{ "model": { "rank": 5011, "code": "thing-q103537", "model_id": "vr.tr.antigen", "name": "antigen", "purpose": "Enable an agent to identify an antigen, assess evidence of immune recognition and preparation quality, and determine its suitability for a specified research, diagnostic, or immunological use.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q103537/", "tier": 2, "score": 70, "payload": { "layer": "wikidata", "aliases": [ "recombinant antigen", "microbial antigen", "synthetic antigen", "Cancer/testis antigens", "pathogen-associated molecular pattern", "anthrax toxin", "tumor antigen", "VLA-2", "autoantigen", "ACAMPs", "enterobacterial common antigen", "heterophile antigens", "histocompatibility antigen", "induced-self antigen", "T-Cell differentiation antigen", "helminth antigen", "viral antigens", "histocompatibility antigens class I", "surface antigen", "isoantigens", "fungal antigen", "archaeal antigens", "nuclear antigens", "Dermatophagoides antigens", "protozoan antigens", "neoplasm antigens", "superantigen", "blood antigen", "T-independent antigens", "tissue polypeptide antigen", "Heymann nephritis antigenic complex", "minor lymphocyte stimulatory antigens" ], "aliasCount": 32, "merged": 32, "knownIn": 70, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": "vr.tr.antigen", "source": { "dataset": "wikidata", "item": "Q103537", "url": "https://www.wikidata.org/wiki/Q103537", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-09T21:28:35Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 21.7, "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: 01a08811-a85a-78c1-933c-08abd8436ff3\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: antigen\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 005: 1001 registe", "usd": 0, "recall": true }, "codex": { "seconds": 62.3, "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: 01a08811-a84e-7250-88b4-911040a48dd0\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: antigen\nRegistry id: vr.tr.antigen\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext " } } }, "metaModel": { "id": "THING-Q103537", "registryId": "vr.tr.antigen", "name": "antigen", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q103537/", "model": { "registry_id": "vr.tr.antigen", "name": "antigen", "purpose": "Enable an agent to identify an antigen, assess evidence of immune recognition and preparation quality, and determine its suitability for a specified research, diagnostic, or immunological use.", "definition": "An antigen is a molecular structure specifically recognized by an antibody or B-cell receptor, or by a T-cell receptor in an appropriate molecular presentation context, whether or not it induces an immune response.", "scope_statement": "This model owns antigen as a context-dependent role of a molecular entity or material recognized by antibodies or antigen receptors, including its epitopes, presentation requirements, recognition evidence, and preparation state.", "in_scope": [ "Molecular identity, biological origin, and material boundaries of the antigen", "Epitopes and their accessibility in specified molecular conformations", "Recognition by specified antibodies, B-cell receptors, or T-cell receptors", "Processing and presentation requirements where recognition depends on them", "Preparation quality, stability, and suitability for a stated use", "Evidence distinguishing antigen recognition from immune-response induction" ], "out_of_scope": [ "Complete models of the organism, cell, or tissue carrying the antigen", "Antibody or receptor engineering beyond its relationship to antigen recognition", "Complete vaccine, diagnostic kit, or therapeutic product formulations", "Host immune-system state, disease diagnosis, and treatment decisions", "Manufacturing facilities and production processes beyond preparation provenance" ], "distinguishing_features": [ "An antigen assignment requires a specified immune-recognition relationship or an explicitly unverified candidate status; biological origin alone does not establish antigenicity.", "Recognition and immune-response induction are separate tests: evidence of binding alone does not establish that the material is an immunogen.", "An epitope is a recognized feature of an antigen; identifying one epitope does not necessarily identify or characterize the whole antigen.", "For presentation-dependent recognition, the tested entity must distinguish the source material, presented component, and presenting molecule.", "A cell, pathogen, or formulated product carrying an antigen is not interchangeable with the particular antigenic determinant or preparation under investigation." ], "characteristics": [ { "name": "Antigen entity and molecular identity", "kind": "category", "unit_or_values": "Defined molecule, molecular complex, heterogeneous material, or unresolved candidate; sequence, structure, and identifiers where applicable", "why_it_matters": "Prevents treating antigen as a single chemical substance or assigning one chemical identifier to an unresolved mixture." }, { "name": "Biological source and variant", "kind": "relation", "unit_or_values": "Source organism, strain, tissue, cell type, allele, or synthetic design", "why_it_matters": "Connects recognition claims to the source and variation actually represented." }, { "name": "Epitope identity and