{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T09:30:47Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 18.4, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a094f3-5bce-7923-b80b-e364f1df2d1b\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: Epiboly\nSense to describe: (none recorded)\nDomain code: ACT.PRC\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001 registe", "usd": 0.0, "recall": true }, "codex": { "seconds": 76.4, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a094f3-5bda-7f00-9d97-7a615c8431ad\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: Epiboly\nRegistry id: vr.tr.epiboly\nPlane / domain: ACT / ACT.PRC\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext " } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:16:20+00:00", "fields": [ "agent_conduct", "ethics", "owners" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:26+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q1484637", "registryId": "vr.tr.epiboly", "name": "Epiboly", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q1484637/", "model": { "registry_id": "vr.tr.epiboly", "name": "Epiboly", "purpose": "Enable an agent to recognise epiboly, assess the progress and coordination of tissue spreading, and identify evidence needed to explain or investigate abnormal progression.", "definition": "Epiboly is a morphogenetic movement in which a tissue sheet thins and spreads over underlying cells or yolk, contributing to embryonic coverage and body organisation during early development.", "scope_statement": "This model owns vr.tr.epiboly in ACT / ACT.PRC: the developmental process in which a tissue thins and spreads over an underlying surface, including its participating tissues, changing geometry, progression and supported mechanisms; species-specific implementations must be identified explicitly.", "in_scope": [ "Recognition of an epibolic movement in a specified embryo and tissue", "Changes in tissue coverage, thickness and advancing-margin geometry", "Coordination between spreading tissues and their underlying substrate", "Cell behaviours and mechanical processes implicated in spreading", "Progression, completion and experimentally observed disruptions" ], "out_of_scope": [ "Gastrulation as a whole and its complete sequence of movements", "Germ-layer specification and lineage determination except as context for identifying participants", "Invagination, involution, ingression and convergence-extension as independently modelled processes", "Complete anatomy or developmental staging of a species", "General molecular functions of adhesion proteins and cytoskeletal regulators", "Wound closure and pathological tissue overgrowth unless separately established as within this registry entry" ], "distinguishing_features": [ "Require evidence of tissue spreading across an underlying surface; displacement of a cell group alone does not establish epiboly.", "Assess spreading together with tissue thickness and cell rearrangement; increased tissue size alone can reflect growth without establishing epibolic deformation.", "Distinguish outward surface coverage from inward bending, rolling or individual-cell internalisation, while allowing these movements to occur concurrently.", "Distinguish increased surface coverage from tissue narrowing and elongation; document coupled convergence-extension without treating the two processes as interchangeable.", "Treat zebrafish yolk enclosure as a species-specific instance, not a requirement that every epiboly event possess a yolk syncytial layer." ], "characteristics": [ { "name": "Developmental context", "kind": "relation", "unit_or_values": "Species, embryo identifier, developmental stage and staging reference", "why_it_matters": "Determines which tissues, landmarks and progression criteria apply." }, { "name": "Spreading tissue and substrate", "kind": "relation", "unit_or_values": "Named tissue or cell population linked to the surface it covers", "why_it_matters": "Prevents different participating layers from being treated as one moving boundary." }, { "name": "Coverage", "kind": "measurement", "unit_or_values": "Percent of a defined reference surface, or a named staging convention with its formula", "why_it_matters": "Quantifies advancement while preventing surface-area coverage from being confused with axial margin position." }, { "name": "Tissue thickness", "kind": "measurement", "unit_or_values": "Micrometres or cell layers at specified positions and times", "why_it_matters": "Tests whether surface expansion accompanies thinning and whether thinning is spatially uneven." }, { "name": "Margin position and velocity", "kind": "measurement", "unit_or_values": "Micrometres, degrees or normalised coordinates; corresponding change per minute", "why_it_matters": "Reveals progression, local stalling and differences between tissue margins." }, { "name": "Layer coordination", "kind": "measurement", "unit_or_values": "Separation between identified margins in micrometres or time lag in minutes", "why_it_matters": "Detects uncoupling that an embryo-level stage label could conceal." }, { "name": "Observed cell behaviour", "kind": "category", "unit_or_values": "Flattening, radial intercalation, neighbour exchange, division, other documented behaviour or unresolved", "why_it_matters": "Connects tissue deformation to observed cellular events without assuming a universal