{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:57:10Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 22.8, "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: 01a094d4-8f4c-7952-935f-8b5060d4f3ee\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: CX3CL1\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 register", "usd": 0.0, "recall": true }, "codex": { "seconds": 78.0, "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: 01a094d4-8f54-7ee2-9697-c373aa45a307\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: CX3CL1\nRegistry id: vr.tr.cx3cl1\nPlane / domain: PHY / PHY.OBJ\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext fo" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:57:13+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", "in_scope", "out_of_scope", "owners", "purpose", "scope_statement", "visual_identification" ], "answering_review": "eb2df3143b1e502b10ace0aca6e7ed7f0192fe55ff4b7be57faee2af7a11cb49" } ], "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-Q14907780", "registryId": "vr.tr.cx3cl1", "name": "CX3CL1", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q14907780/", "model": { "registry_id": "vr.tr.cx3cl1", "name": "CX3CL1", "purpose": "Enable an agent to identify the human CX3CL1 gene, assess evidence about its variants and expression, and distinguish gene and transcript observations from measurements of its protein product.", "definition": "CX3CL1 is a human protein-coding gene that encodes fractalkine, a chemokine whose membrane-bound and soluble forms act through CX3CR1 to regulate leukocyte adhesion and migration.", "scope_statement": "This model owns CX3CL1 as a protein-coding gene in Homo sapiens, including genomic identity, variants, regulation, transcripts and gene expression, with fractalkine functions represented as relationships to its encoded product.", "in_scope": [ "Human CX3CL1 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 chemokine are included." ], "out_of_scope": [ "The CX3CL1 protein's membrane-associated, soluble and engineered forms as independent molecular entities are excluded.", "The CX3CR1 gene and receptor as independent entities are excluded.", "Complete models of CX3CL1-producing or responding cell types are excluded.", "Disease mechanisms, diagnostic criteria and treatment recommendations are excluded.", "Antibodies, inhibitors and assay platforms as independent entities are excluded." ], "distinguishing_features": [ "Identity requires a human gene reference record or genomic sequence evidence specific to CX3CL1.", "CX3CL1 encodes a ligand and is distinct from CX3CR1, which encodes its receptor.", "Genomic coordinates and variants require an explicit reference assembly or sequence accession.", "RNA expression measurements describe transcriptional output rather than directly establishing protein abundance or activity.", "Membrane-bound and soluble fractalkine are protein forms rather than separate gene identities." ], "characteristics": [ { "name": "Molecular reference", "kind": "relation", "unit_or_values": "Species, protein accession with version, sequence and relationship to the encoding gene", "why_it_matters": "Resolves gene-versus-protein ambiguity and prevents silent mixing of orthologues." }, { "name": "Physical form", "kind": "category", "unit_or_values": "Membrane-associated protein; released soluble form; isolated chemokine domain; engineered fusion; unresolved", "why_it_matters": "Determines which localization and functional comparisons are meaningful." }, { "name": "Sequence coverage", "kind": "measurement", "unit_or_values": "Residue interval against a named reference; length in amino acids", "why_it_matters": "Distinguishes full-length material from fragments with different retained domains." }, { "name": "Processing and modification status", "kind": "state", "unit_or_values": "Observed termini, cleavage evidence, glycosylation evidence and unresolved modifications", "why_it_matters": "Helps interpret molecular heterogeneity and differences between endogenous and recombinant material." }, { "name": "Observed molecular mass", "kind": "measurement", "unit_or_values": "kDa, with analytical method and molecular form", "why_it_matters": "Supports identity and integrity assessment without treating apparent gel mass as a universal constant." }, { "name": "Abundance and presentation", "kind": "measurement", "unit_or_values": "Soluble concentration in pg/mL or nM; calibrated surface molecules/cell; assay-relative surface signal", "why_it_matters": "Separates soluble exposure from cell-surface presentation and preserves measurement comparability." }, { "name": "CX3CR1 interaction", "kind": "relation", "unit_or_values": "Receptor species, binding method, measured affinity where available and specificity controls", "why_it_matters": "Connects material identity to receptor recognition without assuming downstream activity." }, { "name": "Functional response", "kind": "measurement", "unit_or_values": "Assay-defined adhesion, migration or signaling response with dose, time and controls", "why_it_matters": "Establishes what the particular molecular form actually does in the tested system." }, { "name": "Preparation