dependence", "kind": "category", "unit_or_values": "Mapped or unresolved; sequence, structural region, chemical determinant, and conformation or modification dependence", "why_it_matters": "Identifies what is recognized and what changes could remove or alter recognition." }, { "name": "Recognition partner", "kind": "relation", "unit_or_values": "Specified antibody, B-cell receptor, T-cell receptor, or characterized polyclonal population", "why_it_matters": "Makes antigenicity an evidenced relationship rather than an unconditional material label." }, { "name": "Presentation context", "kind": "relation", "unit_or_values": "Direct recognition, specified presenting molecule and presented component, other demonstrated context, or unresolved", "why_it_matters": "Prevents transferring recognition claims between incompatible presentation settings." }, { "name": "Binding affinity", "kind": "measurement", "unit_or_values": "Dissociation constant in mol/L, with partner, method, temperature, and binding model; unresolved when unavailable", "why_it_matters": "Supports comparison when the experiment measures affinity and its assumptions are appropriate." }, { "name": "Immune-response induction evidence", "kind": "state", "unit_or_values": "Not tested, response detected, response not detected, or inconclusive; qualified by host, endpoint, dose, route, and formulation", "why_it_matters": "Separates antigen recognition from context-dependent immunogenicity." }, { "name": "Preparation composition and concentration", "kind": "measurement", "unit_or_values": "Purity or component fraction with method; concentration in mg/mL or mol/L where meaningful", "why_it_matters": "Determines what material was tested and whether preparations can be compared." }, { "name": "Recognition-relevant preparation state", "kind": "state", "unit_or_values": "Measured folding, aggregation, degradation, modification, and epitope-accessibility state", "why_it_matters": "A nominally identical antigen can behave differently after processing or storage." }, { "name": "Use qualification", "kind": "state", "unit_or_values": "Qualified, unqualified, or unresolved for a named application and acceptance criteria", "why_it_matters": "Keeps suitability specific to the intended assay or intervention." } ], "affordances": [ "Resolve an antigen candidate to a defined molecular entity or explicitly bounded material.", "Map recognition evidence to specific epitopes, partners, and presentation contexts.", "Compare variants or preparations for demonstrated changes in recognition.", "Select a preparation for a specified assay using measured quality and recognition criteria.", "Identify missing controls or experiments needed to test specificity or immunogenicity.", "Flag storage, handling, or processing changes that require recognition to be reassessed." ] }, "sources": [], "structure": { "bundles": [ { "id": "antigen-identity", "name": "Antigen identity", "description": "Define the physical entity bearing the antigen role and connect it to its source.", "rationale": "Antigen is a recognition role spanning different materials, so a name alone cannot establish molecular identity.", "layers": [ { "id": "molecular-boundary", "name": "Molecular boundary", "description": "Separate the antigen entity from its epitopes, carriers, and surrounding material.", "findings": [ { "id": "recognized-entity", "name": "Recognized entity", "description": "Record whether the entry concerns a defined molecule, complex, or bounded heterogeneous preparation.", "questions": [ { "text": "What molecular entity or material does the antigen name denote, and which identifiers or structural descriptions support that identity?", "kind": "definition", "id": "recognized-entity-q01" }, { "text": "Does the name refer to a whole antigen, an epitope, a carrier conjugate, or a preparation containing multiple antigens?", "kind": "boundary", "id": "recognized-entity-q02" } ] } ] }, { "id": "source-and-variation", "name": "Source and variation", "description": "Connect identity to biological origin or synthetic design and distinguish relevant variants.", "findings": [ { "id": "source-linked-variant", "name": "Source-linked variant", "description": "Record the source, sequence or chemical variant, and modifications represented by the material.", "questions": [ { "text": "Which organism, strain, tissue, allele, or synthetic design produced the antigen being described?", "kind": "provenance", "id": "source-linked-variant-q01" }, { "text": "Which sequence changes, chemical modifications, or conjugations distinguish this antigen from related variants?", "kind": "definition", "id": "source-linked-variant-q02" } ] } ] } ] }, { "id": "epitopes-and-recognition", "name": "Epitopes and recognition", "description": "Describe the determinants recognized and the experimental relationships supporting antigenicity.", "rationale": "Recognition must be tied to a determinant and partner rather than inferred from the antigen label.", "layers": [ { "id": "epitope-structure", "name": "Epitope structure", "description": "Locate recognized determinants and identify dependencies on molecular state.", "findings": [ { "id": "determinant-and-accessibility", "name": "Determinant and accessibility", "description": "Record epitope mapping and evidence that the determinant is accessible in the relevant