{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:21:02Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 21.9, "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: 01a09558-655d-7f00-b78b-e52411683c65\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: mitochondrial ribosome\nSense to describe: (none recorded)\nDomain code: PHY.LIV\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 04", "usd": 0.0, "recall": true }, "codex": { "seconds": 68.9, "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: 01a09558-6557-7542-bf56-4b3a1ea15bab\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: mitochondrial ribosome\nRegistry id: vr.tr.mitochondrial-ribosome\nPlane / domain: PHY / PHY.LIV\nRegistry definition: (none recorded)\nNames folded into" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:49:49+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:28+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q21234507", "registryId": "vr.tr.mitochondrial-ribosome", "name": "mitochondrial ribosome", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.LIV" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q21234507/", "model": { "registry_id": "vr.tr.mitochondrial-ribosome", "name": "mitochondrial ribosome", "purpose": "Enable an agent to recognise a mitochondrial ribosome, assess its assembly and translation competence, and evaluate observations or interventions within the correct organism and mitochondrial context.", "definition": "A mitochondrial ribosome, or mitoribosome, is a ribonucleoprotein complex within mitochondria that translates mitochondrial messenger RNA into proteins using transfer RNAs and the applicable mitochondrial genetic code.", "scope_statement": "This model owns the mitochondrial ribosome as a ribonucleoprotein translation complex, including its constituent subunits, assembly states, mitochondrial interactions and functional evidence, while distinguishing lineage-specific forms from universal requirements.", "in_scope": [ "Identification of mitochondrial ribosomes and their small and large subunits in a specified organism", "Ribosomal RNA and protein composition, architecture and component occupancy", "Assembly, maturation, subunit association and turnover states", "Translation of mitochondrial messenger RNA and interactions with translation factors", "Mitochondrial localisation, membrane association and nascent-chain delivery", "Evidence for functional impairment, experimental perturbation and recovery" ], "out_of_scope": [ "Whole mitochondria, their biogenesis and overall metabolic state", "Cytosolic, bacterial and plastid ribosomes as independently modelled complexes", "Mitochondrial genomes and transcripts beyond their direct relationship to ribosome composition or translation", "Free ribosomal proteins, ribosomal RNA and assembly factors outside their participation in the complex", "Respiratory-chain complexes after their translation and delivery", "Organism-level diseases, diagnosis and treatment decisions" ], "distinguishing_features": [ "Identification requires evidence connecting the complex to mitochondrial translation; similarity to a bacterial ribosome alone is insufficient.", "Assignment uses a lineage-appropriate combination of ribosomal RNA, ribosomal proteins and structural evidence; a mammalian composition or sedimentation value is not a universal test.", "Small-subunit and large-subunit particles must be distinguished from an associated mitochondrial ribosome and from immature assembly intermediates.", "Mitochondrial localisation alone does not establish identity: associated translation factors and other mitochondrial ribonucleoprotein particles require separate classification.", "An intact-looking particle is distinguished from an actively translating particle by evidence of substrate engagement or peptide synthesis." ], "characteristics": [ { "name": "Organism and biological context", "kind": "relation", "unit_or_values": "Taxon identifier, strain or genotype, tissue or cell type, and experimental condition", "why_it_matters": "Composition, architecture and interpretation of function depend on the biological context." }, { "name": "Particle class", "kind": "category", "unit_or_values": "Small subunit; large subunit; associated ribosome; assembly intermediate; unresolved particle", "why_it_matters": "Prevents isolated subunits or precursors from being recorded as complete functional complexes." }, { "name": "Constituent inventory", "kind": "relation", "unit_or_values": "Identified ribosomal RNA and protein components with reference identifiers, occupancy evidence and uncertainty", "why_it_matters": "Supports identity assignment and identifies missing, substituted or incompletely resolved components." }, { "name": "Sedimentation coefficient", "kind": "measurement", "unit_or_values": "Svedberg units (S), with preparation and assay