{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:37:06Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 16.3, "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: 01a09566-f3be-7f63-a4c3-5cf798051e2e\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: NOD1\nSense to describe: (none recorded)\nDomain code: PHY.OBJ\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 044: 1001 registered", "usd": 0.0, "recall": true }, "codex": { "seconds": 78.8, "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: 01a09566-f3ca-7cf0-b432-7de144e71f2a\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: NOD1\nRegistry id: vr.tr.nod1\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": "2026-10-06T08:49:25+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation" ] }, "revisions": [ { "at": "2026-10-07T11:16:32+00:00", "engine": "codex", "fields": [ "definition", "distinguishing_features", "in_scope", "out_of_scope", "purpose", "scope_statement" ], "answering_review": "841170197e65ad42227af2e0ea1dd6e4603c8ee2d527401b4d02c5e4a3d12127" } ], "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T12:16:29+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q18035347", "registryId": "vr.tr.nod1", "name": "NOD1", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q18035347/", "model": { "registry_id": "vr.tr.nod1", "name": "NOD1", "purpose": "Enable an agent to identify the human NOD1 gene, interpret evidence about its sequence variants, transcripts and expression, and distinguish gene-level findings from functions and states of its encoded protein.", "definition": "NOD1 is a protein-coding gene in Homo sapiens that encodes an intracellular innate immune receptor involved in detecting bacterial peptidoglycan fragments and activating inflammatory signalling through RIPK2.", "scope_statement": "This model owns the human NOD1 protein-coding gene, including its genomic identity, sequence variation, transcriptional regulation, transcripts and expression; protein structure, ligand recognition and signalling are included only as relationships to its encoded product.", "in_scope": [ "Human NOD1 gene identity, reference records and genomic locus are included.", "Gene sequence variants and their evidence-supported consequences are included.", "Transcriptional regulation, transcripts and gene expression are included.", "Relationships between the gene, its transcripts and encoded protein are included.", "Evidence linking NOD1 variation or expression to cellular functions is included with explicit uncertainty.", "Reference sequence provenance and the distinction between gene-level and protein-level measurements are included." ], "out_of_scope": [ "NOD1 protein preparations, localization and activation states are outside scope as independently modelled entities.", "NOD1 genes in other species are outside scope except for explicit comparative relationships.", "NOD2 and other genes are outside scope beyond identification and specificity comparisons.", "Peptidoglycan ligands and inhibitors are outside scope as independently characterized chemical substances.", "Whole pathogens and host infection processes are outside scope.", "Complete downstream inflammatory networks are outside scope.", "Patient diagnosis, disease causation and treatment selection are outside scope." ], "distinguishing_features": [ "The entity is the Homo sapiens protein-coding gene identified by NCBI Gene 10392; UniProt Q9Y239 identifies its encoded protein rather than the gene itself.", "A gene-level identification requires a human genomic reference or curated gene record; a protein name or immune response alone is insufficient.", "Genomic variants, transcript variants and protein variants must be distinguished and linked to their respective reference records.", "CARD, nucleotide-binding and leucine-rich-repeat regions describe the encoded protein and do not define the gene as a receptor.", "Recognition of peptidoglycan fragments and signalling through RIPK2 are functions associated with the encoded protein, while attribution to gene variation or expression requires supporting evidence.", "NOD1 must be distinguished from NOD2 and from NOD1 counterparts in other species." ], "characteristics": [ { "name": "Reference identity", "kind": "relation", "unit_or_values": "Protein accession and version, linked gene identifier, organism and taxonomy identifier", "why_it_matters": "Prevents conflating the protein with its gene or another species' ortholog." }, { "name": "Molecular form", "kind": "category", "unit_or_values": "Endogenous isoform, full-length recombinant protein, fragment, tagged construct or sequence variant", "why_it_matters": "Different forms may retain different NOD1 recognition and signaling functions." }, { "name": "Domain integrity", "kind": "state", "unit_or_values": "CARD, nucleotide-binding region and LRR region: intact, altered, absent or unverified", "why_it_matters": "Supports interpretation of changes in recruitment, nucleotide handling or ligand response." }, { "name": "Protein abundance", "kind": "measurement", "unit_or_values": "Molecules per cell, mol/L or explicitly normalized assay units", "why_it_matters": "Separates altered receptor quantity from altered activity per receptor." }, { "name": "Cellular distribution", "kind": "category", "unit_or_values": "Observed cellular compartments and membrane association, with cell type and method", "why_it_matters": "Places receptor