{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T10:57:00Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 22.1, "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: 01a09541-f75e-7b03-bfb9-2d4093322862\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: leukocidin\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 044: 1001 regi", "usd": 0.0, "recall": true }, "codex": { "seconds": 97.4, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09541-f769-70a0-9a74-7c8befb982b6\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: leukocidin\nRegistry id: vr.tr.leukocidin\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nCo" } } }, "metaModel": { "id": "THING-Q16889545", "registryId": "vr.tr.leukocidin", "name": "leukocidin", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q16889545/", "model": { "registry_id": "vr.tr.leukocidin", "name": "leukocidin", "purpose": "Enable an agent to identify a leukocidin, assess its molecular and biological state, and determine whether evidence supports a proposed interpretation or use.", "definition": "A leukocidin is a bacterial protein exotoxin that damages or kills leukocytes, commonly by forming pores in their cell membranes.", "scope_statement": "This model owns vr.tr.leukocidin in PHY / PHY.MAT as a bacterial protein toxin category associated with leukocyte injury, recording named members and preparations without equating the registry entry with Panton-Valentine leukocidin alone; its precise taxonomic boundary remains provisional.", "in_scope": [ "Named leukocidins, aliases, sequence identities and component relationships", "Protein integrity, preparation composition and demonstrated activity", "Host species, leukocyte targets and receptor relationships", "Evidence for membrane injury and other measured cellular effects", "Attribution limits and preparation-specific handling constraints" ], "out_of_scope": [ "Whole bacterial organisms, strain classification and culture processes", "Toxin genes and their genomic vehicles as independently modelled entities", "Host leukocytes and receptors beyond their relationships to the toxin", "Infectious diseases, patient diagnosis and treatment decisions", "Manufacturing protocols and experimental optimization of toxin activity" ], "distinguishing_features": [ "Resolve the name to a toxin category or named member: evidence about Panton-Valentine leukocidin does not identify every leukocidin.", "Require protein identity and relevant functional evidence; leukocyte death alone does not establish that an unknown material is a leukocidin.", "Distinguish a toxin protein preparation from detection of its encoding genes; gene presence does not establish the preparation's protein content or activity.", "For a claimed bicomponent leukocidin, identify both components and distinguish individual subunits from the assembled toxin. [Primary structural study](https://pubmed.ncbi.nlm.nih.gov/11910032/).", "Use member-specific receptor evidence to distinguish related toxins: LukAB targets CD11b, whereas PVL and HlgCB interact with human C5a receptors. [LukAB study](https://pmc.ncbi.nlm.nih.gov/articles/PMC3696772/), [PVL and HlgCB study](https://pmc.ncbi.nlm.nih.gov/articles/PMC4506853/)." ], "characteristics": [ { "name": "Leukocidin identity", "kind": "category", "unit_or_values": "Named member, documented alias, unresolved leukocidin or disputed assignment", "why_it_matters": "Prevents a generic label from inheriting the properties of one named toxin." }, { "name": "Component identity", "kind": "relation", "unit_or_values": "Protein accessions, sequence versions and documented component pairing", "why_it_matters": "Distinguishes related proteins, isolated subunits and complete toxin preparations." }, { "name": "Molecular mass", "kind": "measurement", "unit_or_values": "kDa, with component or assembly specified and calculated versus measured status", "why_it_matters": "Supports identity and integrity assessment without assigning one mass to the whole category." }, { "name": "Component concentration", "kind": "measurement", "unit_or_values": "nmol/L or µg/mL for each identified component", "why_it_matters": "Makes reported amounts interpretable when preparations contain multiple proteins." }, { "name": "Purity and co-occurring material", "kind": "measurement", "unit_or_values": "Percentage by stated method, with identified contaminants and detection limits", "why_it_matters": "Other constituents can confound attribution of leukocyte injury." }, { "name": "Protein integrity and assembly", "kind": "state", "unit_or_values": "Intact, fragmented, aggregated, unassembled, assembled or uncharacterized, with evidence", "why_it_matters": "Protein abundance alone does not establish a functional toxin state." }, { "name": "Target context", "kind": "relation", "unit_or_values": "Host species, cell type, receptor identity and receptor evidence", "why_it_matters": "Activity claims must remain attached to the biological system in which they were established." }, { "name": "Observed cellular effect", "kind": "measurement", "unit_or_values": "Percentage permeabilization, lysis or viability change, with endpoint, duration and uncertainty", "why_it_matters": "Separates