conditions", "why_it_matters": "Helps characterise particles within a reference context but cannot establish identity or completeness by itself." }, { "name": "Assembly and maturation state", "kind": "state", "unit_or_values": "Precursor; maturing; mature; defective; disassembling; unresolved", "why_it_matters": "Separates normal maturation from persistent assembly defects or degradation." }, { "name": "Translation engagement", "kind": "state", "unit_or_values": "Unengaged; initiating; elongating; terminating; recycling; stalled; unresolved", "why_it_matters": "Connects particle state to the translation step that an observation or intervention concerns." }, { "name": "Translation activity", "kind": "measurement", "unit_or_values": "Assay-defined peptide synthesis rate or relative activity, with denominator, time interval and controls", "why_it_matters": "Provides functional evidence while distinguishing per-particle activity from changes in particle abundance." }, { "name": "Mitochondrial spatial association", "kind": "relation", "unit_or_values": "Observed submitochondrial location and contacts with membranes, insertion machinery or other partners", "why_it_matters": "Links the ribosome to its cellular setting and possible delivery routes for newly synthesised proteins." } ], "affordances": [ "Classify an observed particle against organism-specific mitochondrial ribosome references.", "Compare constituent occupancy and architecture across mature particles, intermediates and perturbed samples.", "Assess whether evidence supports assembly competence, active translation or a specific stalled state.", "Trace a candidate component defect to a proposed assembly or translation mechanism.", "Select discriminating localisation, structural, composition or translation assays.", "Evaluate a perturbation by comparing mitochondrial translation effects with cytosolic translation and broader mitochondrial effects." ], "agent_conduct": { "may": [ "Describe mitochondrial ribosomes and their function from reliable sources.", "Explain how some antibiotics can affect mitochondrial ribosomes, citing published research." ], "must_not": [ "Diagnose a mitochondrial disease in a particular person.", "Advise starting, stopping or changing a medicine because of its effect on mitochondria.", "Present early research findings as established treatments.", "Disclose a person's genetic test results without consent." ], "requires_human": [ "Clinical decisions for patients with suspected mitochondrial disorders." ] }, "ethics": { "considerations": [ "Mitochondrial diseases are rare and serious; families need accurate information.", "Genetic data reveal information about whole families." ], "affected_parties": [ "Patients with mitochondrial disease", "Families", "Clinicians and researchers" ] }, "owners": { "steward": "Nobody owns it; it is a component of living cells.", "master_systems": [] }, "failure_modes_and_hazards": [ "Defects in mitoribosome components can cause serious inherited diseases.", "Some antibiotics can impair mitochondrial ribosomes and cause side effects." ], "what_it_is_for": [ "Mitochondrial ribosomes operate inside mitochondria to synthesize proteins encoded by the mitochondrial genome.", "They are studied in mitochondrial biology, inherited disease research and investigations of compounds that affect mitochondrial translation." ], "standards_and_regulation": [ "The Gene Ontology Consortium provides the cellular component classification mitochondrial ribosome for annotating this complex." ], "visual_identification": [ "Cryo-electron microscopy can resolve a small and a large subunit whose detailed architecture differs from cytosolic ribosomes.", "Mammalian mitochondrial ribosomes show extensive protein components and reduced ribosomal RNA relative to bacterial ribosomes in resolved structural maps.", "Localization within mitochondria supports identification, but molecular markers or structural evidence are needed to distinguish the complex reliably." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q21234507: mitochondrial ribosome", "url": "https://www.wikidata.org/wiki/Q21234507", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Mitochondrial ribosome", "url": "https://en.wikipedia.org/wiki/Mitochondrial_ribosome", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "mitochondrial-ribosome-identity", "name": "Mitochondrial ribosome identity", "description": "Establishes which mitochondrial translation particle is being represented and which biological reference applies.", "rationale": "Mitochondrial ribosomes must be recognised without treating one organism's architecture as the definition for all organisms.", "layers": [ { "id": "lineage-and-context", "name": "Lineage and context", "description": "Anchors particle identity to the organism and sample.", "findings": [ { "id": "applicable-reference", "name": "Applicable