mechanism." }, { "name": "Progression state", "kind": "state", "unit_or_values": "Not initiated, progressing, delayed relative to reference, stalled within observation window, completed or indeterminate", "why_it_matters": "Supports decisions about continued observation and comparison with suitable controls." } ], "affordances": [ "Classify a recorded tissue movement as epiboly, a coupled movement or an unresolved candidate.", "Measure coverage, thinning and margin advance from calibrated time-series observations.", "Compare tissue-specific progression with a species- and condition-matched reference.", "Locate asymmetric spreading, persistent uncovered regions or separation between participating margins.", "Compare candidate cellular and mechanical explanations against direct observations and perturbation evidence.", "Select follow-up observations that distinguish delayed progression from persistent failure." ], "agent_conduct": { "may": [ "Explain epiboly and its role in development from scientific sources.", "Annotate imaging data from approved developmental studies." ], "must_not": [ "Misrepresent findings from embryo studies or invent results.", "Assist in animal experiments without approved ethics review.", "Apply findings from model organisms to humans without stating the limits." ], "requires_human": [ "Approving experiments on vertebrate embryos." ] }, "ethics": { "considerations": [ "Research on embryos raises questions about animal welfare and the limits of use.", "Overstated claims mislead patients and the public." ], "affected_parties": [ "Research animals", "Researchers", "The public" ] }, "owners": { "steward": "Nobody owns the process; research institutions answer for the studies.", "master_systems": [] }, "what_it_is_for": [ "Epiboly is studied in developmental biology when embryonic tissues spread over underlying cells or yolk.", "Microscopy and tissue tracking are used to compare its timing, coverage and coordination across embryos and experimental conditions." ], "visual_identification": [ "Time series microscopy shows a tissue sheet expanding its coverage over underlying embryonic material.", "The spreading sheet becomes thinner as its surface coverage increases.", "In embryos with a prominent yolk mass, the tissue margin advances around the yolk rather than folding inward as a localized pocket." ], "failure_modes_and_hazards": [ "Disrupted tissue spreading can contribute to incomplete embryonic coverage and abnormal development.", "Confusing epiboly with other tissue movements can lead to incorrect developmental staging or mechanistic conclusions.", "Observation conditions that damage embryos can create apparent abnormalities and compromise research findings." ], "facets_not_applicable": { "interfaces": "No specific standard, law or official classification applies universally to epiboly itself." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q1484637: Epiboly", "url": "https://www.wikidata.org/wiki/Q1484637", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Epiboly", "url": "https://en.wikipedia.org/wiki/Epiboly", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "epibolic-identity", "name": "Epibolic identity", "description": "Establish whether the recorded event is epiboly and define the biological instance.", "rationale": "The registry provides no definition, and a familiar species example must not become the universal boundary.", "layers": [ { "id": "movement-recognition", "name": "Movement recognition", "description": "Identify surface spreading and its relationship to tissue deformation.", "findings": [ { "id": "spreading-over-substrate", "name": "Spreading over a substrate", "description": "Record which tissue expands over which surface and what observations establish the movement. Zebrafish blastoderm spreading over the yolk provides one experimentally studied instance. [Primary research](https://pmc.ncbi.nlm.nih.gov/articles/PMC5773767/)", "questions": [ { "text": "Which tissue spreads over which underlying surface in this instance?", "kind": "definition", "id": "spreading-over-substrate-q01" }, { "text": "What time-resolved evidence separates surface spreading from translation or growth alone?", "kind": "boundary", "id": "spreading-over-substrate-q02" } ] } ] }, { "id": "instance-and-neighbours", "name": "Instance and neighbouring movements", "description": "Bind the process to an embryo and separate concurrently occurring movements.", "findings": [ { "id": "developmental-event-boundary", "name": "Developmental event boundary", "description": "Record species, tissue identity and event limits, with separate annotations for internalisation or axis-elongating movements.", "questions": [ { "text": "Which embryo, species and staging reference identify this epiboly event?", "kind": "provenance", "id": "developmental-event-boundary-q01" }, { "text": "Which observed movements are assigned to epiboly, and which require linked models for other gastrulation movements?", "kind": "boundary", "id": "developmental-event-boundary-q02" } ] } ] } ] }, { "id": "coverage-and-deformation", "name": "Coverage and deformation", "description": "Describe how the spreading tissue changes shape relative to the embryo.", "rationale": "A stage label alone cannot reveal the extent, direction or uniformity of spreading.", "layers": [ { "id": "surface-and-margin", "name": "Surface and margin", "description": "Define the