{ "model": { "rank": 7080, "code": "thing-q184726", "model_id": "vr.tr.phagocytosis", "name": "phagocytosis", "purpose": "Let an agent explain phagocytosis and its steps, relay its roles in immunity, tissue clearance and feeding, describe related processes and disorders, and distinguish it from other forms of endocytosis.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q184726/", "tier": 2, "score": 57, "payload": { "layer": "wikidata", "aliases": [ "apoptotic cell clearance", "hemophagocytosis", "cytophagocytosis" ], "aliasCount": 3, "merged": 3, "knownIn": 57, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": "vr.tr.phagocytosis", "source": { "dataset": "wikidata", "item": "Q184726", "url": "https://www.wikidata.org/wiki/Q184726", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T23:41:49Z", "providers": [ "Claude" ], "breadth": "written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify", "pass": 2, "wave": 3, "engine": "claude" }, "metaModel": { "id": "THING-Q184726", "registryId": "vr.tr.phagocytosis", "name": "phagocytosis", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q184726/", "model": { "registry_id": "vr.tr.phagocytosis", "name": "phagocytosis", "purpose": "Let an agent explain phagocytosis and its steps, relay its roles in immunity, tissue clearance and feeding, describe related processes and disorders, and distinguish it from other forms of endocytosis.", "definition": "The process by which a cell engulfs a large particle such as a bacterium, dead cell or debris by extending its membrane around it to form an internal vesicle, the phagosome, which fuses with lysosomes for digestion; phagocytosis is carried out by specialised immune cells such as macrophages and neutrophils and by amoebae as feeding, includes the clearance of apoptotic cells, and its dysregulation appears in conditions such as haemophagocytosis.", "what_it_is_for": "Removing pathogens, debris and dead cells; feeding in some organisms.", "affordances": [ "explain the process and steps", "relay roles in immunity and clearance", "describe related disorders", "distinguish from other endocytosis" ], "distinguishing_features": [ "Large particle uptake", "Receptor recognition", "Phagosome-lysosome fusion", "Immune and feeding roles" ], "appearance": "Not visible to the eye; seen by microscopy as a cell engulfing a particle.", "visual_identification": [ "Engulfment of large particles into a phagosome", "By macrophages, neutrophils, amoebae and others", "Pinocytosis takes fluid; receptor-mediated endocytosis takes small cargo" ], "physical_properties": [ { "quantity": "particle size", "typical_range": "over about 0.5", "unit": "micrometres", "note": "typical threshold" } ], "families_and_kinds": [ "phagocytosis of pathogens by immune cells", "clearance of apoptotic cells, or efferocytosis", "phagocytosis as feeding in amoebae and other protists", "cytophagocytosis of whole cells", "haemophagocytosis as a pathological form" ], "related_models": [ { "relation": "is a kind of", "target": "vesicle-mediated transport", "why": "in registry terms" }, { "relation": "is a kind of", "target": "endocytosis", "why": "the large-particle form" }, { "relation": "is performed by", "target": "phagocyte", "why": "such as macrophages" }, { "relation": "is part of", "target": "innate immunity", "why": "the defence system" } ], "identifiers": [ { "scheme": "Gene Ontology", "value_or_pattern": "GO:0006909", "note": "phagocytosis" } ], "standards_and_regulation": [ "No regulation; research standards and nomenclature" ], "failure_modes_and_hazards": [ "Immune deficiency when impaired", "Pathological haemophagocytosis in haemophagocytic syndromes", "Pathogens evading phagocytosis" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "How phagocytosis works.", "rationale": "Science.", "layers": [ { "id": "steps", "name": "Steps", "description": "Steps.", "findings": [ { "id": "steps-finding", "name": "Steps", "description": "Steps.", "questions": [ { "text": "What are the steps of phagocytosis, from recognition to digestion?", "kind": "definition" }, { "text": "Is the process phagocytosis or another form of endocytosis?", "kind": "boundary" } ] } ] }, { "id": "cells", "name": "Cells", "description": "Phagocytes.", "findings": [ { "id": "cells-finding", "name": "Cells", "description": "Cells.", "questions": [ { "text": "Which cells perform phagocytosis, and how do they recognise targets?", "kind": "definition" }, { "text": "Which entry fits macrophage?", "kind": "action" } ] } ] } ] }, { "id": "roles", "name": "Roles", "description": "Roles.", "rationale": "Science.", "layers": [ { "id": "immunity", "name": "Immunity", "description": "Immunity.", "findings": [ { "id": "immunity-finding", "name": "Immunity", "description": "Immunity.", "questions": [ { "text": "How does phagocytosis defend against pathogens and link to adaptive immunity?", "kind": "provenance" }, { "text": "Which entry fits innate immunity?", "kind": "action" } ] } ] }, { "id": "clearance", "name": "Clearance", "description": "Clearance of dead cells.", "findings": [ { "id": "clearance-finding", "name": "Clearance", "description": "Clearance.", "questions": [ { "text": "How are apoptotic cells cleared, and why does it matter for inflammation?