reference", "description": "Record the taxonomic and experimental context needed to choose an appropriate mitochondrial ribosome reference.", "questions": [ { "text": "Which organism, strain or genotype and tissue or cell type supplied the particle?", "kind": "provenance", "id": "applicable-reference-q01" }, { "text": "Which reference establishes the expected mitochondrial ribosome components for this lineage?", "kind": "definition", "id": "applicable-reference-q02" } ] } ] }, { "id": "particle-boundaries", "name": "Particle boundaries", "description": "Separates mitochondrial ribosomes from related particles and neighbouring ribosome systems.", "findings": [ { "id": "identity-and-completeness", "name": "Identity and completeness", "description": "Require an explicit particle assignment supported by mitochondrial identity and subunit evidence.", "questions": [ { "text": "What evidence distinguishes this particle from cytosolic, bacterial or plastid ribosomes and other mitochondrial RNA-protein complexes?", "kind": "boundary", "id": "identity-and-completeness-q01" }, { "text": "Is the observation an associated ribosome, an isolated subunit or an assembly intermediate?", "kind": "definition", "id": "identity-and-completeness-q02" } ] } ] } ] }, { "id": "rna-protein-architecture", "name": "RNA-protein architecture", "description": "Represents the constituent inventory and structural organisation of the particle.", "rationale": "Recognition and defect assessment require lineage-specific evidence about both RNA and protein components.", "layers": [ { "id": "constituent-composition", "name": "Constituent composition", "description": "Records components assigned to each subunit and the strength of their identification.", "findings": [ { "id": "component-occupancy", "name": "Component occupancy", "description": "Distinguish expected components, detected components and uncertain occupancy without equating non-detection with absence.", "questions": [ { "text": "Which ribosomal RNA species and ribosomal proteins are assigned to each subunit?", "kind": "definition", "id": "component-occupancy-q01" }, { "text": "For each apparently missing component, what evidence separates true absence from incomplete detection or structural resolution?", "kind": "measurement", "id": "component-occupancy-q02" } ] } ] }, { "id": "functional-architecture", "name": "Functional architecture", "description": "Relates structural observations to the translation machinery within the particle.", "findings": [ { "id": "translation-site-integrity", "name": "Translation-site integrity", "description": "Record evidence concerning the decoding region, catalytic region, subunit interface and nascent-chain exit path.", "questions": [ { "text": "Which translation sites and intersubunit contacts are resolved, altered or unresolved in the observed structure?", "kind": "measurement", "id": "translation-site-integrity-q01" }, { "text": "Which proposed architectural differences are supported for this lineage, and which were inferred from another organism?", "kind": "provenance", "id": "translation-site-integrity-q02" } ] } ] } ] }, { "id": "assembly-and-maintenance", "name": "Assembly and maintenance", "description": "Tracks maturation of mitochondrial ribosomal subunits and the fate of incomplete or damaged particles.", "rationale": "A deficit in mature ribosomes must be distinguished from reduced activity of otherwise assembled particles.", "layers": [ { "id": "subunit-maturation", "name": "Subunit maturation", "description": "Connects RNA maturation, protein incorporation and assembly-factor interactions to particle state.", "findings": [ { "id": "maturation-evidence", "name": "Maturation evidence", "description": "Assign maturation states from observed components and processing evidence rather than from particle size alone.", "questions": [ { "text": "What RNA processing, component incorporation or assembly-factor evidence supports the assigned maturation state?", "kind": "measurement", "id": "maturation-evidence-q01" }, { "text": "Which observations distinguish a normal transient intermediate from a persistently blocked assembly intermediate?", "kind": "boundary", "id": "maturation-evidence-q02" } ] } ] }, { "id": "particle-maintenance", "name": "Particle maintenance", "description": "Captures subunit association, stability and turnover under defined conditions.", "findings": [ { "id": "assembly-versus-loss", "name": "Assembly versus loss", "description": "Separate changes in production, association and degradation when interpreting particle abundance.", "questions": [ { "text": "How do small-subunit, large-subunit and associated-ribosome abundances change over the observation period?", "kind": "measurement", "id": "assembly-versus-loss-q01" }, { "text": "What experiment could distinguish impaired assembly from accelerated turnover or preparation-induced