identity from its molecular products, and judge what expression, processing and activity evidence supports.", "definition": "CASP7 is the human gene encoding caspase-7, a cysteine protease that is synthesized as an inactive precursor and activated by proteolytic processing to cleave cellular proteins during apoptosis.", "scope_statement": "This draft provisionally treats vr.tr.casp7 as the CASP7 gene, with human CASP7 as the reference anchor, and owns its identity and relationships to transcripts and caspase-7 protein; the registry's intended species and gene-versus-protein boundary remain unresolved. Human CASP7 is a protein-coding gene according to [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/840/).", "in_scope": [ "Species-qualified CASP7 identity and reference accessions", "Genomic variants and their reference sequence context", "Relationships between CASP7 transcripts and encoded protein forms", "Evidence connecting CASP7 expression to caspase-7 processing and activity", "CASP7-specific attribution of experimental observations" ], "out_of_scope": [ "Other caspase genes as independently modelled entities", "The complete apoptosis pathway", "Whole-cell or organism state beyond its relevance to CASP7 observations", "Antibodies, inhibitors and assay kits as product models", "Disease diagnosis or treatment decisions", "The CASP7 protein-structure prediction assessment event, if encountered as a naming collision" ], "distinguishing_features": [ "Resolve the name against a species-qualified gene accession; human CASP7 maps to NCBI Gene 840.", "Distinguish a genomic CASP7 sequence from a transcript accession or caspase-7 protein accession before assigning observations.", "Require sequence or reagent specificity evidence to distinguish CASP7 from CASP3 and other caspases.", "Separate CASP7 expression, caspase-7 protein abundance, protein processing and measured catalytic activity.", "Reject records describing a protein-structure prediction assessment round unless the registry provenance establishes that meaning." ], "characteristics": [ { "name": "Entity interpretation", "kind": "category", "unit_or_values": "gene; transcript; protein; assessment event; unresolved", "why_it_matters": "CASP7 alone does not establish which entity an imported record describes." }, { "name": "Organism", "kind": "relation", "unit_or_values": "Taxonomy identifier and scientific name", "why_it_matters": "The symbol occurs in multiple species, whose records must remain distinguishable." }, { "name": "Reference identity", "kind": "relation", "unit_or_values": "Authority, accession, sequence version and genome assembly where applicable", "why_it_matters": "Provides a reproducible anchor for sequence and variant claims." }, { "name": "Sequence variation", "kind": "category", "unit_or_values": "Reference-qualified variant description; reference sequence; unresolved", "why_it_matters": "A reported alteration cannot be interpreted without its sequence context." }, { "name": "Transcript identity", "kind": "relation", "unit_or_values": "Versioned transcript accession linked to its encoded product", "why_it_matters": "Expression and sequence observations may apply to particular transcripts." }, { "name": "CASP7 transcript abundance", "kind": "measurement", "unit_or_values": "TPM, normalized counts or relative expression with method and normalization specified", "why_it_matters": "Supports expression comparisons without equating RNA abundance with enzyme activity." }, { "name": "Linked caspase-7 processing state", "kind": "state", "unit_or_values": "Precursor detected; processed forms detected; mixed; undetermined", "why_it_matters": "Records protein processing separately from gene identity and catalytic evidence." }, { "name": "CASP7-attributed catalytic activity", "kind": "measurement", "unit_or_values": "Substrate conversion per time, with substrate, normalization, conditions and specificity evidence", "why_it_matters": "Makes activity interpretable and exposes signals that cannot be assigned specifically to caspase-7." }, { "name": "Attribution strength", "kind": "category", "unit_or_values": "CASP7-specific evidence; shared caspase signal; indirect association; unresolved", "why_it_matters": "Prevents a broad assay result from becoming a CASP7-specific conclusion." } ], "affordances": [ "Resolve a CASP7-labelled record to its species and molecular entity.", "Link a sequence variant to the appropriate reference and affected transcript.", "Trace an expression observation to its sample, assay and normalization.", "Compare protein processing and activity observations without conflating them.", "Determine whether an experiment supports CASP7-specific attribution.", "Identify missing controls before accepting a claim about CASP7 function." ], "agent_conduct": { "may": [ "Describe CASP7 and caspase-7 as an executioner of apoptosis, citing sources.", "Report what an experimental result shows, with source and limits." ], "must_not": [ "Interpret a person's CASP7 variant as a diagnosis.", "Share genetic data without consent.", "Present apoptosis research as available treatment.", "Confuse caspase-7 with caspase-3 or other caspases in reports." ], "requires_human": [ "Using results in clinical decisions.", "Research on patient samples without documented consent." ] }, "ethics": { "considerations": [ "Gene findings can be overstated and cause needless worry.", "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 with caspase-3, which has overlapping activity.", "Overinterpretation of variant associations." ], "standards_and_regulation": [ "Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol." ], "what_it_is_for": [ "CASP7 is encountered in human genome databases and research on apoptosis and cellular responses to stress.", "Its sequence and expression are studied alongside measurements of caspase-7 processing and substrate cleavage to distinguish gene expression from enzyme activation." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q17855901: CASP7", "url": "https://www.wikidata.org/wiki/Q17855901", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Caspase 7", "url": "https://en.wikipedia.org/wiki/Caspase_7", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "casp7-identity", "name": "CASP7 identity", "description": "Resolve what CASP7 denotes in this registry and in incoming evidence.", "rationale": "An unresolved gene, protein or event interpretation would make every later observation ambiguous.", "layers": [ { "id": "registry-referent", "name": "Registry referent", "description": "Establish the entity intended by vr.tr.casp7.", "findings": [ { "id": "gene-protein-boundary", "name": "Gene and product boundary", "description": "The symbol is anchored provisionally to the gene; protein observations must identify the linked product rather than silently change the entry's meaning.", "questions": [ { "text": "Does the originating registry record identify a gene, a protein or the CASP7 assessment event?", "kind": "boundary", "id": "gene-protein-boundary-q01" }, { "text": "Which original identifier or description establishes that interpretation?", "kind": "provenance", "id": "gene-protein-boundary-q02" } ] } ] }, { "id": "species-and-accessions", "name": "Species and accessions", "description": "Separate species-specific identities and preserve authoritative cross-references.", "findings": [ { "id": "species-qualified-anchor", "name": "Species-qualified anchor", "description": "Human CASP7 provides a provisional reference, not evidence that every CASP7-labelled observation concerns humans.", "questions": [ { "text": "Which organism and gene accession does the registry entry intend?", "kind": "definition", "id": "species-qualified-anchor-q01" }, { "text": "Are records from another species ortholog relationships or observations of the same intended entity?", "kind": "boundary", "id": "species-qualified-anchor-q02" } ] } ] } ] }, { "id": "casp7-sequence-and-products", "name": "CASP7 sequence and products", "description": "Connect genomic identity, transcripts and encoded molecular forms.", "rationale": "Variant effects and expression claims depend on which sequence and product were examined.", "layers": [ { "id": "reference-and-variation", "name": "Reference and variation", "description": "Anchor CASP7 sequence differences to explicit references.", "findings": [ { "id": "reference-qualified-variant", "name": "Reference-qualified variant", "description": "A CASP7 variant record must preserve its reference sequence and distinguish predicted consequences from measured effects.", "questions": [ { "text": "Which assembly or versioned sequence defines the reported CASP7 position?", "kind": "provenance", "id": "reference-qualified-variant-q01" }, { "text": "Was the proposed effect on CASP7 expression or protein function predicted or experimentally measured?", "kind": "measurement", "id": "reference-qualified-variant-q02" } ] } ] }, { "id": "transcript-product-mapping", "name": "Transcript-to-product mapping", "description": "Maintain explicit links between observed RNA and encoded protein forms.", "findings": [ { "id": "resolved-transcript-product", "name": "Resolved transcript and product", "description": "Transcript-level evidence must specify whether the measurement distinguishes individual CASP7 transcripts or aggregates them.", "questions": [ { "text": "Which CASP7 transcript accession and encoded protein sequence are represented?", "kind": "definition", "id": "resolved-transcript-product-q01" }, { "text": "Can the primers, reads or other assay features distinguish that transcript from other CASP7 transcripts?", "kind": "measurement", "id": "resolved-transcript-product-q02" } ] } ] } ] }, { "id": "casp7-expression-and-processing", "name": "CASP7 expression and processing", "description": "Separate RNA abundance, protein detection and protein processing in a defined biological context.", "rationale": "These observations answer different questions and cannot substitute for one another.", "layers": [ { "id": "expression-context", "name": "Expression context", "description": "Interpret CASP7 abundance within the sampled system.", "findings": [ { "id": "contextualized-abundance", "name": "Contextualized abundance", "description": "A CASP7 abundance observation needs the biological sample, measured molecular species and normalization method.", "questions": [ { "text": "Which tissue, cell population, condition and time point produced the CASP7 