{ "model": { "rank": 5654, "code": "thing-q14599311", "model_id": "vr.tr.apoptotic-process", "name": "apoptotic process", "purpose": "Let an agent explain apoptosis by mechanism, roles and research, distinguish other forms of cell death, and avoid personal medical advice.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q14599311/", "tier": 2, "score": 65, "payload": { "layer": "wikidata", "aliases": [ "neuron apoptotic process", "cuproptosis", "inflammatory cell apoptotic process", "retinal cell apoptotic process", "fibroblast apoptotic process", "glial cell apoptotic process", "apoptotic process in bone marrow cell", "melanocyte apoptotic process", "mesenchymal cell apoptotic process", "apoptotic process involved in development", "muscle cell apoptotic process", "myeloid cell apoptotic process", "hepatoblast apoptotic process", "leukocyte apoptotic process", "fat cell apoptotic process", "myofibroblast cell apoptotic process", "epithelial cell apoptotic process", "natural apoptosis", "chromatolysis", "apoptotic process in response to mitochondrial fragmentation", "anoikis", "eryptosis" ], "aliasCount": 22, "merged": 22, "knownIn": 65, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q14599311", "url": "https://www.wikidata.org/wiki/Q14599311", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-11T14:09:48Z", "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": 1, "engine": "claude" }, "metaModel": { "id": "THING-Q14599311", "registryId": "vr.tr.apoptotic-process", "name": "apoptotic process", "version": "0.2.0-wave.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q14599311/", "model": { "registry_id": "vr.tr.apoptotic-process", "name": "apoptotic process", "purpose": "Let an agent explain apoptosis by mechanism, roles and research, distinguish other forms of cell death, and avoid personal medical advice.", "definition": "A form of programmed cell death in which a cell dismantles itself in a controlled way, with shrinkage, chromatin condensation, DNA fragmentation and membrane blebbing, driven by caspase enzymes through intrinsic mitochondrial and extrinsic death-receptor pathways; it shapes development and immunity, and its dysregulation is linked to cancer and neurodegeneration. Other regulated deaths such as cuproptosis are distinct.", "what_it_is_for": "Cell biology, development and disease research.", "affordances": [ "explain apoptotic pathways", "distinguish apoptosis from necrosis and other deaths", "describe roles in development and disease", "find research ontologies and data" ], "distinguishing_features": [ "Programmed and controlled", "Caspase-driven", "Little inflammation", "Essential in development" ], "appearance": "Microscopic changes such as cell shrinkage, blebbing and apoptotic bodies.", "visual_identification": [ "Shrunken cells and apoptotic bodies", "Caspase activation markers", "Necrosis causes swelling and inflammation" ], "physical_properties": [], "families_and_kinds": [ "intrinsic (mitochondrial) apoptosis", "extrinsic (death receptor) apoptosis", "cell-type specific apoptosis", "anoikis", "other regulated deaths such as ferroptosis and cuproptosis" ], "related_models": [ { "relation": "is a kind of", "target": "programmed cell death", "why": "category" }, { "relation": "occurs in", "target": "cell", "why": "unit" }, { "relation": "is related to", "target": "neuroglia", "why": "example of cell types" }, { "relation": "is dysregulated in", "target": "cancer", "why": "disease" } ], "identifiers": [], "standards_and_regulation": [ "Gene Ontology term apoptotic process", "Research ethics for animal and human studies" ], "failure_modes_and_hazards": [ "Confusing forms of cell death", "Overstating therapeutic claims", "Agents giving personal medical advice" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "mechanism", "name": "Mechanism", "description": "Pathways.", "rationale": "Pathways control death.", "layers": [ { "id": "pathways", "name": "Pathways", "description": "Intrinsic and extrinsic.", "findings": [ { "id": "pathways-finding", "name": "Pathways", "description": "Pathways.", "questions": [ { "text": "How do the intrinsic and extrinsic pathways trigger apoptosis?", "kind": "definition" }, { "text": "What role do caspases and BCL-2 proteins play?", "kind": "definition" } ] } ] }, { "id": "markers", "name": "Markers", "description": "Detection.", "findings": [ { "id": "markers-finding", "name": "Markers", "description": "Detection.", "questions": [ { "text": "How is apoptosis detected in the lab, such as by annexin V or TUNEL assays?", "kind": "definition" }, { "text": "What are the limits of each assay?", "kind": "boundary" } ] } ] } ] }, { "id": "roles", "name": "Roles", "description": "Biology.", "rationale": "Apoptosis shapes organisms.", "layers": [ { "id": "development", "name": "Development", "description": "Shaping tissues.", "findings": [ { "id": "development-finding", "name": "Development", "description": "Development.", "questions": [ { "text": "How does apoptosis shape tissues during development, such as separating fingers?", "kind": "definition" }, { "text": "Which