{ "model": { "rank": 11314, "code": "thing-q1141026", "model_id": "vr.tr.gastrulation", "name": "gastrulation", "purpose": "Let an agent explain gastrulation and its mechanisms, relay differences across animal groups and model organisms from developmental biology references, describe its significance and disorders, and distinguish gastrulation from cleavage, neurulation and organogenesis.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q1141026/", "tier": 2, "score": 42, "payload": { "layer": "wikidata", "aliases": [ "mouse gastrulation", "gastrulation with mouth forming second", "gastrulation with mouth forming first" ], "aliasCount": 3, "merged": 3, "knownIn": 42, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": "vr.tr.gastrulation", "source": { "dataset": "wikidata", "item": "Q1141026", "url": "https://www.wikidata.org/wiki/Q1141026", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T06:04:02Z", "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-Q1141026", "registryId": "vr.tr.gastrulation", "name": "gastrulation", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q1141026/", "model": { "registry_id": "vr.tr.gastrulation", "name": "gastrulation", "purpose": "Let an agent explain gastrulation and its mechanisms, relay differences across animal groups and model organisms from developmental biology references, describe its significance and disorders, and distinguish gastrulation from cleavage, neurulation and organogenesis.", "definition": "A phase of early embryonic development in animals in which the single-layered blastula is reorganised by coordinated cell movements into a multilayered structure with the germ layers ectoderm, mesoderm and endoderm, establishing the body plan and the primitive gut, through processes such as invagination, involution, ingression and epiboly that differ between groups, as in mouse gastrulation with its primitive streak; in protostomes the blastopore forms the mouth first, while in deuterostomes such as vertebrates the mouth forms second.", "what_it_is_for": "Not applicable; a developmental process.", "affordances": [ "explain mechanisms", "relay differences across groups", "describe significance and disorders", "distinguish related stages" ], "distinguishing_features": [ "Germ layer formation", "Coordinated cell movements", "Body plan establishment", "Group-specific mechanisms" ], "appearance": "Not a visible object without microscopy; an embryo folding into layers.", "visual_identification": [ "Formation of germ layers in the embryo", "Mouse gastrulation with the primitive streak; protostome and deuterostome gastrulation", "Cleavage precedes it; neurulation and organogenesis follow" ], "physical_properties": [ { "quantity": "human gastrulation", "typical_range": "about day 14-16", "unit": "after fertilisation", "note": "" }, { "quantity": "germ layers", "typical_range": "3", "unit": "count", "note": "ectoderm, mesoderm, endoderm" }, { "quantity": "14-day rule", "typical_range": "research limit", "unit": "note", "note": "in many jurisdictions" } ], "families_and_kinds": [ "gastrulation in sea urchins and amphibians", "gastrulation in birds and mammals including mouse gastrulation with the primitive streak", "protostome gastrulation with the mouth forming first", "deuterostome gastrulation with the mouth forming second", "gastrulation in insects and other invertebrates", "gastruloids and stem cell models" ], "related_models": [ { "relation": "is a kind of", "target": "embryonic morphogenesis", "why": "in registry terms" }, { "relation": "follows", "target": "blastula", "why": "formation" }, { "relation": "produces", "target": "germ layer", "why": "ectoderm, mesoderm and endoderm" }, { "relation": "precedes", "target": "neurulation", "why": "in vertebrates" } ], "identifiers": [ { "scheme": "GO", "value_or_pattern": "GO:0007369", "note": "gastrulation" }, { "scheme": "MeSH", "value_or_pattern": "D054262", "note": "gastrulation" } ], "standards_and_regulation": [ "Research rules such as the 14-day limit on human embryo culture", "Gene Ontology definitions" ], "failure_modes_and_hazards": [ "Confusing gastrulation with cleavage or neurulation", "Overgeneralising one model organism", "Ethical sensitivity of human embryo research, to be presented with attribution" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What gastrulation is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is gastrulation, and how does it differ from cleavage, neurulation and organogenesis?", "kind": "definition" }, { "text": "Is the question about gastrulation in general, a specific organism or human embryo research?", "kind": "boundary" } ] } ] }, { "id": "mechanisms", "name": "Mechanisms", "description": "Mechanisms.", "findings": [ { "id": "mechanisms-finding", "name": "Mechanisms", "description": "Mechanisms.", "questions": [ { "text": "How do invagination, involution, ingression and epiboly form the germ layers, and how does mouse gastrulation with the primitive streak differ?", "kind": "definition" }, { "text": "Which entry fits the specific mechanism?", "kind": "action" } ] } ] } ] }, { "id": "groups", "name": "Groups", "description": "Across animals.", "rationale": "Science.", "layers": [ { "id": "protostomes", "name": "Protostomes", "description": "Protostomes and deuterostomes.", "findings": [ { "id": "protostomes-finding", "name": "Protostomes", "description": "Protostomes.", "questions": [ { "text": "How does the fate of the blastopore differ between protostomes and deuterostomes?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "models", "name": "Models", "description": "Model organisms.", "findings": [ { "id": "models-finding", "name": "Models", "description": "Models.", "questions": [ { "text": "What have sea urchins, frogs, zebrafish, chicks and mice revealed about gastrulation?