{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:29:11Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 22.0, "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: 01a094ba-ee92-7123-9679-8d25c692cda0\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: CD38\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 registered", "usd": 0.0, "recall": true }, "codex": { "seconds": 78.6, "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: 01a094ba-ee9b-7c21-b911-a19c091f9f73\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: CD38\nRegistry id: vr.tr.cd38\nPlane / domain: PHY / PHY.OBJ\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext for th" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:56:30+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "visual_identification" ] }, "revisions": [ { "at": "2026-10-07T11:11:27+00:00", "engine": "codex", "fields": [ "agent_conduct", "definition", "distinguishing_features", "failure_modes_and_hazards", "in_scope", "out_of_scope", "owners", "purpose", "scope_statement", "visual_identification" ], "answering_review": "a7a98f437905958f364a45ed5e44999083778b8a974a2ef947c1ebbe52cf4c9e" } ], "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T12:16:28+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q14885119", "registryId": "vr.tr.cd38", "name": "CD38", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q14885119/", "model": { "registry_id": "vr.tr.cd38", "name": "CD38", "purpose": "Enable an agent to identify the human CD38 gene, distinguish its genomic variants and transcripts from its protein product, and report gene-related evidence with appropriate limits.", "definition": "CD38 is a human protein-coding gene whose encoded cell-surface glycoprotein metabolizes NAD-related substrates, contributes to calcium-signalling pathways and serves as a marker of several immune-cell populations.", "scope_statement": "This model owns CD38 as a protein-coding gene in Homo sapiens, including genomic identity, variants, regulation, transcripts and gene expression, with encoded protein functions represented as relationships.", "in_scope": [ "Human CD38 gene identity and reference genomic sequence are included.", "Genomic coordinates qualified by reference assembly are included.", "Gene variants and their evidence-supported annotations are included.", "Transcript models, transcriptional regulation and RNA expression are included.", "Relationships between the gene, its transcripts and its encoded protein are included." ], "out_of_scope": [ "The CD38 protein's molecular forms, localization and catalytic state as an independent entity are excluded.", "Whole-cell identity, immune activation and differentiation models are excluded.", "Complete NAD metabolism and calcium-signaling networks are excluded.", "Disease diagnosis, prognosis and treatment selection are excluded.", "Antibody, inhibitor and laboratory instrument models are excluded." ], "distinguishing_features": [ "Human CD38 gene identity is represented by NCBI Gene 952 and must be distinguished from the encoded protein.", "Genomic coordinates and variants require an explicit reference assembly or sequence accession.", "Transcript records describe RNA products of the gene rather than the genomic locus itself.", "Protein abundance, antibody staining and catalytic activity do not directly establish gene sequence or genotype.", "Genes named CD38 in other species are distinct from this human gene." ], "characteristics": [ { "name": "Molecular identity", "kind": "relation", "unit_or_values": "Species-qualified protein accession, sequence version and linked encoding gene", "why_it_matters": "Prevents conflating human CD38, orthologs and gene-level observations." }, { "name": "Protein form", "kind": "category", "unit_or_values": "Full-length native protein, soluble form, recombinant construct or sequence variant; modifications recorded", "why_it_matters": "Different forms can change accessibility and experimental interpretation." }, { "name": "Localization and catalytic-domain orientation", "kind": "state", "unit_or_values": "Compartment and membrane orientation, each measured, inferred or unknown", "why_it_matters": "Determines which substrates and binding reagents can reach CD38." }, { "name": "Cell-surface abundance", "kind": "measurement", "unit_or_values": "Calibrated molecules per cell, or explicitly instrument-dependent fluorescence units", "why_it_matters": "Supports comparisons only when calibration and cell-population definitions are compatible." }, { "name": "CD38-positive fraction", "kind": "measurement", "unit_or_values": "Percent of a defined cell population, with positivity threshold and controls", "why_it_matters": "Separates the prevalence of expression from expression intensity." }, { "name": "Reaction-specific activity", "kind": "measurement", "unit_or_values": "nmol product/min/mg CD38 or another explicitly normalized rate; substrate, product, pH and temperature required", "why_it_matters": "Separates protein detection from demonstrated catalytic function." }, { "name": "Binding-reagent occupancy", "kind": "measurement", "unit_or_values": "Percent occupied binding sites, with reagent identity and measurement method", "why_it_matters": "Helps interpret target engagement and possible interference with detection." }, { "name": "Experimental