material.", "questions": [ { "text": "Which residues, chemical groups, or structural regions define the epitope, and how was that assignment established?", "kind": "measurement", "id": "determinant-and-accessibility-q01" }, { "text": "Does recognition depend on folding, modification, cleavage, or exposure that differs between the tested preparation and its native context?", "kind": "boundary", "id": "determinant-and-accessibility-q02" } ] } ] }, { "id": "binding-specificity", "name": "Binding specificity", "description": "Associate recognition measurements with partners, controls, and assay conditions.", "findings": [ { "id": "partner-qualified-recognition", "name": "Partner-qualified recognition", "description": "Record binding or recognition evidence without conflating assay signal, affinity, and avidity.", "questions": [ { "text": "Which antibody or receptor recognizes the antigen, by what assay, and with which negative and competition controls?", "kind": "measurement", "id": "partner-qualified-recognition-q01" }, { "text": "What related or unrelated materials were tested for cross-reactivity, and does the reported measurement represent affinity, avidity, or assay response?", "kind": "boundary", "id": "partner-qualified-recognition-q02" } ] } ] } ] }, { "id": "presentation-and-immune-response", "name": "Presentation and immune response", "description": "Specify recognition context and separately assess evidence of immune-response induction.", "rationale": "Recognition may depend on processing and presentation, while immunogenicity requires additional contextual evidence.", "layers": [ { "id": "processing-and-presentation", "name": "Processing and presentation", "description": "Distinguish source antigen from the component and molecular context encountered by a receptor.", "findings": [ { "id": "presented-recognition-unit", "name": "Presented recognition unit", "description": "Record direct or presentation-dependent recognition and the evidence connecting source material to the recognized unit.", "questions": [ { "text": "Is recognition direct or presentation-dependent, and which presented component and presenting molecule are required?", "kind": "definition", "id": "presented-recognition-unit-q01" }, { "text": "What demonstrates that the source antigen generates the recognized component in the relevant cells, rather than only after experimental loading?", "kind": "measurement", "id": "presented-recognition-unit-q02" } ] } ] }, { "id": "immunogenicity-context", "name": "Immunogenicity context", "description": "Qualify induced responses by host, exposure, formulation, and endpoint.", "findings": [ { "id": "recognition-versus-induction", "name": "Recognition versus induction", "description": "Keep evidence of an induced immune response distinct from evidence of recognition by existing immune reagents.", "questions": [ { "text": "Has response induction been tested, and in which host, dose, route, formulation, and observation period?", "kind": "measurement", "id": "recognition-versus-induction-q01" }, { "text": "Which controls distinguish the response to this antigen from responses to its carrier, adjuvant, or contaminants?", "kind": "boundary", "id": "recognition-versus-induction-q02" } ] } ] } ] }, { "id": "preparation-integrity", "name": "Preparation integrity", "description": "Characterize the physical preparation whose antigenic behavior is being assessed.", "rationale": "Composition, processing, and deterioration can change recognition or confound immune-response measurements.", "layers": [ { "id": "composition-and-confounders", "name": "Composition and confounders", "description": "Measure antigen content and identify constituents that could affect interpretation.", "findings": [ { "id": "tested-material-composition", "name": "Tested material composition", "description": "Record preparation identity, concentration, purity, and assay-relevant impurities.", "questions": [ { "text": "How were antigen identity, concentration, and purity measured for the tested lot?", "kind": "measurement", "id": "tested-material-composition-q01" }, { "text": "Which carrier proteins, expression tags, residual host materials, or immune-active contaminants could contribute to the observed result?", "kind": "boundary", "id": "tested-material-composition-q02" } ] } ] }, { "id": "stability-and-accessibility", "name": "Stability and accessibility", "description": "Assess whether handling preserves the antigen features required for recognition.", "findings": [ { "id": "retained-antigenic-state", "name": "Retained antigenic state", "description": "Link storage and processing history to measured structural integrity and recognition.", "questions": [ { "text": "What changes in aggregation, degradation, folding, or recognition occur under the proposed storage and handling conditions?", "kind": "measurement", "id": "retained-antigenic-state-q01" }, { "text": "Which acceptance criteria determine whether a stored, thawed, fixed, or immobilized preparation remains suitable for its intended recognition assay?", "kind": "action", "id": "retained-antigenic-state-q02" } ] } ] } ] }, { "id": "application-and-evidence-limits", "name": "Application and evidence limits", "description": "Translate antigen evidence into bounded use decisions and explicit unresolved claims.", "rationale": "Suitability depends