availability and signaling observations in their cellular context." }, { "name": "Nucleotide occupancy", "kind": "state", "unit_or_values": "ATP-associated, ADP-associated, mixed, unoccupied or undetermined", "why_it_matters": "Allows nucleotide measurements to be evaluated separately from inferred activation." }, { "name": "Assembly state", "kind": "state", "unit_or_values": "Monomeric, oligomeric, aggregated, mixed or undetermined under stated conditions", "why_it_matters": "Distinguishes receptor assembly from nonspecific aggregation." }, { "name": "Ligand-response profile", "kind": "measurement", "unit_or_values": "Response versus ligand concentration in mol/L and exposure time; EC50 only when supported", "why_it_matters": "Makes potency comparisons conditional on ligand delivery and assay context." }, { "name": "RIPK2 coupling", "kind": "relation", "unit_or_values": "Interaction or dependency evidence linked to RIPK2 identity, assay and conditions", "why_it_matters": "Distinguishes partner association from successful downstream signaling." } ], "affordances": [ "Resolve an observed sequence or reagent to a NOD1 species, isoform and construct.", "Assess whether a NOD1 preparation retains the regions required for a proposed experiment.", "Compare ligand responses while accounting for delivery, abundance and cellular context.", "Select measurements that distinguish NOD1 presence, assembly and downstream activity.", "Evaluate NOD1 perturbations using receptor-specific controls and rescue evidence.", "Flag conclusions that exceed the evidence for NOD1-specific signaling." ], "agent_conduct": { "may": [ "Describe NOD1 and its role in sensing bacterial cell wall fragments from curated sources.", "Report the evidence behind a claim, such as a database record or published assay." ], "must_not": [ "Present research findings on NOD1 as an approved diagnosis or treatment for inflammatory disease.", "Share a person's genetic data about NOD1 without consent.", "Confuse NOD1 with NOD2 or other receptors in a report.", "Invent results or citations to support a claim." ], "requires_human": [ "Returning a genetic finding about immune function to a patient." ] }, "ethics": { "considerations": [ "Overstated links between immune genes and disease can mislead patients.", "Genetic data identifies a person and their relatives." ], "affected_parties": [ "Patients with inflammatory conditions", "Research participants", "Researchers" ] }, "owners": { "steward": "Nobody owns the gene or receptor; curated gene and protein databases keep its reference records.", "master_systems": [ "HGNC gene symbol registry", "Protein sequence databases" ] }, "failure_modes_and_hazards": [ "Misannotation between related receptors propagates errors into later research.", "Overinterpreted variant links can lead to wrong clinical expectations." ], "standards_and_regulation": [ "HGNC guidelines for human gene nomenclature, HUGO Gene Nomenclature Committee." ], "what_it_is_for": [ "The human NOD1 gene is studied in genetics and immunology to understand how cells detect bacterial components and initiate inflammatory signalling.", "Its sequence, variants and expression are examined in research on innate immunity and host responses to infection." ], "facets_not_applicable": { "recognition": "The human NOD1 gene has no distinctive visual appearance and is identified through sequence evidence and genomic annotation." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q18035347: NOD1", "url": "https://www.wikidata.org/wiki/Q18035347", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: NOD1", "url": "https://en.wikipedia.org/wiki/NOD1", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "nod1-identity", "name": "NOD1 identity and reference boundary", "description": "Establish which molecular entity the registry name and each observation denote.", "rationale": "NOD1 names both a gene and its protein product, and an unspecified species leaves sequence-based judgments ambiguous.", "layers": [ { "id": "registry-referent", "name": "Registry referent", "description": "Resolve the intended entity without creating a second registry thing.", "findings": [ { "id": "gene-protein-boundary", "name": "Gene versus protein boundary", "description": "Document why this entry is interpreted as a receptor protein and retain the encoding gene as a linked entity.", "questions": [ { "text": "Does the registry's originating identifier denote NOD1 protein, its gene or a combined gene-product concept?", "kind": "boundary", "id": "gene-protein-boundary-q01" }, { "text": "Which original registry or external record supports the chosen interpretation?", "kind": "provenance", "id": "gene-protein-boundary-q02" } ] } ] }, { "id": "sequence-reference", "name": "Species and molecular form", "description": "Anchor NOD1 observations to a specified sequence.", "findings": [ { "id": "ortholog-isoform-construct", "name": "Ortholog, isoform and construct", "description": "Record species, accession, isoform and experimental sequence changes before transferring functional expectations.", "questions": [ { "text": "Which organism, protein accession and sequence version identify this NOD1?", "kind": "definition", "id": "ortholog-isoform-construct-q01" }, { "text": "Which substitutions, deletions, tags or isoform differences separate the observed material from that reference?", "kind": "measurement", "id": "ortholog-isoform-construct-q02" } ] } ] } ] }, { "id": "nod1-molecular-competence", "name": "Domain