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] } ] }, { "id": "disease", "name": "Disease", "description": "Disorders and evasion.", "rationale": "Clinical.", "layers": [ { "id": "disorders", "name": "Disorders", "description": "Disorders.", "findings": [ { "id": "disorders-finding", "name": "Disorders", "description": "Disorders.", "questions": [ { "text": "Which disorders involve defective or excessive phagocytosis, such as chronic granulomatous disease and haemophagocytic syndromes?", "kind": "provenance" }, { "text": "Is the user asking about a personal condition, which needs a clinician?", "kind": "boundary" } ] } ] }, { "id": "evasion", "name": "Evasion", "description": "Pathogen evasion.", "findings": [ { "id": "evasion-finding", "name": "Evasion", "description": "Evasion.", "questions": [ { "text": "How do pathogens evade or exploit phagocytosis?", "kind": "provenance" }, { "text": "Which entry fits immune evasion?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Feeding and history.", "rationale": "Context.", "layers": [ { "id": "feeding", "name": "Feeding", "description": "Feeding in protists.", "findings": [ { "id": "feeding-finding", "name": "Feeding", "description": "Feeding.", "questions": [ { "text": "How do amoebae and other protists use phagocytosis to feed?", "kind": "provenance" }, { "text": "Which entry fits amoeba?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How did Metchnikoff discover phagocytosis, and how did the field develop?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should efferocytosis be a separate entry?", "How should Gene Ontology terms be linked?", "The registry entry has merged aliases naming subtypes and a pathological form; should they be split off?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "disease or condition", "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 phagocytosis, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain phagocytosis and its steps, relay its roles in immunity, tissue clearance and feeding, describe related processes and disorders, and distinguish it from other forms of endocytosis.", "characteristics": { "substance": "activity", "origin": "conceptual", "agency": "inert" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: apoptotic cell clearance, hemophagocytosis, cytophagocytosis.", "3 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 57 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 phagocytosis, and on what evidence are they told apart?" ], "whatItIsMadeOf": "something that happens over time", "physicalCharacter": [ "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" ], "howItIsRecognised": [ "Recognised by criteria applied to signs and findings, not by appearance. Two conditions can look identical and be distinguished only by test." ], "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": [ "apoptotic cell clearance", "hemophagocytosis", "cytophagocytosis" ] } ], "standing": "Described in 57 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 3 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 phagocytosis from another, and a phagocytosis 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 phagocytosis, 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 phagocytosis, 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 phagocytosis 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 phagocytosis, 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 phagocytosis, 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 phagocytosis 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 phagocytosis 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 phagocytosis, 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 phagocytosis, 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 phagocytosis 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 phagocytosis from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a phagocytosis, 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 phagocytosis, 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 phagocytosis 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 phagocytosis 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 phagocytosis between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a phagocytosis, 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 phagocytosis, 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 phagocytosis 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 phagocytosis, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a phagocytosis 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 phagocytosis, 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 phagocytosis, 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 phagocytosis is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "process-and-outcome", "name": "Process, inputs and outcome", "description": "How a phagocytosis proceeds, what it needs and what it leaves behind.", "rationale": "An activity is