{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:30:06Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 19.8, "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: 01a094bc-05da-7750-a4a4-6398610e70ac\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: cellular compartment\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:", "usd": 0.0, "recall": true }, "codex": { "seconds": 62.1, "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: 01a094bc-05d5-75d0-885a-b1fb10794be0\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: cellular compartment\nRegistry id: vr.tr.cellular-compartment\nPlane / domain: ACT / ACT.PRC\nRegistry definition: (none recorded)\nNames folded into thi" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:08:21+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "revisions": [ { "at": "2026-10-07T11:19:24+00:00", "engine": "codex", "fields": [ "agent_conduct", "definition", "distinguishing_features", "in_scope", "out_of_scope", "scope_statement", "visual_identification" ], "answering_review": "3e87cd4f07b49a82f4a59414ee9f398fb9f1d5c8b04af12f8990b32163f43330" } ], "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T12:16:30+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q189055", "registryId": "vr.tr.cellular-compartment", "name": "cellular compartment", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q189055/", "model": { "registry_id": "vr.tr.cellular-compartment", "name": "cellular compartment", "purpose": "Enable an agent to recognise a cellular compartment, assess how it maintains a distinct local environment, and judge which observations or interventions are appropriate.", "definition": "A cellular compartment is a closed, membrane-enclosed part within the cytosol that maintains an internal molecular composition or biochemical environment distinct from its surroundings while permitting regulated exchange.", "scope_statement": "This model owns the criteria, evidence and state needed to identify a closed, membrane-enclosed part within the cytosol as a compartment, including its boundary, contents, exchanges and functional organisation; it distinguishes these compartments from non-enclosed regions, membrane domains, computational partitions and annotation categories.", "in_scope": [ "Operational definitions of compartment identity in a specified cell type and condition.", "Closed, membrane-enclosed parts within the cytosol, with evidence of enclosure recorded.", "Boundary organisation, internal composition and distinction from adjacent regions.", "Transport and reactions that maintain or modify compartment state.", "Compartment formation, remodelling, inheritance and disappearance.", "Evidence supporting localisation, compartment integrity and functional attribution." ], "out_of_scope": [ "Whole-cell identity, physiology and life-cycle models.", "Complete models of particular organelles and their specialised machinery.", "Molecular identities and intrinsic properties of constituent proteins, lipids and metabolites.", "Extracellular tissue compartments and anatomical spaces.", "Complete biochemical pathway models independent of spatial localisation.", "Purely computational compartments without an asserted correspondence to a cellular region.", "Non-enclosed intracellular regions, membraneless condensates and membrane domains considered independently of an enclosed space." ], "distinguishing_features": [ "An instance must identify a region in a particular cellular context; a cellular-component vocabulary term alone identifies a class rather than a physical instance.", "A compartment claim must support a closed membrane boundary enclosing an internal space within the cytosol; a drawn image region or selective molecular partitioning alone is insufficient.", "A local concentration peak does not establish a compartment without evidence of enclosure.", "Compartment and organelle must not be assumed synonymous, and a membrane domain alone does not constitute an enclosed compartment.", "A functional label must map to a spatially supported enclosed region; participation in the same pathway does not by itself establish a shared compartment." ], "characteristics": [ { "name": "Cellular context", "kind": "relation", "unit_or_values": "Host cell, organism, cell type, developmental stage and experimental condition", "why_it_matters": "Compartment identity and expected behaviour must be interpreted within the cell and condition observed." }, { "name": "Compartment inclusion criterion", "kind": "category", "unit_or_values": "Membrane enclosure, selective partitioning, restricted exchange, other explicitly defined criterion or unresolved", "why_it_matters": "Makes competing uses of the term explicit and prevents unsupported classification." }, { "name": "Boundary organisation", "kind": "category", "unit_or_values": "Membrane-bounded, membrane-free interface, mixed, diffuse or unresolved", "why_it_matters": "Determines what evidence is needed to assess separation and exchange." }, { "name": "Spatial extent", "kind": "measurement", "unit_or_values": "Volume in µm³, area in µm² or characteristic length in µm, with segmentation method and uncertainty", "why_it_matters": "Supports comparison of size, concentration and changes in compartment organisation." }, { "name": "Topological relationships", "kind": "relation", "unit_or_values": "Contained within, encloses, adjacent to, contacts or continuous with an identified region", "why_it_matters": "Separates spatial proximity from physical continuity and