on the application, and results from one preparation or recognition context may not transfer.", "layers": [ { "id": "application-qualification", "name": "Application qualification", "description": "Connect a proposed use to recognition performance and preparation-specific requirements.", "findings": [ { "id": "fit-for-intended-use", "name": "Fit for intended use", "description": "Define the evidence needed to use the antigen in a particular experimental or product context.", "questions": [ { "text": "For the proposed assay or immunological use, which recognition, specificity, and preparation-quality criteria must be met?", "kind": "action", "id": "fit-for-intended-use-q01" }, { "text": "Which handling restrictions or regulatory requirements apply to this actual preparation and use, including its source material and formulation?", "kind": "action", "id": "fit-for-intended-use-q02" } ] } ] }, { "id": "claim-transfer-and-gaps", "name": "Claim transfer and gaps", "description": "Bound the transfer of results across variants, lots, hosts, and presentation settings.", "findings": [ { "id": "evidence-bounded-conclusions", "name": "Evidence-bounded conclusions", "description": "Associate each conclusion with the material and context tested, and identify further validation needs.", "questions": [ { "text": "Which records connect each recognition or immune-response claim to its tested antigen variant, preparation lot, and experimental context?", "kind": "provenance", "id": "evidence-bounded-conclusions-q01" }, { "text": "What additional evidence is required before transferring the claim to another variant, lot, host population, or presentation context?", "kind": "action", "id": "evidence-bounded-conclusions-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": [ "Antigen denotes an immunological role across diverse molecular structures, not one chemical substance; no universal CAS number, purity, melting point or GHS classification applies.", "The listed kinds overlap and represent different classification axes rather than mutually exclusive categories.", "For a concrete entry, establish the molecular identity, epitope, preparation and recognition context; most conventional T cells recognize peptide-MHC complexes, but other presentation systems exist." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of antigen 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": [ "Self antigens (autoantigens)", "Alloantigens differing among individuals of the same species", "Microbial antigens", "Tumour-associated antigens", "T-dependent antigens", "T-independent antigens" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of antigen 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": "UniProt accession", "value_or_pattern": "Accession identifying a particular protein sequence record", "note": "Applicable to protein antigens; it does not by itself specify the recognized epitope or antigen preparation." }, { "scheme": "Immune Epitope Database (IEDB) epitope identifier", "value_or_pattern": "Numeric epitope record identifier", "note": "Identifies a recorded epitope rather than necessarily the entire antigen." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of antigen 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": [ "Vaccine components intended to elicit antigen-specific immunity", "Targets detected by diagnostic immunoassays", "Reagents used to detect antigen-specific antibodies or cellular responses", "Blood-group and tissue-compatibility testing", "Targets for therapeutic antibodies and cellular immunotherapies" ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of antigen 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": "Antigen mass concentration", "typical_range": "Preparation- and assay-dependent; no class-wide range", "unit": "ng/mL or µg/mL" }, { "quantity": "Antibody-antigen equilibrium dissociation constant", "typical_range": "Specific to the binding pair and experimental conditions", "unit": "mol/L" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of antigen 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": [ "Cross-reactive recognition can produce misleading diagnostic results or unintended biological effects.", "Denaturation, degradation or chemical modification can destroy or alter epitopes.", "Antigenic variation can reduce recognition by existing antibodies or T cells.", "Some antigens participate in allergic or autoimmune responses; antigenicity alone does not establish a hazard.", "Contaminants such as endotoxin can confound experiments or make an antigen preparation unsafe." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of antigen this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-regional-variation", "name": "Regional variation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Regulatory requirements depend on whether an antigen preparation is used as a vaccine component, diagnostic reagent or research material, and on the jurisdiction." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of antigen 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": "immunogen", "difference": "An immunogen induces an immune response under specified conditions; an antigen need only be specifically recognized." }, { "name": "epitope", "difference": "An epitope is the particular molecular feature recognized; an antigen can contain multiple epitopes." }, { "name": "hapten", "difference": "A hapten can be specifically bound but generally requires association with a carrier to induce an antibody response." }, { "name": "allergen", "difference": "An allergen is an antigen that elicits an allergic immune response in a susceptible individual." }, { "name": "antibody", "difference": "An antibody is an immunoglobulin recognition molecule; the antigen is its binding target, although antibodies can themselves act as antigens." }, { "name": "adjuvant", "difference": "An adjuvant enhances responses to an antigen rather than defining the target of antigen-specific recognition." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of antigen this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which authoritative definition should anchor the registry's antigen scope, particularly for heterogeneous materials and nonclassical presentation contexts?", "Does an existing Vercy model already own antigen, epitope, or immunogen, and which relationships would preserve one source of truth?", "What minimum recognition evidence should distinguish a candidate antigen from a demonstrated antigen in the catalogue?", "Which criteria should determine whether molecular variants and carrier conjugates are separate antigen instances or states of the same instance?", "Which application-specific standards should govern preparation qualification and the transfer of recognition claims between contexts?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 18, "questions": 28 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "chemical substance or material", "method": "Written from the archetype playbook - what this kind of thing needs beyond identity and provenance - and from the structure that recurred across 6,333 models already researched by two engines. Applied to this entry by rule. No source was read for this thing and no claim here is researched. This entry carries no facets of its own, so they were inferred from its domain - a guess about a whole domain applied to one thing.", "facetsInferred": true, "nextPass": "A researcher replaces this draft with a sourced specification. Treat every sentence below as a proposal to argue with.", "purpose": "Give an agent a durable, checkable way to recognise a antigen, record what state it is in, and decide what may be done with it.", "whatItIs": "Enable an agent to identify an antigen, assess evidence of immune recognition and preparation quality, and determine its suitability for a specified research, diagnostic, or immunological use.", "characteristics": { "substance": "material", "origin": "natural", "agency": "inert", "mobility": "varies" }, "whatYouCanDoWithIt": [ "observed and measured", "consumed or used up" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: recombinant antigen, microbial antigen, synthetic antigen, Cancer/testis antigens, pathogen-associated molecular pattern, anthrax toxin, tumor antigen, VLA-2, autoantigen, ACAMPs, enterobacterial common antigen, heterophile antigens.", "32 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 70 Wikipedia languages, which is a measure of how widely the thing is known, not of how important it is." ], "openQuestionsForResearch": [ "Which of the bundles below does a real task actually need, and which are ceremony?", "What does this thing have that the facets do not capture at all?", "Which neighbouring kind is most often confused with a antigen, and on what evidence are they told apart?" ], "whatItIsMadeOf": "matter you can touch", "physicalCharacter": [ "Mobility varies between examples.", "Does nothing on its own; everything it does, something else did to it.", "These come from the domain this entry sits in rather than from the entry itself, so treat them as a first guess about the whole domain applied to one thing." ], "whatCanBeDoneWithIt": [ "observe it, measure it, record its state", "use it up, and then need more of it" ], "howItIsRecognised": [ "Not recognisable by sight in any reliable way. Appearance varies with grade, form and additives; identification is by label, by documentation, or by assay." ], "relatedModels": [ { "relation": "covers", "note": "Finer kinds folded into this entry because telling them apart needs a task that asks for it. Each is a model waiting to be split out when one does.", "targets": [ "recombinant antigen", "microbial antigen", "synthetic antigen", "Cancer/testis antigens", "pathogen-associated molecular pattern", "anthrax toxin", "tumor antigen", "VLA-2", "autoantigen", "ACAMPs", "enterobacterial common antigen", "heterophile antigens" ] } ], "standing": "Described in 70 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 32 finer distinctions are held inside this entry as names rather than as separate models.", "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one antigen from another, and a antigen from things that resemble it.", "rationale": "Recognition comes before every other claim. Without stable identity nothing else in the model can be trusted to be about the same thing twice.", "layers": [ { "id": "naming-and-identifiers", "name": "Names and identifiers", "description": "The names this thing goes by and the identifiers that survive translation and time.", "findings": [ { "id": "preferred-name-and-aliases", "name": "Preferred name, aliases and local