attribution", "kind": "category", "unit_or_values": "Direct molecular measurement, controlled perturbation, association or unresolved", "why_it_matters": "Prevents attributing an entire cellular response to CD38 from correlation alone." } ], "affordances": [ "Identify a protein observation as CD38 using species-qualified molecular evidence.", "Measure CD38 abundance within a defined cell population using validated detection controls.", "Determine whether a substrate or binding reagent can access the observed CD38 form.", "Compare CD38 reaction rates under matched substrate and environmental conditions.", "Evaluate experimental CD38 binding or inhibition while checking assay interference.", "Link CD38 observations to cell-state or pathway models with explicit limits on causal attribution." ], "agent_conduct": { "may": [ "Describe the human CD38 gene and the functions of its encoded protein, citing sources.", "Report what a CD38 gene variant or RNA expression measurement shows, with method and limits." ], "must_not": [ "Interpret a person's CD38 test or flow cytometry result as a diagnosis.", "Recommend CD38-targeted treatment for a person.", "Share a person's laboratory results without consent.", "Present supplement claims about NAD levels and CD38 as proven." ], "requires_human": [ "Any clinical decision using CD38 results.", "Using patient samples in research without consent." ] }, "ethics": { "considerations": [ "Blood test results are private health data.", "Anti-ageing claims linked to CD38 exploit hopes without evidence." ], "affected_parties": [ "Patients", "Consumers of supplements", "Researchers" ] }, "owners": { "steward": "The person whose genome carries it has interests in associated samples and data; laboratories and biobanks steward the records.", "master_systems": [] }, "visual_identification": [ "The gene is identified through human genomic sequence records and reference identifiers.", "Antibody staining identifies the encoded protein rather than the gene." ], "failure_modes_and_hazards": [ "Confusing gene variants, RNA expression and protein marker measurements can mislead interpretation.", "Reference sequence or assembly mismatches can produce incorrect variant annotations." ], "standards_and_regulation": [ "Cluster of Differentiation nomenclature, Human Cell Differentiation Molecules (HCDM) organization." ], "what_it_is_for": [ "The human CD38 gene is encountered in genomic and gene expression studies of immune cells and their differentiation.", "Its identity connects DNA and transcript observations to research on the encoded cell-surface enzyme, while protein abundance and catalytic activity require separate measurements." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q14885119: CD38", "url": "https://www.wikidata.org/wiki/Q14885119", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: CD38", "url": "https://en.wikipedia.org/wiki/CD38", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "molecular-identity-and-form", "name": "Molecular identity and form", "description": "Establish which CD38 protein the observation concerns.", "rationale": "The registry has no definition, and CD38 can label a gene, a protein or a staining result.", "layers": [ { "id": "species-and-sequence", "name": "Species and sequence", "description": "Anchor CD38 identity to a species-qualified protein record.", "findings": [ { "id": "protein-reference", "name": "Protein reference", "description": "Human CD38 has a reviewed protein record at P28907; this is a provisional reference anchor rather than evidence that the registry excludes orthologs. [UniProt CD38](https://www.uniprot.org/uniprotkb/P28907/entry)", "questions": [ { "text": "Which species, protein accession and sequence version identify this CD38?", "kind": "definition", "id": "protein-reference-q01" }, { "text": "Does the evidence identify protein directly, or only its encoding gene or transcript?", "kind": "boundary", "id": "protein-reference-q02" } ] } ] }, { "id": "native-and-engineered-forms", "name": "Native and engineered forms", "description": "Specify the actual molecular form used or observed.", "findings": [ { "id": "construct-and-processing", "name": "Construct and processing", "description": "Record retained sequence, tags, substitutions and processing so an engineered preparation is not silently treated as native membrane CD38.", "questions": [ { "text": "Is this full-length CD38, a soluble preparation or a recombinant fragment?", "kind": "definition", "id": "construct-and-processing-q01" }, { "text": "Which sequence changes, tags and post-translational modifications were established experimentally?", "kind": "provenance", "id": "construct-and-processing-q02" } ] } ] } ] }, { "id": "topology-and-substrate-access", "name": "Topology and substrate access", "description": "Connect CD38 location to the molecules that can reach it.", "rationale": "A catalytic or binding claim requires access to the relevant CD38 domain.", "layers": [ { "id": "membrane-orientation", "name": "Membrane orientation", "description": "Describe the catalytic region relative to the membrane.", "findings": [ { "id": "type-ii-reference-topology", "name": "Type II reference topology", "description": "The conventional CD38 topology places its C-terminal region outside the cell and its N-terminal tail inside; observations must distinguish this reference arrangement