nesting." }, { "name": "Local molecular enrichment", "kind": "measurement", "unit_or_values": "Dimensionless inside-to-reference concentration ratio for a named constituent under stated conditions", "why_it_matters": "Tests compositional differentiation without treating a marker as conclusive evidence of identity." }, { "name": "Exchange behaviour", "kind": "measurement", "unit_or_values": "Species-specific flux in mol/s, residence time in s or recovery timescale in s, with the measurement model stated", "why_it_matters": "Indicates how rapidly constituents cross or redistribute across the proposed boundary." }, { "name": "Observed organisational state", "kind": "state", "unit_or_values": "Forming, maintained, remodelling, dividing, merging, disassembling, disrupted or unresolved", "why_it_matters": "Connects observations and possible interventions to the compartment's current trajectory." } ], "affordances": [ "Classify a candidate region under an explicit compartment definition and record competing interpretations.", "Map compartment nesting, adjacency and continuity within a cell.", "Compare composition, geometry and exchange across conditions using compatible measurements.", "Select localisation and boundary assays that distinguish a compartment from an imaging or preparation artefact.", "Assess proposed perturbations of transport, boundary organisation or local chemistry against compartment-specific evidence.", "Track compartment formation, remodelling and loss while preserving uncertainty about identity over time." ], "agent_conduct": { "may": [ "Explain cellular compartments and their functions, citing cell biology sources.", "Annotate compartments in microscopy images or data using a controlled vocabulary." ], "must_not": [ "Assign a protein or molecule to a compartment with more certainty than the evidence supports.", "Falsify or manipulate microscopy images used as evidence of localization.", "Classify non-enclosed regions, membraneless condensates or membrane domains as cellular compartments in this closed-part sense." ], "requires_human": [ "Publishing curated localization annotations to shared databases." ] }, "ethics": { "considerations": [ "Research findings on cell compartments feed into medicine; errors mislead later work.", "Image manipulation in biology undermines trust in science." ], "affected_parties": [ "Researchers", "Patients relying on research", "Database users" ] }, "owners": { "steward": "Nobody owns the concept; ontology curators maintain its shared vocabulary.", "master_systems": [ "Gene and cell component ontologies" ] }, "visual_identification": [ "Membrane-enclosed structures such as nuclei, mitochondria or vesicles can provide evidence of cellular compartments.", "Fluorescent markers can support localisation, but a labelled region alone does not establish a closed boundary." ], "failure_modes_and_hazards": [ "Misassigned localization leads to wrong conclusions about how proteins work.", "Mislabelled annotations propagate through many databases." ], "what_it_is_for": [ "Cellular compartments are studied in cell biology to explain how cells separate biochemical activities and maintain distinct local environments.", "They provide a framework for interpreting microscopy, molecular localization and transport between regions of a cell." ], "standards_and_regulation": [ "The Gene Ontology Cellular Component ontology, maintained by the Gene Ontology Consortium, provides standardized terms for annotating cellular compartments and the locations of gene products." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q189055: cellular compartment", "url": "https://www.wikidata.org/wiki/Q189055", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Cellular compartment", "url": "https://en.wikipedia.org/wiki/Cellular_compartment", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "compartment-identity-and-topology", "name": "Compartment identity and topology", "description": "Establish what counts as the compartment and where its extent lies within cellular organisation.", "rationale": "An agent must distinguish a physical region from a terminology category and avoid conflating an organelle with its constituent compartments.", "layers": [ { "id": "definition-and-inclusion", "name": "Definition and inclusion", "description": "Record the operational meaning of compartment used for the candidate.", "findings": [ { "id": "explicit-compartment-criterion", "name": "Explicit compartment criterion", "description": "The model must state which spatial and organisational properties qualify the candidate, including whether membrane-free regions are admitted.", "questions": [ { "text": "Which definition is being applied, and what observable properties must this region satisfy?", "kind": "definition", "id": "explicit-compartment-criterion-q01" }, { "text": "Which publication, ontology or experimental convention supplies that definition?", "kind": "provenance", "id": "explicit-compartment-criterion-q02" } ] } ] }, { "id": "extent-and-nesting", "name": "Extent and nesting", "description": "Resolve the candidate's boundaries and relationships to other cellular regions.", "findings": [ { "id": "region-versus-containing-structure", "name": "Region versus containing structure", "description": "The model must distinguish a lumen, its bounding membrane and the larger structure containing both, while allowing explicitly defined composite regions.", "questions": [ { "text": "Does the named compartment include its bounding membrane, only