examples are well studied?", "kind": "provenance" } ] } ] }, { "id": "immunity", "name": "Immunity", "description": "Immune function.", "findings": [ { "id": "immunity-finding", "name": "Immunity", "description": "Immune function.", "questions": [ { "text": "How does apoptosis help remove infected or unwanted immune cells?", "kind": "definition" }, { "text": "What happens when it fails?", "kind": "provenance" } ] } ] } ] }, { "id": "disease", "name": "Disease", "description": "Health links.", "rationale": "General information only.", "layers": [ { "id": "links", "name": "Links", "description": "Disease links.", "findings": [ { "id": "links-finding", "name": "Links", "description": "Disease links.", "questions": [ { "text": "How is dysregulated apoptosis linked to cancer or neurodegeneration, according to reviews?", "kind": "provenance" }, { "text": "How strong is the evidence?", "kind": "boundary" } ] } ] }, { "id": "personal", "name": "Personal", "description": "Personal questions.", "findings": [ { "id": "personal-finding", "name": "Personal", "description": "Personal advice limits.", "questions": [ { "text": "Is the user asking about their own diagnosis or treatment?", "kind": "boundary" }, { "text": "How should the agent refer them to a clinician?", "kind": "action" } ] } ] } ] }, { "id": "other", "name": "Other", "description": "Other cell deaths.", "rationale": "Distinguish forms.", "layers": [ { "id": "compare", "name": "Compare", "description": "Necrosis and others.", "findings": [ { "id": "compare-finding", "name": "Compare", "description": "Other forms.", "questions": [ { "text": "How does apoptosis differ from necrosis, ferroptosis or cuproptosis?", "kind": "definition" }, { "text": "Which nomenclature committee defines them?", "kind": "provenance" } ] } ] }, { "id": "data", "name": "Data", "description": "Ontologies.", "findings": [ { "id": "data-finding", "name": "Data", "description": "Ontologies.", "questions": [ { "text": "Which Gene Ontology terms describe this process?", "kind": "provenance" }, { "text": "Which databases annotate genes to it?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should pathways be separate entries?", "How should Gene Ontology be linked?", "How should new death forms be tracked?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "abstract concept", "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 apoptotic process, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain apoptosis by mechanism, roles and research, distinguish other forms of cell death, and avoid personal medical advice.", "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: neuron apoptotic process, cuproptosis, inflammatory cell apoptotic process, retinal cell apoptotic process, fibroblast apoptotic process, glial cell apoptotic process, apoptotic process in bone marrow cell, melanocyte apoptotic process, mesenchymal cell apoptotic process, apoptotic process involved in development, muscle cell apoptotic process, myeloid cell apoptotic process.", "22 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 65 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 apoptotic process, 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": [ "Nothing to see. What is recognised is an instance of it, and which instances count is exactly what is argued about." ], "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": [ "neuron apoptotic process", "cuproptosis", "inflammatory cell apoptotic process", "retinal cell apoptotic process", "fibroblast apoptotic process", "glial cell apoptotic process", "apoptotic process in bone marrow cell", "melanocyte apoptotic process", "mesenchymal cell apoptotic process", "apoptotic process involved in development", "muscle cell apoptotic process", "myeloid cell apoptotic process" ] } ], "standing": "Described in 65 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 22 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 apoptotic process from another, and a apoptotic process 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 apoptotic process, 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 apoptotic process, 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 apoptotic process 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 apoptotic process, 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 apoptotic process, 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 apoptotic process 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 apoptotic process 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 apoptotic process, 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 apoptotic process, 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 apoptotic process 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 apoptotic process from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a apoptotic process, 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 apoptotic process, 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 apoptotic process 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 apoptotic process 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 