distinct biological readouts and prevents unsupported comparisons." }, { "name": "Preparation history", "kind": "state", "unit_or_values": "Formulation, recorded storage history, integrity assessment and activity verification date", "why_it_matters": "Supports assessment of whether earlier characterization still applies." }, { "name": "Handling determination", "kind": "category", "unit_or_values": "Documented permitted use, restricted use, pending assessment or disposal designation", "why_it_matters": "Connects decisions to the actual preparation and applicable institutional requirements." } ], "affordances": [ "Resolve a leukocidin label to a named toxin, component or explicitly unresolved category.", "Check whether a preparation contains the components its identity claim requires.", "Compare published activity observations only across adequately matched biological contexts.", "Identify missing evidence before attributing cell injury to a particular leukocidin.", "Flag preparations whose identity, integrity or handling determination is insufficient for the proposed use." ], "what_it_is_for": [ "Leukocidins are studied in microbiology, infectious disease research and investigations of bacterial virulence.", "Their identification and activity help researchers interpret interactions between bacterial pathogens and immune cells." ], "standards_and_regulation": [ "The Occupational Exposure to Hazardous Chemicals in Laboratories standard, issued by the United States Occupational Safety and Health Administration as 29 CFR 1910.1450, applies to laboratory use of leukocidin preparations that meet its hazardous chemical criteria." ], "failure_modes_and_hazards": [ "Exposure to biologically active leukocidin can damage susceptible immune cells.", "Misidentified or contaminated preparations can produce misleading experimental results and incorrect conclusions about bacterial virulence.", "Unrecognised differences in toxin activity or target species can undermine exposure assessments and experimental interpretation." ], "facets_not_applicable": { "recognition": "Leukocidin identity cannot be established from visual appearance because these proteins lack distinctive visible features." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q16889545: leukocidin", "url": "https://www.wikidata.org/wiki/Q16889545", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Leukocidin", "url": "https://en.wikipedia.org/wiki/Leukocidin", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "leukocidin-identity", "name": "Leukocidin identity", "description": "Resolve what the leukocidin name denotes and how narrowly its properties can be assigned.", "rationale": "A category label, named toxin and isolated component support different conclusions.", "layers": [ { "id": "name-and-boundary", "name": "Name and boundary", "description": "Separate registry scope from narrower toxin names and broader descriptions of leukocyte toxicity.", "findings": [ { "id": "named-member-resolution", "name": "Named member resolution", "description": "Record the intended member or retain an explicit unresolved identity.", "questions": [ { "text": "Does leukocidin denote the general category, a named toxin such as PVL, or an isolated protein component here?", "kind": "definition", "id": "named-member-resolution-q01" }, { "text": "Which source establishes the supplied name or alias for this material?", "kind": "provenance", "id": "named-member-resolution-q02" } ] } ] }, { "id": "molecular-attribution", "name": "Molecular attribution", "description": "Connect toxin identity to protein evidence and its biological source.", "findings": [ { "id": "protein-versus-gene-evidence", "name": "Protein versus gene evidence", "description": "Keep protein identification distinct from evidence that an organism carries a corresponding gene.", "questions": [ { "text": "Which protein accessions or sequence observations support this leukocidin assignment?", "kind": "provenance", "id": "protein-versus-gene-evidence-q01" }, { "text": "Does the evidence establish toxin protein, encoding genes, or only a leukocytotoxic phenotype?", "kind": "boundary", "id": "protein-versus-gene-evidence-q02" } ] } ] } ] }, { "id": "components-and-integrity", "name": "Components and integrity", "description": "Describe the molecular constituents and physical state of the toxin being represented.", "rationale": "A component, component mixture and functional assembly must not be treated as interchangeable.", "layers": [ { "id": "component-architecture", "name": "Component architecture", "description": "Record the architecture supported for the identified leukocidin.", "findings": [ { "id": "bicomponent-identity", "name": "Bicomponent identity", "description": "For applicable staphylococcal leukocidins, distinguish the two protein classes and the assembled pore. [Primary structural study](https://pubmed.ncbi.nlm.nih.gov/11910032/).", "questions": [ { "text": "What component architecture is established for this named toxin?", "kind": "definition", "id": "bicomponent-identity-q01" }, { "text": "Which required components are identified in the represented preparation?", "kind": "measurement", "id": "bicomponent-identity-q02" } ] } ] }, { "id": "preparation-state", "name": "Preparation