from an experimentally established alternative. [NCBI CD38](https://www.ncbi.nlm.nih.gov/gene/952)", "questions": [ { "text": "Which side of the membrane contains the catalytic region in this preparation?", "kind": "measurement", "id": "type-ii-reference-topology-q01" }, { "text": "Was orientation measured directly or inferred from the reference protein?", "kind": "provenance", "id": "type-ii-reference-topology-q02" } ] } ] }, { "id": "compartment-and-accessibility", "name": "Compartment and accessibility", "description": "Track surface, intracellular and soluble observations separately.", "findings": [ { "id": "accessible-cd38-pool", "name": "Accessible CD38 pool", "description": "Distinguish the CD38 pool present in a sample from the pool accessible to a particular substrate, antibody or inhibitor.", "questions": [ { "text": "Which CD38 compartment does the assay actually sample?", "kind": "boundary", "id": "accessible-cd38-pool-q01" }, { "text": "Can the applied substrate or reagent reach that compartment under the recorded conditions?", "kind": "action", "id": "accessible-cd38-pool-q02" } ] } ] } ] }, { "id": "catalysis-and-product-attribution", "name": "Catalysis and product attribution", "description": "Describe CD38-dependent substrate conversion as measured reactions.", "rationale": "The CD38 name does not specify which catalytic output an assay measures.", "layers": [ { "id": "reaction-resolution", "name": "Reaction resolution", "description": "Separate substrates and products instead of recording undifferentiated enzyme activity.", "findings": [ { "id": "resolved-catalytic-output", "name": "Resolved catalytic output", "description": "CD38 supports multiple nucleotide-converting activities, including cADPR synthesis and hydrolysis and condition-dependent NAADP synthesis; each asserted reaction needs its own evidence. [UniProt CD38](https://www.uniprot.org/uniprotkb/P28907/entry)", "questions": [ { "text": "Which substrate-product pair is measured, and are cyclic and noncyclic products resolved?", "kind": "measurement", "id": "resolved-catalytic-output-q01" }, { "text": "Does the assay measure a native substrate reaction or turnover of a surrogate substrate?", "kind": "boundary", "id": "resolved-catalytic-output-q02" } ] } ] }, { "id": "assay-conditions-and-specificity", "name": "Assay conditions and specificity", "description": "Make activity measurements comparable and attributable.", "findings": [ { "id": "conditional-activity", "name": "Conditional activity", "description": "A CD38 activity record needs reaction conditions, normalization and controls that distinguish CD38 contribution from other sample activities.", "questions": [ { "text": "What pH, temperature, substrate concentration and normalization define the reported rate?", "kind": "measurement", "id": "conditional-activity-q01" }, { "text": "Which depletion, genetic or orthogonal biochemical control establishes the CD38-dependent contribution?", "kind": "provenance", "id": "conditional-activity-q02" } ] } ] } ] }, { "id": "expression-and-detection", "name": "Expression and detection", "description": "Represent CD38 expression as a population- and assay-dependent observation.", "rationale": "CD38 positivity requires a denominator, threshold and validated detection method.", "layers": [ { "id": "population-resolved-expression", "name": "Population-resolved expression", "description": "Locate expression measurements within defined cells and sampling conditions.", "findings": [ { "id": "abundance-versus-prevalence", "name": "Abundance versus prevalence", "description": "Record the fraction of CD38-positive cells separately from CD38 abundance per cell.", "questions": [ { "text": "Which independently defined cell population supplies the denominator for CD38 positivity?", "kind": "boundary", "id": "abundance-versus-prevalence-q01" }, { "text": "What are the positive fraction and per-cell signal distribution at the recorded sampling time?", "kind": "measurement", "id": "abundance-versus-prevalence-q02" } ] } ] }, { "id": "reagent-and-signal-validity", "name": "Reagent and signal validity", "description": "Establish whether the reported signal specifically measures accessible CD38.", "findings": [ { "id": "validated-cd38-detection", "name": "Validated CD38 detection", "description": "Record antibody clone or alternative identification method, species validation, preparation conditions and background controls.", "questions": [ { "text": "Which reagent and specificity controls support assignment of the signal to CD38?", "kind": "provenance", "id": "validated-cd38-detection-q01" }, { "text": "Could fixation, permeabilization or prior binding-reagent exposure alter the detected signal?", "kind": "measurement", "id": "validated-cd38-detection-q02" }, { "text": "What calibration and threshold make this result comparable with another sample?", "kind": "measurement", "id": "validated-cd38-detection-q03" } ] } ] } ] }, { "id": "perturbation-and-functional-interpretation", "name": "Perturbation and functional interpretation", "description": "Connect experimental interventions to demonstrated CD38 effects.", "rationale": "Binding, catalytic inhibition and downstream cellular responses are distinct outcomes.", "layers": [ { "id": "target-engagement", "name": "Target engagement", "description": "Specify what an intervention