measurement?", "kind": "provenance", "id": "contextualized-abundance-q01" }, { "text": "Does the result measure RNA or protein, and in what units relative to which reference?", "kind": "measurement", "id": "contextualized-abundance-q02" } ] } ] }, { "id": "protein-processing", "name": "Protein processing", "description": "Represent precursor and processed caspase-7 observations as properties of linked protein products.", "findings": [ { "id": "processing-evidence", "name": "Processing evidence", "description": "Detection of a processed form must retain the molecular evidence and remain distinct from a direct activity measurement.", "questions": [ { "text": "Which epitope, peptide or fragment identifies the detected caspase-7 form?", "kind": "measurement", "id": "processing-evidence-q01" }, { "text": "What additional evidence is needed before treating the processing observation as evidence of catalytic activity?", "kind": "action", "id": "processing-evidence-q02" } ] } ] } ] }, { "id": "casp7-function-and-attribution", "name": "CASP7 function and attribution", "description": "Assess whether activity and perturbation results support claims specifically about CASP7.", "rationale": "Shared caspase readouts and indirect cellular effects require explicit attribution before an agent can act on them.", "layers": [ { "id": "activity-specificity", "name": "Activity specificity", "description": "Examine what a catalytic assay measures and which enzyme it identifies.", "findings": [ { "id": "casp7-specific-readout", "name": "CASP7-specific readout", "description": "An assay label alone does not establish CASP7 specificity; substrate, controls and alternative contributors must be recorded.", "questions": [ { "text": "Which substrate, conditions and rate calculation define the reported activity?", "kind": "measurement", "id": "casp7-specific-readout-q01" }, { "text": "What evidence separates caspase-7 activity from caspase-3 or other contributors to the signal?", "kind": "boundary", "id": "casp7-specific-readout-q02" } ] } ] }, { "id": "perturbation-and-causality", "name": "Perturbation and causality", "description": "Connect CASP7-directed interventions to measured molecular and cellular outcomes.", "findings": [ { "id": "supported-functional-inference", "name": "Supported functional inference", "description": "A functional claim must distinguish verified CASP7 perturbation, associated outcomes and evidence supporting a causal link.", "questions": [ { "text": "How was the intended change to CASP7 verified independently of the downstream outcome?", "kind": "measurement", "id": "supported-functional-inference-q01" }, { "text": "Which rescue experiment or independent perturbation would address alternative explanations?", "kind": "action", "id": "supported-functional-inference-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 missing sense leaves the referent uncertain; this description assumes the human gene CASP7.", "The batch's device-oriented guidance does not fit the biological interpretation and should not determine its properties.", "Confirm the registry's originating identifier and organism before deciding whether this entry represents a gene or its protein product." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of CASP7 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": "CASP7", "note": "Human gene symbol; caspase-7 denotes the encoded protein." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of CASP7 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 executioner caspases and apoptotic cell death.", "Combined caspase-3/7 activity assays for monitoring apoptosis.", "Studies of cell responses to experimental anticancer treatments." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of CASP7 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": [ "Combined caspase-3/7 assays do not establish that measured activity specifically originates from caspase-7.", "CASP7 transcript abundance or total protein abundance alone does not establish protease activation." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of CASP7 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-7", "difference": "CASP7 names the gene; caspase-7 is its protein product." }, { "name": "CASP3", "difference": "A distinct gene encoding caspase-3, another executioner caspase with overlapping but nonidentical substrate preferences." }, { "name": "CASP9", "difference": "Encodes an initiator caspase associated with the apoptosome, rather than the executioner caspase encoded by CASP7." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of CASP7 this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry's original source identify CASP7 as a gene, caspase-7 protein or the protein-structure prediction assessment event?", "Is this entry human-specific, species-neutral or anchored to another organism?", "Does an existing Vercy model already own the intended CASP7 concept, requiring a link instead of a separate publication?", "Which reference sequences, transcripts and protein forms should be authoritative for the intended scope?", "Which assays and controls provide adequate CASP7-specific evidence, and which functional claims remain unresolved?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 13, "questions": 21 } }