reference geometry and quantify boundary advancement.", "findings": [ { "id": "explicit-coverage-convention", "name": "Explicit coverage convention", "description": "Keep measured surface coverage, axial margin position and conventional percentage-stage labels distinct unless their conversion is specified.", "questions": [ { "text": "Does the reported percentage denote surface area, normalised margin position or a published staging convention?", "kind": "measurement", "id": "explicit-coverage-convention-q01" }, { "text": "Which anatomical landmarks and geometric reconstruction define the reference surface?", "kind": "measurement", "id": "explicit-coverage-convention-q02" } ] } ] }, { "id": "thinning-and-uniformity", "name": "Thinning and uniformity", "description": "Relate area expansion to local thickness and spatial differences.", "findings": [ { "id": "local-deformation-pattern", "name": "Local deformation pattern", "description": "Record thickness and margin trajectories at multiple positions rather than inferring uniform deformation from one view.", "questions": [ { "text": "How does tissue thickness change at matched positions as coverage increases?", "kind": "measurement", "id": "local-deformation-pattern-q01" }, { "text": "Which regions advance unevenly, and could projection or embryo orientation explain the apparent asymmetry?", "kind": "measurement", "id": "local-deformation-pattern-q02" } ] } ] } ] }, { "id": "participating-tissues", "name": "Participating tissues", "description": "Identify the spreading populations, substrate and coordination between them.", "rationale": "An apparently single spreading front can conceal distinct tissues with different behaviours.", "layers": [ { "id": "tissue-specific-participants", "name": "Tissue-specific participants", "description": "Record anatomical participants without imposing teleost anatomy on other organisms.", "findings": [ { "id": "identified-layer-roster", "name": "Identified layer roster", "description": "In zebrafish, distinguish the enveloping layer, deep cells and yolk syncytial layer; establish the applicable participants independently in other species. [Primary research](https://pmc.ncbi.nlm.nih.gov/articles/PMC5773767/)", "questions": [ { "text": "Which labels, lineage observations or anatomical criteria identify each participating population?", "kind": "provenance", "id": "identified-layer-roster-q01" }, { "text": "Which zebrafish tissue terms are applicable here, and which would create an unsupported equivalence?", "kind": "boundary", "id": "identified-layer-roster-q02" } ] } ] }, { "id": "intertissue-coordination", "name": "Intertissue coordination", "description": "Track relative motion and contact between identified participants.", "findings": [ { "id": "relative-margin-motion", "name": "Relative margin motion", "description": "Assess synchrony through tissue-specific trajectories and interface observations rather than a shared whole-embryo score.", "questions": [ { "text": "How do the positions and velocities of the identified tissue margins differ through time?", "kind": "measurement", "id": "relative-margin-motion-q01" }, { "text": "What observations support maintained contact, slippage or separation between participating tissues?", "kind": "measurement", "id": "relative-margin-motion-q02" } ] } ] } ] }, { "id": "spreading-mechanisms", "name": "Spreading mechanisms", "description": "Connect observed deformation with cellular behaviours and tested mechanical explanations.", "rationale": "Similar spreading geometry can arise from different contributions, so morphology alone cannot establish causation.", "layers": [ { "id": "cellular-contributions", "name": "Cellular contributions", "description": "Resolve how individual cell behaviours contribute to tissue expansion and thinning.", "findings": [ { "id": "observed-cell-rearrangement", "name": "Observed cell rearrangement", "description": "Treat flattening, radial intercalation, neighbour exchange and division as candidate contributions to test in the specified tissue.", "questions": [ { "text": "Which tracked cells flatten or change position through the tissue thickness during spreading?", "kind": "measurement", "id": "observed-cell-rearrangement-q01" }, { "text": "What evidence separates contributions from cell rearrangement, division and changes in individual cell shape?", "kind": "measurement", "id": "observed-cell-rearrangement-q02" } ] } ] }, { "id": "mechanical-explanations", "name": "Mechanical explanations", "description": "Distinguish measured forces and perturbation results from inferred driving mechanisms.", "findings": [ { "id": "force-generation-and-transmission", "name": "Force generation and transmission", "description": "Record competing explanations with tissue and stage limits. Zebrafish experiments have implicated cortical contractility, differential tension and membrane removal in epiboly mechanics. [Primary research](https://pubmed.ncbi.nlm.nih.gov/28590839/)", "questions": [ { "text": "Which tissue is proposed to generate force, and what measurements support force transmission to the spreading tissue?", "kind": "provenance", "id": "force-generation-and-transmission-q01" }, { "text": "Which perturbation and control could distinguish altered force production from altered adhesion or general tissue damage?", "kind": "action", "id": "force-generation-and-transmission-q02" } ] } ] } ] }, { "id": "progression-and-disruption", "name": "Progression