actually does to CD38.", "findings": [ { "id": "binding-versus-functional-change", "name": "Binding versus functional change", "description": "Measure reagent binding separately from changes in CD38 catalysis, abundance or localization.", "questions": [ { "text": "Does the intervention demonstrate CD38 binding, catalytic inhibition, altered localization or altered abundance?", "kind": "measurement", "id": "binding-versus-functional-change-q01" }, { "text": "Which dose, exposure time and controls support repeating this experimental perturbation?", "kind": "action", "id": "binding-versus-functional-change-q02" } ] } ] }, { "id": "downstream-attribution", "name": "Downstream attribution", "description": "Limit interpretation of metabolic and signaling responses to demonstrated evidence.", "findings": [ { "id": "cd38-dependent-response", "name": "CD38-dependent response", "description": "A change in calcium signaling or nucleotide pools needs independent attribution before being recorded as a CD38-caused effect.", "questions": [ { "text": "Which downstream response was measured alongside the CD38-specific change?", "kind": "measurement", "id": "cd38-dependent-response-q01" }, { "text": "What rescue or independent perturbation distinguishes CD38 dependence from reagent-specific effects?", "kind": "provenance", "id": "cd38-dependent-response-q02" }, { "text": "Which conclusions require a separate pathway, cell-state or disease model?", "kind": "boundary", "id": "cd38-dependent-response-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": [ "The name is interpreted as the biological CD38 protein; the supplied device-oriented batch context does not fit this interpretation.", "Sequence length and accession refer specifically to human CD38; species and protein forms should be checked before applying these details elsewhere.", "This is recalled knowledge without source consultation; apparent molecular mass depends on glycosylation and measurement conditions." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of CD38 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": "Cluster of differentiation nomenclature", "value_or_pattern": "CD38", "note": "Designation for the protein antigen; CD means cluster of differentiation." }, { "scheme": "HGNC gene symbol", "value_or_pattern": "CD38", "note": "Human gene encoding the protein; distinguish the gene from its protein product." }, { "scheme": "UniProtKB accession", "value_or_pattern": "P28907", "note": "Human CD38 protein." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of CD38 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": [ "Flow-cytometric immunophenotyping of immune cells, including plasma cells and activated lymphocytes.", "Therapeutic target of monoclonal antibodies such as daratumumab and isatuximab in multiple myeloma.", "Research on NAD metabolism, cyclic ADP-ribose production, and intracellular calcium signalling." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of CD38 this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Canonical human protein sequence length", "typical_range": "300", "unit": "amino-acid residues" }, { "quantity": "Apparent molecular mass of glycosylated protein", "typical_range": "approximately 45", "unit": "kDa" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of CD38 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": [ "CD38 expression is not specific to malignancy, so its detection alone does not establish a cancer diagnosis.", "Therapeutic anti-CD38 antibodies can interfere with some laboratory antibody-detection assays, including pretransfusion testing.", "Changes in CD38 expression or accessibility can complicate immunophenotyping during anti-CD38 treatment." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of CD38 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": "CD38 gene", "difference": "The gene is a DNA sequence encoding CD38; the described thing is its protein product." }, { "name": "CD157 / BST1", "difference": "A related cell-surface protein encoded by a different gene; CD157 is GPI-anchored, whereas canonical CD38 spans the membrane." }, { "name": "Anti-CD38 antibody", "difference": "An antibody binds CD38 as its target and is not the CD38 protein itself." }, { "name": "CD138 / syndecan-1", "difference": "A distinct cell-surface proteoglycan also used in plasma-cell identification, rather than an NAD-metabolizing enzyme." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of CD38 this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does vr.tr.cd38 designate human CD38 specifically, a cross-species protein kind, or a gene/protein concept requiring registry clarification?", "Which native soluble forms, sequence variants and alternative membrane orientations need explicit representation for the intended use cases?", "Which physiological compartments and assay conditions establish the relative contributions of CD38 to NAD turnover, cADPR metabolism and NAADP formation?", "Which detection reagents and calibration procedures support comparable CD38 abundance measurements across species, preparations and prior reagent exposures?", "Which context-specific signaling or adhesion relationships have sufficient direct evidence to add beyond the catalytic and detection capabilities modeled here?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 16, "questions": 28 } }