state", "description": "Assess whether measured protein content corresponds to the intended molecular material.", "findings": [ { "id": "integrity-and-composition", "name": "Integrity and composition", "description": "Record component amounts, integrity and contamination without treating nominal purity as proof of activity.", "questions": [ { "text": "What concentrations and purity measurements are available for the individual toxin components?", "kind": "measurement", "id": "integrity-and-composition-q01" }, { "text": "What evidence identifies fragmentation, aggregation or other material that could affect interpretation?", "kind": "measurement", "id": "integrity-and-composition-q02" } ] } ] } ] }, { "id": "host-and-cell-recognition", "name": "Host and cell recognition", "description": "Attach toxin activity to a defined host, leukocyte population and receptor context.", "rationale": "Target recognition distinguishes leukocidins and limits transfer of findings between biological systems.", "layers": [ { "id": "receptor-relations", "name": "Receptor relations", "description": "Record receptor relationships at the named-toxin level.", "findings": [ { "id": "member-specific-receptor-evidence", "name": "Member-specific receptor evidence", "description": "LukAB recognition of CD11b illustrates why receptor assignments require toxin-specific evidence. [Primary study](https://pmc.ncbi.nlm.nih.gov/articles/PMC3696772/).", "questions": [ { "text": "Which receptor interaction is demonstrated for this toxin and host species?", "kind": "provenance", "id": "member-specific-receptor-evidence-q01" }, { "text": "Does the evidence establish binding, functional dependence or merely association?", "kind": "boundary", "id": "member-specific-receptor-evidence-q02" } ] } ] }, { "id": "species-and-cell-context", "name": "Species and cell context", "description": "Preserve the biological limits of observed susceptibility.", "findings": [ { "id": "susceptibility-boundaries", "name": "Susceptibility boundaries", "description": "PVL and HlgCB receptor studies demonstrate that related toxins can differ in their response to receptor variation. [Primary study](https://pmc.ncbi.nlm.nih.gov/articles/PMC4506853/).", "questions": [ { "text": "Which host species and leukocyte populations were actually examined?", "kind": "measurement", "id": "susceptibility-boundaries-q01" }, { "text": "What evidence supports extending the observation to a different species, cell population or activation state?", "kind": "boundary", "id": "susceptibility-boundaries-q02" } ] } ] } ] }, { "id": "activity-and-attribution", "name": "Activity and attribution", "description": "Represent observed effects while distinguishing molecular mechanism, cellular injury and disease relevance.", "rationale": "A positive biological readout does not by itself establish mechanism or clinical importance.", "layers": [ { "id": "cellular-endpoints", "name": "Cellular endpoints", "description": "Keep binding, membrane permeabilization, lysis and other responses separately interpretable.", "findings": [ { "id": "endpoint-specific-activity", "name": "Endpoint-specific activity", "description": "Attach every activity observation to its endpoint, preparation and biological context.", "questions": [ { "text": "Was the measured endpoint receptor binding, pore formation, membrane injury, cell death or another response?", "kind": "measurement", "id": "endpoint-specific-activity-q01" }, { "text": "Are component amounts, observation duration, cell context and uncertainty reported well enough to interpret the result?", "kind": "measurement", "id": "endpoint-specific-activity-q02" } ] } ] }, { "id": "causal-interpretation", "name": "Causal interpretation", "description": "Assess how specifically an observation can be attributed to the identified leukocidin.", "findings": [ { "id": "toxin-specific-causation", "name": "Toxin-specific causation", "description": "Distinguish effects of an identified toxin preparation from effects of a bacterial mixture or clinical association.", "questions": [ { "text": "What evidence separates this leukocidin's contribution from other constituents or virulence factors?", "kind": "provenance", "id": "toxin-specific-causation-q01" }, { "text": "Does the available evidence support a cellular effect, a contribution to infection, or only an association?", "kind": "boundary", "id": "toxin-specific-causation-q02" } ] } ] } ] }, { "id": "preparation-fitness-and-handling", "name": "Preparation fitness and handling", "description": "Connect the preparation's documented condition to permitted interpretation and use.", "rationale": "The toxin name alone cannot establish current activity, fitness for use or applicable handling requirements.", "layers": [ { "id": "condition-and-reliability", "name": "Condition and reliability", "description": "Determine whether preparation history undermines existing characterization.", "findings": [ { "id": "current-characterization", "name": "Current characterization", "description": "Record formulation and handling history alongside the date and scope of integrity or activity evidence.", "questions": [ { "text": "What formulation and storage history accompany this leukocidin preparation?", "kind": "provenance", "id": "current-characterization-q01" }, { "text": "What evidence shows that its present integrity and activity remain consistent with its characterization?", "kind": "measurement", "id": "current-characterization-q02" } ] } ] }, { "id": "use-determination", "name": "Use determination", "description": "Link preparation-specific documentation to decisions about handling and use.", "findings": [ { "id": "documented-use-constraints", "name": "Documented use constraints", "description": "Record applicable institutional assessments and supplier documentation without inventing a universal classification for all leukocidins.", "questions": [ { "text": "Which documented handling requirements and use restrictions apply to this exact preparation?", "kind": "provenance", "id": "documented-use-constraints-q01" }, { "text": "Do unresolved identity, activity or documentation gaps require withholding the proposed use pending assessment?", "kind": "action", "id": "documented-use-constraints-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 is recorded: confirm whether the registry means the broad functional class, staphylococcal bicomponent leukocidins or Panton-Valentine leukocidin specifically.", "The listed kinds and subunit mass range concern staphylococcal bicomponent toxins and do not describe every bacterial leukocyte toxin.", "This is recall without source verification; exact protein identifiers, strain-specific properties and disease associations require checking." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of leukocidin 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": [ "Panton-Valentine leukocidin (PVL) of Staphylococcus aureus", "LukED of Staphylococcus aureus", "LukAB, also called LukGH, of Staphylococcus aureus", "Gamma-haemolysin HlgAB of Staphylococcus aureus", "Gamma-haemolysin HlgCB of Staphylococcus aureus" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of leukocidin 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": "UniProtKB accession", "value_or_pattern": "6- or 10-character alphanumeric accession", "note": "Identifies a particular protein record; bicomponent leukocidins have separate protein components, and the class has no single accession." }, { "scheme": "Bacterial gene symbols", "value_or_pattern": "lukS-PV and lukF-PV", "note": "These encode the two components of Panton-Valentine leukocidin specifically, not leukocidins as a whole." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of leukocidin 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 into bacterial virulence and interactions with host immune cells.", "Detection of leukocidin genes when characterising bacterial isolates.", "Evaluation of experimental toxin-neutralising antibodies and vaccine candidates." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of leukocidin 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": "Approximate molecular mass of an individual mature staphylococcal bicomponent leukocidin subunit", "typical_range": "30-40", "unit": "kDa" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of leukocidin 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": [ "Susceptible leukocytes can undergo membrane permeabilisation and lysis.", "Toxin activity can impair immune defence and contribute to inflammation and tissue injury.", "Host species and leukocyte receptor differences can make experimental results poorly transferable between models.", "Detection of a toxin gene does not establish toxin expression, biological activity or its contribution to a particular infection." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of leukocidin 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": "Panton-Valentine leukocidin", "difference": "A particular two-component leukocidin, rather than the entire toxin class." }, { "name": "Haemolysin", "difference": "Named for erythrocyte-damaging activity; leukocidin denotes leukocyte-damaging activity, and some toxins have both." }, { "name": "Leukotoxin", "difference": "An overlapping functional term whose relationship to leukocidin depends on the organism and naming convention." }, { "name": "Staphylococcus aureus", "difference": "A bacterial organism that can produce leukocidins, rather than a toxin itself." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of leukocidin this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry intend leukocidin broadly as a leukocyte-damaging bacterial toxin category or specifically as the staphylococcal bicomponent family?", "Which named members, historical aliases and overlapping hemolysin labels belong under this entry without creating duplicate concepts?", "Which sequence variants and preparations have directly established receptor and host-cell relationships, and which assignments remain inferred?", "Which available activity measurements are sufficiently comparable to support cross-study conclusions?", "Which preparation-specific identity records, stability evidence and handling determinations can be verified from authoritative documentation?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 17, "questions": 27 } }