and assembly competence", "description": "Describe the molecular features needed to interpret NOD1 function.", "rationale": "An identifiable NOD1 fragment or damaged preparation need not retain the capabilities of the intact receptor.", "layers": [ { "id": "functional-regions", "name": "Functional regions", "description": "Assess the CARD, nucleotide-binding region and LRR region in the selected molecular form.", "findings": [ { "id": "domain-retention", "name": "Domain retention and alteration", "description": "Associate each retained or altered region with the function actually tested.", "questions": [ { "text": "Are the CARD, nucleotide-binding region and LRR region present and intact in this NOD1 sequence?", "kind": "measurement", "id": "domain-retention-q01" }, { "text": "Which functional conclusions remain justified if a region is deleted or mutated?", "kind": "boundary", "id": "domain-retention-q02" } ] } ] }, { "id": "nucleotide-and-assembly", "name": "Nucleotide and assembly state", "description": "Separate nucleotide association, receptor assembly and nonspecific aggregation.", "findings": [ { "id": "assembly-evidence", "name": "Evidence for a competent molecular state", "description": "Record nucleotide and assembly observations without equating either automatically with activity.", "questions": [ { "text": "What assay establishes NOD1 nucleotide binding or occupancy under the reported conditions?", "kind": "measurement", "id": "assembly-evidence-q01" }, { "text": "What distinguishes the observed NOD1 oligomers from insoluble or nonspecific aggregates?", "kind": "measurement", "id": "assembly-evidence-q02" }, { "text": "What independent evidence links this molecular state to signaling competence?", "kind": "provenance", "id": "assembly-evidence-q03" } ] } ] } ] }, { "id": "nod1-ligand-recognition", "name": "Peptidoglycan recognition and access", "description": "Represent the stimulus chemistry and intracellular exposure behind a NOD1 response.", "rationale": "A nominal ligand dose does not establish receptor exposure, and different peptidoglycan fragments cannot be treated as interchangeable.", "layers": [ { "id": "stimulus-identity", "name": "Stimulus identity", "description": "Identify the exact peptidoglycan fragment or other proposed stimulus.", "findings": [ { "id": "dap-stimulus-specificity", "name": "Diaminopimelate stimulus specificity", "description": "Distinguish chemically defined NOD1 stimuli from mixed bacterial preparations and NOD2 comparator ligands.", "questions": [ { "text": "What exact chemical structure, stereochemistry and purity define the tested iE-DAP-containing stimulus?", "kind": "definition", "id": "dap-stimulus-specificity-q01" }, { "text": "Which controls distinguish NOD1-associated recognition from NOD2 responses or contaminating stimulants?", "kind": "measurement", "id": "dap-stimulus-specificity-q02" } ] } ] }, { "id": "intracellular-exposure", "name": "Intracellular exposure", "description": "Relate administered ligand to access and response in the tested cellular system.", "findings": [ { "id": "delivery-response-boundary", "name": "Delivery and response boundary", "description": "Keep extracellular dose, intracellular access and receptor recognition as separate observations.", "questions": [ { "text": "How was the stimulus delivered, and what supports its access to intracellular NOD1?", "kind": "provenance", "id": "delivery-response-boundary-q01" }, { "text": "How does the response vary with dose, exposure duration and delivery method?", "kind": "measurement", "id": "delivery-response-boundary-q02" }, { "text": "Does the experiment establish direct molecular binding or only NOD1-dependent cellular responsiveness?", "kind": "boundary", "id": "delivery-response-boundary-q03" } ] } ] } ] }, { "id": "nod1-cellular-signaling", "name": "Cellular availability and signal coupling", "description": "Connect receptor presence and partner availability to observed signaling.", "rationale": "NOD1 activity depends on cellular context, while downstream inflammatory readouts are shared with other receptors.", "layers": [ { "id": "receptor-context", "name": "Receptor context", "description": "Locate and quantify NOD1 in the relevant cells.", "findings": [ { "id": "abundance-localization", "name": "Abundance and localization", "description": "Distinguish measured NOD1 protein from transcript proxies and expression-system effects.", "questions": [ { "text": "What NOD1 protein abundance and distribution were measured in the specified cell type and condition?", "kind": "measurement", "id": "abundance-localization-q01" }, { "text": "Is the evidence from endogenous protein, overexpression or transcript abundance alone?", "kind": "provenance", "id": "abundance-localization-q02" } ] } ] }, { "id": "ripk2-and-output", "name": "RIPK2 coupling and downstream output", "description": "Separate partner recruitment from functional signal transmission.", "findings": [ { "id": "coupling-versus-output", "name": "Coupling versus output", "description": "Treat RIP2 association as a distinct observation from successful NOD1 signaling. [NOD1-RIP2 experimental study](https://pmc.ncbi.nlm.nih.gov/articles/PMC4132792/)", "questions": [ { "text": "What evidence demonstrates NOD1-RIPK2 association or RIPK2 dependence in this system?", "kind": "measurement", "id": "coupling-versus-output-q01" }, { "text": "Which