apoptotic process between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a apoptotic process, 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 apoptotic process, 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 apoptotic process 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 apoptotic process, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a apoptotic process 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 apoptotic process, 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 apoptotic process, 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 apoptotic process 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 apoptotic process 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 apoptotic process, 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 apoptotic process and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a apoptotic process, 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 apoptotic process, 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 apoptotic process 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 apoptotic process consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a apoptotic process 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 apoptotic process, 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 apoptotic process, 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 apoptotic process is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "definitions-in-contest", "name": "Definitions and who holds them", "description": "What apoptotic process is taken to mean, and by whom.", "rationale": "When a field disagrees about a concept, the disagreement is the content. A model that picks one definition silently destroys the information.", "layers": [ { "id": "competing-definitions", "name": "Competing definitions", "description": "The main readings and the traditions behind them.", "findings": [ { "id": "definition-map", "name": "Definitions and their holders", "description": "Each definition with the school or body that holds it.", "questions": [ { "id": "definition-map-q01", "text": "Which definitions of apoptotic process are in use, and which tradition or body holds each?", "kind": "definition" }, { "id": "definition-map-q02", "text": "What turns on the difference between them in practice?", "kind": "boundary" } ] } ] }, { "id": "operationalisation", "name": "Operationalisation", "description": "How it is measured or applied when it has to be.", "findings": [ { "id": "operational-record", "name": "Measures and proxies", "description": "Instruments and indicators used to stand in for it.", "questions": [ { "id": "operational-record-q01", "text": "How is apoptotic process operationalised or measured in practice, and by what instrument?", "kind": "measurement" }, { "id": "operational-record-q02", "text": "What does that operationalisation leave out, and when does that matter?", "kind": "boundary" } ] } ] } ] }, { "id": "instances-and-use", "name": "Instances, use and consequence", "description": "What counts as an instance of apoptotic process and what follows from calling something that.", "rationale": "Applying a concept is an act with consequences, so a model must say what the label licenses and what it does not.", "layers": [ { "id": "instances", "name": "What counts as an instance", "description": "Clear cases, borderline cases and non-cases.", "findings": [ { "id": "instance-tests", "name": "Tests for an instance", "description": "What would settle whether something falls under it.", "questions": [ { "id": "instance-tests-q01", "text": "What would settle whether something is an instance of apoptotic process?", "kind": "boundary" }, { "id": "instance-tests-q02", "text": "Which borderline cases are argued about, and on what grounds?", "kind": "definition" } ] } ] }, { "id": "consequence", "name": "Consequence of application", "description": "Rights, duties or decisions that follow from the label.", "findings": [ { "id": "consequence-record", "name": "What the label licenses", "description": "What an agent may do once something is classified this way.", "questions": [ { "id": "consequence-record-q01", "text": "What follows practically once something is treated as apoptotic process?", "kind": "action" }, { "id": "consequence-record-q02", "text": "What must an agent not infer from the label alone?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a apoptotic process 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 apoptotic process and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a apoptotic process, 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 apoptotic process, 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 apoptotic process 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 apoptotic process is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a apoptotic process, 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 apoptotic process, 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 apoptotic process 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 } } } }