its interior or another specified spatial extent?", "kind": "boundary", "id": "region-versus-containing-structure-q01" }, { "text": "Which neighbouring regions are enclosed, contacted or physically continuous with it?", "kind": "boundary", "id": "region-versus-containing-structure-q02" } ] } ] } ] }, { "id": "boundary-and-selective-exchange", "name": "Boundary and selective exchange", "description": "Represent the mechanisms and observations that support separation while permitting molecular exchange.", "rationale": "A compartment's separation cannot be assessed from appearance alone or treated as identical for every molecular species.", "layers": [ { "id": "boundary-maintenance", "name": "Boundary maintenance", "description": "Describe how the proposed interface is organised and sustained.", "findings": [ { "id": "separation-mechanism", "name": "Separation mechanism", "description": "The model must distinguish observed boundary features from hypotheses about membrane barriers, partitioning or other mechanisms maintaining spatial differentiation.", "questions": [ { "text": "What observation supports a boundary or persistent spatial differentiation rather than a segmentation choice?", "kind": "measurement", "id": "separation-mechanism-q01" }, { "text": "Which proposed separation mechanisms remain compatible with the evidence?", "kind": "definition", "id": "separation-mechanism-q02" } ] } ] }, { "id": "exchange-and-connectivity", "name": "Exchange and connectivity", "description": "Record entry, exit and continuity for specified constituents.", "findings": [ { "id": "species-specific-exchange", "name": "Species-specific exchange", "description": "Exchange claims must identify the constituent, route, direction and conditions rather than assigning a single permeability to the entire compartment.", "questions": [ { "text": "For which molecules have entry, exit or residence times been measured, and by what method?", "kind": "measurement", "id": "species-specific-exchange-q01" }, { "text": "What perturbation could distinguish passive redistribution from mediated transport or physical continuity?", "kind": "action", "id": "species-specific-exchange-q02" } ] } ] } ] }, { "id": "local-environment-and-function", "name": "Local environment and function", "description": "Connect compartment-specific composition and conditions to spatially supported biological activities.", "rationale": "An agent needs evidence that local conditions and activities belong to the compartment, rather than inferring function from its name or a single marker.", "layers": [ { "id": "composition-and-conditions", "name": "Composition and conditions", "description": "Characterise constituents and relevant local physicochemical measurements.", "findings": [ { "id": "measured-local-distinction", "name": "Measured local distinction", "description": "The model must identify how composition or local conditions differ from a specified reference region and preserve measurement limitations.", "questions": [ { "text": "Which constituents or conditions distinguish this compartment from its immediate surroundings?", "kind": "measurement", "id": "measured-local-distinction-q01" }, { "text": "How were localisation, sensor calibration and contamination from adjacent regions assessed?", "kind": "provenance", "id": "measured-local-distinction-q02" } ] } ] }, { "id": "spatial-functional-attribution", "name": "Spatial functional attribution", "description": "Assess whether an activity occurs within the compartment and depends on its organisation.", "findings": [ { "id": "localisation-versus-functional-dependence", "name": "Localisation versus functional dependence", "description": "The model must distinguish component presence, local activity and evidence that compartmental organisation is required for that activity.", "questions": [ { "text": "What evidence places the activity itself in this region rather than merely locating one associated molecule there?", "kind": "measurement", "id": "localisation-versus-functional-dependence-q01" }, { "text": "What intervention could test dependence on compartment organisation while checking effects on the rest of the cell?", "kind": "action", "id": "localisation-versus-functional-dependence-q02" } ] } ] } ] }, { "id": "dynamics-and-evidence-guided-intervention", "name": "Dynamics and evidence-guided intervention", "description": "Track compartment state through time and establish how observations can support intervention decisions.", "rationale": "Compartment boundaries and identities may change during observation, and the act of measurement or perturbation can alter the state being assessed.", "layers": [ { "id": "formation-and-state-transitions", "name": "Formation and state transitions", "description": "Describe emergence, persistence, remodelling and loss of the compartment.", "findings": [ { "id": "identity-through-remodelling", "name": "Identity through remodelling", "description": "The model must specify how instances are tracked across changes in shape, composition, division or merging.", "questions": [ { "text": "What tracking criterion identifies the same compartment across successive observations?", "kind": "definition", "id": "identity-through-remodelling-q01" }, { "text": "Which temporal evidence distinguishes formation or disappearance from movement, marker loss or a change in imaging visibility?", "kind": "measurement", "id": "identity-through-remodelling-q02" } ] } ] }, { "id": "observation-and-perturbation-validity", "name": "Observation