and disruption", "description": "Judge the event's course, completion and response to experimental conditions.", "rationale": "Useful assessment requires explicit endpoints and controls that distinguish a local spreading defect from general developmental delay.", "layers": [ { "id": "trajectory-and-completion", "name": "Trajectory and completion", "description": "Define onset, continued progression and completion for the particular instance.", "findings": [ { "id": "contextual-progress-state", "name": "Contextual progress state", "description": "Assign state from a documented observation interval and an anatomical endpoint appropriate to the species and tissue.", "questions": [ { "text": "What observable landmarks define initiation and completion in this species?", "kind": "definition", "id": "contextual-progress-state-q01" }, { "text": "Over what interval and at what temporal resolution was advancement absent before the event was called stalled?", "kind": "measurement", "id": "contextual-progress-state-q02" } ] } ] }, { "id": "defects-and-follow-up", "name": "Defects and follow-up", "description": "Assess abnormal trajectories and choose observations that resolve their interpretation.", "findings": [ { "id": "specificity-of-disruption", "name": "Specificity of disruption", "description": "Record treatment timing, affected tissues, matched controls and recovery evidence before attributing an abnormal embryo to an epiboly-specific defect.", "questions": [ { "text": "What evidence distinguishes impaired epiboly from general developmental delay, cell loss or imaging-induced damage?", "kind": "boundary", "id": "specificity-of-disruption-q01" }, { "text": "Would longer observation, tissue-specific tracking or a controlled rescue most directly resolve the suspected defect?", "kind": "action", "id": "specificity-of-disruption-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": [ "The intended sense is inferred to be the developmental-biology process; no sense was supplied.", "The tissues involved and their force-generating mechanisms differ among organisms, so findings from zebrafish should not be assumed universal.", "Percent epiboly is a staging convention, not a universally interchangeable measure of surface area covered; its operational definition should be checked for the organism and protocol." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of Epiboly 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": [ "Studied in zebrafish and amphibian embryos to investigate coordinated cell movement, tissue mechanics and gastrulation.", "Used as a developmental staging feature in zebrafish embryology.", "Assessed in experimental studies of how genetic or chemical perturbations affect embryonic morphogenesis." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of Epiboly 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": "Progression of epiboly in zebrafish embryos", "typical_range": "0-100, with intermediate stages assigned using established morphological staging conventions", "unit": "percent epiboly" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of Epiboly 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": [ "Delayed or arrested tissue spreading can disrupt normal gastrulation and embryonic development.", "Disrupted cell adhesion or cytoskeletal force generation can impair tissue integrity and coordinated movement.", "Defective cell rearrangement can prevent normal tissue thinning and expansion." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of Epiboly 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": "Gastrulation", "difference": "Gastrulation encompasses movements that establish and organise germ layers; epiboly is one morphogenetic movement that can contribute to that process." }, { "name": "Invagination", "difference": "Invagination bends a tissue sheet inward to form a pocket, whereas epiboly spreads a sheet over underlying material." }, { "name": "Involution", "difference": "Involution rolls tissue inward over an edge, whereas epiboly extends tissue coverage over an underlying surface." }, { "name": "Convergent extension", "difference": "Convergent extension narrows and lengthens a tissue, whereas epiboly increases its coverage of an underlying surface, generally with thinning." }, { "name": "Radial intercalation", "difference": "Radial intercalation rearranges cells between tissue layers and can help drive epiboly; it is a cellular mechanism rather than the overall spreading movement." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of Epiboly this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does vr.tr.epiboly intend only embryological epiboly, or does its missing registry definition permit additional biological usages?", "Which cross-species definition handles tissue spreading with little measurable thinning without becoming indistinguishable from growth?", "Which participating tissues and mechanisms can be compared across taxa without assuming homology from similar movement?", "How should published percentage-epiboly conventions be mapped to measured geometry without treating unlike quantities as equivalent?", "Which species-, stage- and condition-specific reference trajectories justify thresholds for delay, arrest and completion?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 15, "questions": 25 } }