names", "description": "Which name to use, which names mean the same thing, and which merely sound similar.", "questions": [ { "id": "preferred-name-and-aliases-q01", "text": "What identifies and describes the name of a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "preferred-name-and-aliases-q02", "text": "Who or what asserted this about the name of a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "preferred-name-and-aliases-q03", "text": "What may an agent decide or do once the name of a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "stable-identifiers", "name": "Stable identifiers and external keys", "description": "Identifiers that keep pointing at this kind of thing across systems and languages.", "questions": [ { "id": "stable-identifiers-q01", "text": "What identifies and describes an identifier for a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stable-identifiers-q02", "text": "Who or what asserted this about an identifier for a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stable-identifiers-q03", "text": "What may an agent decide or do once an identifier for a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "classification-and-granularity", "name": "Classification and granularity", "description": "Where a antigen sits among kinds, and how finely a task needs to cut it.", "findings": [ { "id": "kind-and-parents", "name": "Kind, parents and neighbouring kinds", "description": "The classes this thing belongs to and the ones it is next to.", "questions": [ { "id": "kind-and-parents-q01", "text": "What identifies and describes the kind of a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "kind-and-parents-q02", "text": "Who or what asserted this about the kind of a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "kind-and-parents-q03", "text": "What may an agent decide or do once the kind of a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "distinguishing-features", "name": "Distinguishing features", "description": "What separates a antigen from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "distinguishing-features-q02", "text": "Who or what asserted this about what distinguishes a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "distinguishing-features-q03", "text": "What may an agent decide or do once what distinguishes a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "form-and-composition", "name": "Form, composition and condition", "description": "What a antigen is made of, what shape and size it takes, and what state it is in.", "rationale": "A physical thing can be measured, and a model that cannot record its measurements cannot support any decision that depends on them.", "layers": [ { "id": "form-and-dimensions", "name": "Form and dimensions", "description": "Shape, size, mass and the ranges these take across examples.", "findings": [ { "id": "measurable-dimensions", "name": "Measurable dimensions and their units", "description": "The quantities worth recording and the units they are recorded in.", "questions": [ { "id": "measurable-dimensions-q01", "text": "What identifies and describes the dimensions of a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "measurable-dimensions-q02", "text": "Who or what asserted this about the dimensions of a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "measurable-dimensions-q03", "text": "What may an agent decide or do once the dimensions of a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "material-and-composition", "name": "Material and composition", "description": "Materials, parts and how they are put together.", "findings": [ { "id": "parts-and-materials", "name": "Parts and materials", "description": "What a antigen is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "parts-and-materials-q02", "text": "Who or what asserted this about the composition of a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "parts-and-materials-q03", "text": "What may an agent decide or do once the composition of a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "condition-and-integrity", "name": "Condition and integrity", "description": "Wear, damage, health and the difference between working and broken.", "findings": [ { "id": "condition-assessment", "name": "Condition, damage and health", "description": "How the condition of a antigen is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "condition-assessment-q02", "text": "Who or what asserted this about the condition of a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "condition-assessment-q03", "text": "What may an agent decide or do once the condition of a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "place-and-movement", "name": "Place and movement", "description": "Where a antigen is, how it got there and where it may go (varies).", "rationale": "A thing that can move needs its position recorded with a time, or every later claim about it is about a place it has left.", "layers": [ { "id": "location-and-placement", "name": "Location and placement", "description": "Position, containment and the reference frame the position is given in.", "findings": [ { "id": "position-and-frame", "name": "Position, container and reference frame", "description": "Where a antigen is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "position-and-frame-q02", "text": "Who or what asserted this