and perturbation validity", "description": "Assess artefacts, intervention specificity and the evidence needed to interpret a changed compartment state.", "findings": [ { "id": "validated-compartment-response", "name": "Validated compartment response", "description": "The model must connect a proposed intervention to a measurable compartment response and distinguish that response from preparation artefacts or general cellular disruption.", "questions": [ { "text": "Which independent observation could check whether labelling, fixation, fractionation or imaging created the apparent compartment state?", "kind": "measurement", "id": "validated-compartment-response-q01" }, { "text": "Which compartment readout, whole-cell control and recovery observation are needed to interpret the proposed perturbation?", "kind": "action", "id": "validated-compartment-response-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": [ "No sense is recorded; this response assumes the cell-biological meaning. The supplied ACT.PRC domain assignment should be checked against that interpretation.", "Usage varies over whether cellular compartments must be membrane-bounded or also include membraneless regions.", "This is recalled knowledge without source verification; specific ontology mappings and numerical values require checking before publication." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of cellular compartment this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Nuclear compartment", "Cytosolic compartment", "Endoplasmic reticulum lumen", "Endosomal and lysosomal compartments", "Mitochondrial matrix and intermembrane space", "Membraneless compartments, including biomolecular condensates" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of cellular compartment this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "scheme": "Gene Ontology cellular component identifiers", "value_or_pattern": "GO: followed by seven digits", "note": "Specific compartments can be represented by cellular component terms; this ontology branch also includes structures and protein complexes that are not compartments." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of cellular compartment 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": [ "Annotating the subcellular localization of proteins and other molecules.", "Representing spatially separated reactions in biochemical and metabolic models.", "Isolating cellular fractions for biochemical analysis and proteomics.", "Studying intracellular trafficking and selective molecular transport.", "Targeting probes or therapeutic cargo to particular intracellular locations." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of cellular compartment 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": "Compartment volume", "typical_range": "Depends on compartment identity, cell type and physiological state; no universal range.", "unit": "µm³" }, { "quantity": "Internal pH", "typical_range": "Compartment-dependent; lysosomal lumens are typically approximately 4.5-5.0.", "unit": "dimensionless" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of cellular compartment 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": [ "Loss of membrane integrity can release compartment contents and disrupt cellular function.", "Incorrect protein targeting can prevent molecules from reaching the compartment where they function.", "Failure to maintain ion or proton gradients can impair compartment-specific reactions.", "Cross-contamination during subcellular fractionation can produce misleading localization results.", "Apparent colocalization in microscopy does not by itself establish residence within the same compartment." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of cellular compartment 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": "Organelle", "difference": "An organelle is a specialized cellular structure; one organelle can contain multiple distinct compartments." }, { "name": "Cellular component", "difference": "A cellular component can be a structure or molecular complex without defining a distinct intracellular region." }, { "name": "Biomolecular condensate", "difference": "A condensate is a molecularly enriched assembly that can constitute a membraneless compartment; many compartments instead have membrane boundaries." }, { "name": "Cellular compartmentalization", "difference": "Compartmentalization is the organization or process that establishes distinct regions; a compartment is one such region." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of cellular compartment this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does this registry entry intend a physical intracellular region, a cellular-component classification concept or a process-oriented abstraction, and how should its ACT / ACT.PRC placement be interpreted?", "Which authoritative definitions should govern inclusion of membrane-free condensates, diffuse reaction zones and membrane subdomains?", "Which existing Vercy models already own organelles, intracellular regions or compartmentalisation, and where should this entry link rather than duplicate them?", "What evidence and observation timescale are sufficient to distinguish a maintained compartment from transient enrichment in different cellular contexts?", "Which conventions should determine whether bounding membranes belong to the compartment and whether identity persists through division or merging?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 15, "questions": 23 } }