known by its steps and its results, and both have to be recordable while it is still running.", "layers": [ { "id": "steps-and-sequence", "name": "Steps and sequence", "description": "The steps of a phagocytosis, their order and what may run in parallel.", "findings": [ { "id": "steps-and-preconditions", "name": "Steps, preconditions and completion", "description": "What has to be true before each step of a phagocytosis and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a phagocytosis, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "steps-and-preconditions-q02", "text": "Who or what asserted this about a step of a phagocytosis, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "steps-and-preconditions-q03", "text": "What may an agent decide or do once a step of a phagocytosis is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "inputs-and-results", "name": "Inputs, resources and results", "description": "What a phagocytosis consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a phagocytosis takes and the results it leaves, wanted or not.", "questions": [ { "id": "inputs-and-outputs-q01", "text": "What identifies and describes the inputs and results of a phagocytosis, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "inputs-and-outputs-q02", "text": "Who or what asserted this about the inputs and results of a phagocytosis, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "inputs-and-outputs-q03", "text": "What may an agent decide or do once the inputs and results of a phagocytosis is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "diagnosis-and-criteria", "name": "Diagnosis, criteria and coding", "description": "What makes a case of phagocytosis a case, and under which revision.", "rationale": "Criteria change between revisions, so a diagnosis without its coding revision cannot be compared with a later one.", "layers": [ { "id": "criteria", "name": "Diagnostic criteria", "description": "The criteria in force and who issues them.", "findings": [ { "id": "criteria-record", "name": "Criteria, issuer and revision", "description": "What must be true for a diagnosis, according to whom.", "questions": [ { "id": "criteria-record-q01", "text": "What criteria define phagocytosis, issued by which body, in which revision?", "kind": "definition" }, { "id": "criteria-record-q02", "text": "What changed between revisions that would reclassify existing cases?", "kind": "boundary" } ] } ] }, { "id": "coding", "name": "Coding and terminology", "description": "The codes used to record it and their mapping.", "findings": [ { "id": "coding-record", "name": "Codes and mappings", "description": "Which classification codes apply and how they map.", "questions": [ { "id": "coding-record-q01", "text": "Which classification and terminology codes cover phagocytosis, and how do they map to each other?", "kind": "definition" }, { "id": "coding-record-q02", "text": "What is lost when a case is mapped from one scheme to another?", "kind": "boundary" } ] } ] } ] }, { "id": "course-and-population", "name": "Course, population and care", "description": "How phagocytosis develops, whom it affects, and what is done about it.", "rationale": "The condition, the diagnosis and the episode of care are three different things, and an agent must not merge them.", "layers": [ { "id": "course", "name": "Course and stages", "description": "Onset, progression, remission and outcome.", "findings": [ { "id": "course-record", "name": "Stages and transitions", "description": "The stages recorded and what moves a case between them.", "questions": [ { "id": "course-record-q01", "text": "What course does phagocytosis typically take, and what marks each stage?", "kind": "definition" }, { "id": "course-record-q02", "text": "What separates the condition itself from an episode of care for it?", "kind": "boundary" } ] } ] }, { "id": "population", "name": "Affected populations", "description": "Who is affected, how often, and on what evidence.", "findings": [ { "id": "epidemiology", "name": "Prevalence and its basis", "description": "Rates with their population, period and source.", "questions": [ { "id": "epidemiology-q01", "text": "What prevalence or incidence is reported for phagocytosis, in which population and period?", "kind": "measurement" }, { "id": "epidemiology-q02", "text": "What may an agent not conclude about an individual from a population rate?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a phagocytosis 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 phagocytosis and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a phagocytosis, 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 phagocytosis, 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 phagocytosis 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 phagocytosis is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a phagocytosis, 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 phagocytosis, 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 phagocytosis is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 6, "layers": 12, "findings": 14, "questions": 38 } } } }