downstream endpoint was measured, at what time, and relative to which baseline?", "kind": "measurement", "id": "coupling-versus-output-q02" }, { "text": "What establishes that the endpoint reflects NOD1 activity rather than another convergent pathway?", "kind": "boundary", "id": "coupling-versus-output-q03" } ] } ] } ] }, { "id": "nod1-experimental-decisions", "name": "Experimental attribution and material suitability", "description": "Support decisions about NOD1 reagents, perturbations and the conclusions they permit.", "rationale": "Reagent cross-reactivity, construct artifacts and shared signaling targets can produce misleading NOD1 assignments.", "layers": [ { "id": "reagent-fitness", "name": "Reagent fitness", "description": "Determine whether detection reagents and protein preparations support the intended NOD1 measurement.", "findings": [ { "id": "identity-and-integrity-controls", "name": "Identity and integrity controls", "description": "Record specificity evidence for detection and integrity evidence for functional material.", "questions": [ { "text": "How was the NOD1 antibody or detection reagent validated against NOD1-deficient material or an independent method?", "kind": "provenance", "id": "identity-and-integrity-controls-q01" }, { "text": "What confirms the preparation's NOD1 identity, full-length status, purity and retained activity?", "kind": "measurement", "id": "identity-and-integrity-controls-q02" }, { "text": "Which measurements remain valid if identity is established but functional integrity is uncertain?", "kind": "action", "id": "identity-and-integrity-controls-q03" } ] } ] }, { "id": "causal-perturbation", "name": "Causal perturbation", "description": "Evaluate experiments intended to change or isolate NOD1 function.", "findings": [ { "id": "nod1-specific-intervention", "name": "NOD1-specific intervention evidence", "description": "Require controls that distinguish changes to NOD1 from changes to delivery, viability or shared signaling machinery.", "questions": [ { "text": "Which loss-of-function and rescue comparisons support a causal contribution from NOD1?", "kind": "action", "id": "nod1-specific-intervention-q01" }, { "text": "Does the perturbation act on NOD1 itself, its expression, ligand delivery or a shared downstream component?", "kind": "boundary", "id": "nod1-specific-intervention-q02" }, { "text": "Which viability, expression and comparator-pathway controls are needed before interpreting the effect?", "kind": "action", "id": "nod1-specific-intervention-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 registry supplies neither a sense nor a species; this description assumes the NOD1 protein, with human gene nomenclature where specified.", "NOD1 is a biological receptor, not a device or tool; the batch's device-oriented guidance does not apply.", "This is recalled knowledge without source verification; species-specific properties and disease associations require research." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of NOD1 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": "NOD1", "note": "Approved human gene symbol; the same name commonly denotes its protein product." }, { "scheme": "Protein alias", "value_or_pattern": "CARD4", "note": "An established alternative name for NOD1." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of NOD1 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 intracellular recognition of bacterial peptidoglycan.", "Investigation of innate immune signalling, inflammation and host-microbe interactions.", "Experimental testing of NOD1 agonists and inhibitors." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of NOD1 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": [ "Impaired NOD1 signalling can weaken cellular responses to bacteria containing its recognised peptidoglycan motif.", "Excessive or inappropriate activation can contribute to inflammatory tissue injury." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of NOD1 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": "NOD1 gene", "difference": "The gene is the DNA sequence encoding the receptor; the receptor is its protein product." }, { "name": "NOD2", "difference": "NOD2 recognises muramyl dipeptide and has two N-terminal CARD domains; NOD1 recognises diaminopimelic-acid-containing peptidoglycan fragments and has one." }, { "name": "RIPK2", "difference": "RIPK2 is a downstream signalling kinase recruited by NOD1, rather than the peptidoglycan-sensing receptor." }, { "name": "iE-DAP", "difference": "iE-DAP is a minimal peptidoglycan-derived motif recognised by NOD1, rather than the receptor itself." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of NOD1 this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the originating registry record intend the human NOD1 protein, a species-independent protein concept or the NOD1 gene?", "Does an existing Vercy publication already own this concept and require this registry entry to link to it?", "Which isoforms and orthologs have sufficiently established functional differences to require explicit branches within this model?", "Which activation and assembly states can be measured reliably enough to support operational state assignments?", "Which reported ligand-binding mechanisms and non-peptidoglycan responses have direct evidence rather than pathway-level inference?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 15, "questions": 30 } }