about the location of a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "position-and-frame-q03", "text": "What may an agent decide or do once the location of a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "movement-and-transfer", "name": "Movement and transfer", "description": "How a antigen is carried, installed or relocated.", "findings": [ { "id": "movement-events", "name": "Movement events and constraints", "description": "What counts as a movement, what records it and what limits it.", "questions": [ { "id": "movement-events-q01", "text": "What identifies and describes the movement of a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "movement-events-q02", "text": "Who or what asserted this about the movement of a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "movement-events-q03", "text": "What may an agent decide or do once the movement of a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "state-and-lifecycle", "name": "State and lifecycle", "description": "The states a antigen passes through and the events that move it between them.", "rationale": "Most decisions about a thing depend on what state it is in now, which is a claim with a time on it, not a property.", "layers": [ { "id": "lifecycle-stages", "name": "Lifecycle stages", "description": "From coming into existence to ceasing to be one of these.", "findings": [ { "id": "stages-and-transitions", "name": "Stages and transitions", "description": "The stages worth naming and what moves a antigen between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stages-and-transitions-q02", "text": "Who or what asserted this about the lifecycle of a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stages-and-transitions-q03", "text": "What may an agent decide or do once the lifecycle of a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "observations-and-status", "name": "Observations and current status", "description": "What is observed about a antigen, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a antigen is recorded so that it can be superseded rather than overwritten.", "questions": [ { "id": "observation-record-q01", "text": "What identifies and describes an observation of a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "observation-record-q02", "text": "Who or what asserted this about an observation of a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "observation-record-q03", "text": "What may an agent decide or do once an observation of a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "use-and-operation", "name": "Use and operation", "description": "What can be done with a antigen and what it takes to do it.", "rationale": "An agent that can recognise a thing but not act on it has only half a model.", "layers": [ { "id": "intended-use", "name": "Intended use and function", "description": "What a antigen is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a antigen performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "function-and-purpose-q02", "text": "Who or what asserted this about the use of a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "function-and-purpose-q03", "text": "What may an agent decide or do once the use of a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "handling-and-procedure", "name": "Handling and procedure", "description": "The steps, skills and tools involved in using a antigen.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a antigen at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "procedures-and-skills-q02", "text": "Who or what asserted this about handling a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "procedures-and-skills-q03", "text": "What may an agent decide or do once handling a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "supply-and-consumption", "name": "Supply and consumption", "description": "Quantities, rates and what running out means.", "findings": [ { "id": "consumption-and-stock", "name": "Consumption, stock and replenishment", "description": "How much of a antigen there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "consumption-and-stock-q02", "text": "Who or what asserted this about the supply of a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "consumption-and-stock-q03", "text": "What may an agent decide or do once the supply of a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "composition-and-identity", "name": "Composition, grade and chemical identity", "description": "What antigen is made of and how pure the thing in hand is.", "rationale": "Grade decides what a substance may be used for, so a model that records only the name cannot support any decision about use.", "layers": [ { "id": "chemical-identity", "name": "Chemical identity", "description": "Formula, structure and the registry numbers that name it unambiguously.", "findings": [ { "id": "identity-record", "name": "Identity and registry numbers", "description": "What identifies this substance across suppliers and regulators.", "questions": [ { "id": "identity-record-q01", "text": "What formula, structure and registry identifiers name antigen unambiguously?", "kind": "definition" }, { "id": "identity-record-q02", "text": "Which related substances share a name in common use but not an identifier?", "kind": "boundary" } ] } ] }, { "id": "grade-and-impurities", "name": "Grade, purity