suitability", "kind": "state", "unit_or_values": "Purity, aggregation, endotoxin result, storage history and acceptance against experiment-specific criteria", "why_it_matters": "Supports a defensible decision about whether observed responses can be attributed to CX3CL1." } ], "affordances": [ "Resolve a CX3CL1-labelled record to a species-specific protein and molecular form.", "Select detection methods that distinguish soluble CX3CL1 from surface-associated material.", "Compare preparations after reconciling sequence coverage, modifications and concentration basis.", "Design controlled CX3CR1 binding, adhesion or chemotaxis measurements.", "Evaluate whether cleavage, degradation or sample handling explains an observed change.", "Accept, qualify or reject a preparation for a stated experiment using documented criteria." ], "agent_conduct": { "may": [ "Describe the human CX3CL1 gene and the membrane-bound and soluble forms of its encoded protein, citing sources.", "Report what a gene variant or RNA expression measurement shows, with method and limits." ], "must_not": [ "Interpret a person's CX3CL1 level as a diagnosis.", "Share test or genetic results without consent.", "Recommend treatments targeting it to a person.", "Confuse the ligand with its receptor in reports." ], "requires_human": [ "Using results in clinical decisions.", "Research on patient samples without documented consent." ] }, "ethics": { "considerations": [ "Inflammation markers are often overinterpreted in commercial testing.", "Lab results are private health data." ], "affected_parties": [ "Patients", "Consumers of commercial tests", "Researchers" ] }, "owners": { "steward": "The person whose genome carries it has interests in associated samples and data; laboratories and biobanks steward the records.", "master_systems": [ "Gene and variant databases hold relevant reference records." ] }, "visual_identification": [ "The gene is identified through human genomic sequence records and reference identifiers.", "Immunoassays and antibody staining detect its protein product rather than the gene.", "Images of protein localization do not establish genomic variants." ], "failure_modes_and_hazards": [ "Overinterpretation of marker levels.", "Confusion between ligand and receptor." ], "standards_and_regulation": [ "Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol." ], "what_it_is_for": [ "The human CX3CL1 gene is encountered in studies of immune cell recruitment, vascular inflammation and communication between cells in nervous tissue.", "Its expression is studied as a contributor to production of fractalkine, while distinguishing membrane-associated and soluble protein requires additional measurements." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q14907780: CX3CL1", "url": "https://www.wikidata.org/wiki/Q14907780", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: CX3CL1", "url": "https://en.wikipedia.org/wiki/CX3CL1", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "cx3cl1-identity", "name": "CX3CL1 identity and registry boundary", "description": "Resolve what the CX3CL1 label denotes before attaching molecular or functional observations.", "rationale": "The same symbol can label a gene, its transcript measurement or protein material.", "layers": [ { "id": "protein-versus-gene", "name": "Protein versus gene", "description": "Separate the modelled protein from the genetic entity that encodes it.", "findings": [ { "id": "fractalkine-reference", "name": "Fractalkine reference identity", "description": "Human CX3CL1 encodes fractalkine; the registry's intended molecular level needs confirmation. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/6376/)", "questions": [ { "text": "Does the originating registry record identify CX3CL1 protein, the encoding gene or an unresolved combination?", "kind": "boundary", "id": "fractalkine-reference-q01" }, { "text": "Which protein accession and sequence substantiate the identity of the material being modelled?", "kind": "provenance", "id": "fractalkine-reference-q02" } ] } ] }, { "id": "orthologue-and-construct", "name": "Orthologue and construct", "description": "Track species and engineered sequence changes within the existing registry entry.", "findings": [ { "id": "sequence-equivalence", "name": "Sequence equivalence", "description": "Make comparisons conditional on a declared species, residue interval and engineered additions.", "questions": [ { "text": "Which organism and reference sequence define this CX3CL1 material?", "kind": "definition", "id": "sequence-equivalence-q01" }, { "text": "Which truncations, substitutions, tags or fusion partners distinguish it from that reference?", "kind": "boundary", "id": "sequence-equivalence-q02" } ] } ] } ] }, { "id": "cx3cl1-architecture", "name": "CX3CL1 architecture and molecular form", "description": "Describe the domains and processing state that determine how CX3CL1 is physically presented.", "rationale": "A chemokine-domain reagent and membrane-associated CX3CL1 cannot be treated as the same experimental object.", "layers": [ { "id": "domain-coverage", "name": "Domain coverage", "description": "Identify retained structural regions rather than relying on a product name.", "findings": [ { "id": "chemokine-stalk-anchor", "name": "Chemokine, stalk and anchor", "description": "CX3CL1 has a chemokine domain and mucin-like stalk and occurs in membrane-anchored and soluble forms. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/6376/)", "questions": [ { "text": "Which chemokine-domain, stalk, membrane-anchor and intracellular regions are present in this sequence?", "kind": "definition", "id": "chemokine-stalk-anchor-q01" }, { "text": "What evidence distinguishes full-length membrane-associated material from a soluble ectodomain or isolated chemokine domain?", "kind": "measurement", "id": "chemokine-stalk-anchor-q02" } ] } ] }, { "id": "cleavage-and-modification", "name": "Cleavage and modification", "description": "Resolve molecular heterogeneity relevant to presentation and assay interpretation.", "findings": [ { "id": "observed-proteoform", "name": "Observed proteoform", "description": "Record experimentally supported termini and modifications, separating them from predictions.", "questions": [ { "text": "Which cleavage termini and glycosylation features have been measured for this CX3CL1 material?", "kind": "measurement", "id": "observed-proteoform-q01" }, { "text": "Does a mass or band-pattern difference reflect expected processing, an engineered construct or degradation?", "kind": "boundary", "id": "observed-proteoform-q02" } ] } ] } ] }, { "id": "cx3cl1-presentation", "name": "CX3CL1 localization and release", "description": "Connect the protein's measured location with its source and changes over time.", "rationale": "Surface-associated abundance and soluble abundance answer different biological questions.", "layers": [ { "id": "surface-and-fluid-compartments", "name": "Surface and fluid compartments", "description": "Locate the measured protein within a defined biological or experimental compartment.", "findings": [ { "id": "compartment-specific-abundance", "name": "Compartment-specific abundance", "description": "Keep surface measurements, intracellular measurements and soluble concentrations distinguishable.", "questions": [ { "text": "Was CX3CL1 measured on a cell surface, inside cells, in tissue extract or in a specified fluid?", "kind": "measurement", "id": "compartment-specific-abundance-q01" }, { "text": "Which cells, tissue, collection method and sampling time establish the measurement's origin?", "kind": "provenance", "id": "compartment-specific-abundance-q02" } ] } ] }, { "id": "release-dynamics", "name": "Release dynamics", "description": "Evaluate transitions between surface-associated and soluble material.", "findings": [ { "id": "supported-release-mechanism", "name": "Supported release mechanism", "description": "Cell-surface cleavage can generate soluble CX3CL1; attribution of a particular change requires evidence from the system studied. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/6376/)", "questions": [ { "text": "What paired surface and soluble measurements support release rather than altered production or cell damage?", "kind": "measurement", "id": "supported-release-mechanism-q01" }, { "text": "Which perturbation and controls would test the proposed cleavage mechanism in this system?", "kind": "action", "id": "supported-release-mechanism-q02" } ] } ] } ] }, { "id": "cx3cl1-receptor-function", "name": "CX3CR1 interaction and functional evidence", "description": "Separate ligand recognition from measured cellular outcomes.", "rationale": "Binding, adhesion and migration are distinct claims requiring different observations.", "layers": [ { "id": "receptor-recognition", "name": "Receptor recognition", "description": "Establish the receptor and experimental basis of a CX3CL1 interaction.", "findings": [ { "id": "cx3cr1-binding-evidence", "name": "CX3CR1 binding evidence", "description": "CX3CL1 interacts with CX3CR1; a preparation's binding performance still requires assay-specific evidence. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/6376/)", "questions": [ { "text": "Which CX3CR1 species and expression context were used to measure binding of this CX3CL1 form?", "kind": "provenance", "id": "cx3cr1-binding-evidence-q01" }, { "text": "What competition, receptor-negative or receptor-blocking controls establish specificity?", "kind": "measurement", "id": "cx3cr1-binding-evidence-q02" } ] } ] }, { "id": "adhesion-and-migration", "name": "Adhesion and migration", "description": "Interpret functional outcomes against ligand presentation and responding-cell context.", "findings": [ { "id": "presentation-matched-function", "name": "Presentation-matched function", "description": "Membrane-associated CX3CL1 supports adhesion, while soluble CX3CL1 can act as a chemoattractant; test the actual form and context. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/6376/)", "questions": [ { "text": "Does the assay measure adhesion, directional migration or a signaling readout, and under which dose and timing conditions?", "kind": "measurement", "id": "presentation-matched-function-q01" }, { "text": "Which controls distinguish CX3CR1-dependent activity from nonspecific adhesion, random motility or contaminants?", "kind": "action", "id": "presentation-matched-function-q02" } ] } ] } ] }, { "id": "cx3cl1-assay-readiness", "name": "CX3CL1 measurement and preparation readiness", "description": "Determine whether detection results and prepared material support the intended experimental decision.", "rationale": "Detectable CX3CL1 abundance does not by itself establish intact structure or usable biological activity.", "layers": [ { "id": "detection-selectivity", "name": "Detection selectivity", "description": "Define which CX3CL1 forms a measurement can actually detect.", "findings": [ { "id": "epitope-and-calibration", "name": "Epitope and calibration compatibility", "description": "Assess recognition and calibration against the sample's species, sequence coverage and molecular form.", "questions": [ { "text": "Which CX3CL1 region does the detection reagent recognize, and is that region retained in the sample?", "kind": "definition", "id": "epitope-and-calibration-q01" }, { "text": "Do calibration material, sample matrix and recovery checks support comparison of the reported concentrations?", "kind": "measurement", "id": "epitope-and-calibration-q02" } ] } ] }, { "id": "functional-preparation-quality", "name": "Functional preparation quality", "description": "Assess confounders and handling effects before using CX3CL1 in cellular experiments.", "findings": [ { "id": "use-specific-acceptance", "name": "Use-specific acceptance", "description": "Base preparation acceptance on documented integrity, contamination and activity criteria for the intended assay.", "questions": [ { "text": "What lot-specific evidence covers CX3CL1 purity, aggregation, endotoxin and retained activity after storage?", "kind": "provenance", "id": "use-specific-acceptance-q01" }, { "text": "Should this preparation be used, recharacterized or replaced for the proposed receptor or cellular assay?", "kind": "action", "id": "use-specific-acceptance-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": [ "No sense or species was supplied; this description treats the registered thing as the protein, with identifiers and sequence length specific to humans.", "Protein processing and glycosylation affect molecular mass; soluble concentrations depend on specimen, assay and biological condition.", "This is recall-based information, not a source-reviewed account; disease-specific and therapeutic claims require verification." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of CX3CL1 this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Membrane-bound CX3CL1", "Soluble CX3CL1" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of CX3CL1 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": "CX3CL1", "note": "Approved human gene symbol; the same designation commonly denotes its protein product." }, { "scheme": "NCBI Gene", "value_or_pattern": "6376", "note": "Human CX3CL1 gene." }, { "scheme": "UniProtKB accession", "value_or_pattern": "P78423", "note": "Human CX3CL1 protein." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of CX3CL1 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 leukocyte recruitment and vascular inflammation.", "Research on communication between neurons and microglia.", "Measurement in biological samples as an investigational marker of inflammation.", "Experimental study of CX3CL1-CX3CR1 signaling as a therapeutic target." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of CX3CL1 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 precursor length", "typical_range": "397", "unit": "amino acid residues" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of CX3CL1 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": [ "Dysregulated signaling can contribute to inflammatory leukocyte recruitment and tissue injury, depending on biological context.", "Blocking the pathway can also disrupt protective immune or neural functions; its effects are context dependent.", "Assays that do not distinguish soluble from membrane-bound CX3CL1 can support misleading biological interpretations." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of CX3CL1 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": "CX3CR1", "difference": "CX3CR1 is the receptor; CX3CL1 is its chemokine ligand." }, { "name": "CXCL16", "difference": "CXCL16 is another chemokine with membrane-bound and soluble forms, but belongs to the CXC family and signals through CXCR6." }, { "name": "CX3CL1 gene", "difference": "The gene is the DNA sequence encoding CX3CL1; the protein is the adhesion and signaling molecule described here." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of CX3CL1 this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the originating registry identifier denote human CX3CL1 protein, a species-independent protein concept or the gene?", "Which existing Vercy model, if any, already owns this concept and should receive the registry link?", "Which native cleavage products and responsible proteases are experimentally established in each intended biological context?", "How do species, glycosylation, construct boundaries and tags affect equivalence between recombinant material and endogenous CX3CL1?", "Which assays and reference preparations support comparable measurements of soluble abundance, surface presentation and biological activity?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 17, "questions": 27 } }