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "significance", "name": "Significance", "description": "Significance.", "rationale": "Science.", "layers": [ { "id": "bodyplan", "name": "Body plan", "description": "Body plan.", "findings": [ { "id": "bodyplan-finding", "name": "Body plan", "description": "Body plan.", "questions": [ { "text": "How does gastrulation establish axes and the body plan, and what signalling controls it?", "kind": "provenance" }, { "text": "Which entry fits axis specification?", "kind": "action" } ] } ] }, { "id": "disorders", "name": "Disorders", "description": "Disorders.", "findings": [ { "id": "disorders-finding", "name": "Disorders", "description": "Disorders.", "questions": [ { "text": "What happens when gastrulation goes wrong, and how does it relate to birth defects, in general terms?", "kind": "provenance" }, { "text": "Which entry fits congenital abnormality?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Research and history.", "rationale": "Context.", "layers": [ { "id": "research", "name": "Research", "description": "Human and stem cell research.", "findings": [ { "id": "research-finding", "name": "Research", "description": "Research.", "questions": [ { "text": "How are gastruloids and embryo models used, and what ethical rules apply, with positions attributed?", "kind": "provenance" }, { "text": "Is the presentation attributed?", "kind": "boundary" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How was gastrulation discovered and named, from Haeckel to Spemann and Mangold?", "kind": "provenance" }, { "text": "Which entry fits the history of embryology?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should the primitive streak and germ layer be separate primary entries?", "How should developmental biology references be linked?", "The registry entry has merged aliases naming group-specific modes; 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": "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 gastrulation, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain gastrulation and its mechanisms, relay differences across animal groups and model organisms from developmental biology references, describe its significance and disorders, and distinguish gastrulation from cleavage, neurulation and organogenesis.", "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: mouse gastrulation, gastrulation with mouth forming second, gastrulation with mouth forming first.", "3 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 42 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 gastrulation, 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": [ "mouse gastrulation", "gastrulation with mouth forming second", "gastrulation with mouth forming first" ] } ], "standing": "Described in 42 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 gastrulation from another, and a gastrulation 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 gastrulation, 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 gastrulation, 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 gastrulation 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 gastrulation, 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 gastrulation, 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 gastrulation 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 gastrulation 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 gastrulation, 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 gastrulation, 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 gastrulation 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 gastrulation from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a gastrulation, 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 gastrulation, 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 gastrulation 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 gastrulation 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 gastrulation between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a gastrulation, 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 gastrulation, 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 gastrulation 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 gastrulation, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a gastrulation 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 gastrulation, 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 gastrulation, 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 gastrulation 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 gastrulation 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 gastrulation, 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 gastrulation and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a gastrulation, 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 gastrulation, 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 gastrulation 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 gastrulation consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a gastrulation 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 gastrulation, 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 gastrulation, 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 gastrulation 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 gastrulation 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 gastrulation 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 gastrulation 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 gastrulation 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 gastrulation?", "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 gastrulation?", "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 gastrulation 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 gastrulation and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a gastrulation, 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 gastrulation, 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 gastrulation 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 gastrulation is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a gastrulation, 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 gastrulation, 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 gastrulation 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 } } } }