and impurities", "description": "The specification a batch meets and what else is in it.", "findings": [ { "id": "specification", "name": "Specification and assay", "description": "How purity is stated and measured, and which impurities matter.", "questions": [ { "id": "specification-q01", "text": "What grades of antigen exist, how is purity assayed, and which impurities are limited?", "kind": "measurement" }, { "id": "specification-q02", "text": "Which use requires which grade, and what happens when a lower grade is substituted?", "kind": "action" } ] } ] } ] }, { "id": "properties-and-behaviour", "name": "Properties and behaviour", "description": "How antigen behaves under conditions an agent can measure or change.", "rationale": "Physical constants are the part of a substance model that transfers between contexts, and each needs its unit and its conditions.", "layers": [ { "id": "physical-constants", "name": "Physical constants", "description": "Values that hold for the pure substance, with their conditions.", "findings": [ { "id": "constants-record", "name": "Constants and conditions", "description": "The quantities worth recording and the state they apply in.", "questions": [ { "id": "constants-record-q01", "text": "What are the defining physical constants of antigen, in what units and under what conditions?", "kind": "measurement" }, { "id": "constants-record-q02", "text": "Which of these values change with grade or form rather than being fixed?", "kind": "boundary" } ] } ] }, { "id": "stability-and-reactivity", "name": "Stability and reactivity", "description": "What it reacts with, degrades into, and how it is stored.", "findings": [ { "id": "incompatibilities", "name": "Incompatibilities and degradation", "description": "What must not meet it, and what it becomes over time.", "questions": [ { "id": "incompatibilities-q01", "text": "What is antigen incompatible with, and what does it degrade into under storage?", "kind": "definition" }, { "id": "incompatibilities-q02", "text": "What storage and handling does that require, and who is competent to do it?", "kind": "action" } ] } ] } ] }, { "id": "hazard-and-regulation", "name": "Hazard classification and regulation", "description": "How antigen can harm, and what the law says about holding and moving it.", "rationale": "A substance model without its hazard class and its regulatory identity is unusable in exactly the situations that matter.", "layers": [ { "id": "hazard-class", "name": "Hazard classification", "description": "Classified hazards, exposure limits and protective measures.", "findings": [ { "id": "classified-hazards", "name": "Classified hazards and limits", "description": "The classification, the scheme it belongs to, and the limits set.", "questions": [ { "id": "classified-hazards-q01", "text": "How is antigen classified for hazard, under which scheme, and what exposure limits apply?", "kind": "definition" }, { "id": "classified-hazards-q02", "text": "What protection does handling require, and what must an agent refuse to do without it?", "kind": "action" } ] } ] }, { "id": "regulatory-identity", "name": "Regulatory identity and control", "description": "Registration, restriction and transport rules by jurisdiction.", "findings": [ { "id": "controls", "name": "Controls and jurisdiction", "description": "Where it is restricted and what the restriction attaches to.", "questions": [ { "id": "controls-q01", "text": "Which registrations, restrictions or transport rules cover antigen, and where?", "kind": "provenance" }, { "id": "controls-q02", "text": "Does the control attach to the substance, its concentration, or its intended use?", "kind": "boundary" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a antigen came from and when it held.", "rationale": "A claim without a source and a time cannot be superseded, only overwritten, and an agent that overwrites loses the ability to explain itself.", "layers": [ { "id": "source-and-authority", "name": "Source and authority", "description": "Who said it, on what evidence, and how strongly.", "findings": [ { "id": "claim-provenance", "name": "Claim provenance and confidence", "description": "The authority behind each claim about a antigen and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "claim-provenance-q02", "text": "Who or what asserted this about a claim about a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "claim-provenance-q03", "text": "What may an agent decide or do once a claim about a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "time-and-versions", "name": "Time, versions and supersession", "description": "When a claim was true, when it was learnt, and what replaced it.", "findings": [ { "id": "validity-and-supersession", "name": "Validity period and supersession", "description": "How an old claim about a antigen is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a antigen, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "validity-and-supersession-q02", "text": "Who or what asserted this about the validity of a claim about a antigen, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "validity-and-supersession-q03", "text": "What may an agent decide or do once the validity of a claim about a antigen is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 9, "layers": 20, "findings": 22, "questions": 60 } } } }