dissociation?", "kind": "action", "id": "assembly-versus-loss-q02" } ] } ] } ] }, { "id": "mitochondrial-translation", "name": "Mitochondrial translation", "description": "Represents substrate engagement, translation-cycle state and production of mitochondrial gene products.", "rationale": "Particle presence alone cannot establish whether mitochondrial protein synthesis is proceeding correctly.", "layers": [ { "id": "substrates-and-cycle-state", "name": "Substrates and cycle state", "description": "Identifies messenger RNA, transfer RNA and factor interactions associated with translation.", "findings": [ { "id": "engaged-translation-complex", "name": "Engaged translation complex", "description": "Record the substrates and factors supporting a particular translation-state assignment.", "questions": [ { "text": "Which mitochondrial transcript, transfer RNAs and translation factors are associated with the observed particle?", "kind": "measurement", "id": "engaged-translation-complex-q01" }, { "text": "What evidence supports initiation, elongation, termination, recycling or stalling rather than an unengaged state?", "kind": "definition", "id": "engaged-translation-complex-q02" } ] } ] }, { "id": "output-and-decoding", "name": "Output and decoding", "description": "Assesses peptide synthesis and interpretation under the organism's mitochondrial decoding system.", "findings": [ { "id": "translation-performance", "name": "Translation performance", "description": "Connect activity measurements to their substrates, normalisation and applicable mitochondrial genetic code.", "questions": [ { "text": "Which mitochondrial genetic code and transcript annotations are required to interpret the measured translation products?", "kind": "definition", "id": "translation-performance-q01" }, { "text": "What assay measures peptide output, and how does it separate particle abundance, synthesis rate and product degradation?", "kind": "measurement", "id": "translation-performance-q02" } ] } ] } ] }, { "id": "cellular-coupling-and-perturbation", "name": "Cellular coupling and perturbation", "description": "Places the particle in its mitochondrial environment and evaluates interventions affecting its function.", "rationale": "Spatial interactions and indirect mitochondrial defects can change apparent ribosome performance and confound intervention claims.", "layers": [ { "id": "localisation-and-product-delivery", "name": "Localisation and product delivery", "description": "Records submitochondrial location and evidence for connections to nascent-chain delivery machinery.", "findings": [ { "id": "spatial-and-functional-contacts", "name": "Spatial and functional contacts", "description": "Distinguish proximity, physical contact and demonstrated functional coupling.", "questions": [ { "text": "What evidence locates the particle within mitochondria and establishes any association with the inner membrane?", "kind": "measurement", "id": "spatial-and-functional-contacts-q01" }, { "text": "Which contacts support nascent-chain delivery, and where does responsibility pass to membrane insertion or protein-complex assembly models?", "kind": "boundary", "id": "spatial-and-functional-contacts-q02" } ] } ] }, { "id": "perturbation-and-causal-assessment", "name": "Perturbation and causal assessment", "description": "Evaluates whether a genetic, chemical or environmental change acts on the ribosome itself.", "findings": [ { "id": "direct-versus-indirect-impairment", "name": "Direct versus indirect impairment", "description": "Link a perturbation to a specific ribosomal mechanism while retaining plausible upstream and downstream explanations.", "questions": [ { "text": "What evidence separates a direct ribosomal defect from altered transcript availability, transfer RNA function, protein import or mitochondrial energetic state?", "kind": "boundary", "id": "direct-versus-indirect-impairment-q01" }, { "text": "Which controlled comparison or rescue experiment would test the proposed mechanism while monitoring cytosolic translation?", "kind": "action", "id": "direct-versus-indirect-impairment-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": [ "This is a molecular complex, not an organism; taxonomic authorities and conservation status do not apply.", "The sedimentation values given are mammalian conventions, not universal mitochondrial values; sedimentation coefficients are not additive.", "Composition, architecture and genetic-code usage vary substantially among lineages; the kinds listed are broad biological groupings, not a formal classification." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of mitochondrial ribosome 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": [ "Animal mitoribosomes", "Fungal mitoribosomes", "Plant mitoribosomes", "Protist mitoribosomes" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of mitochondrial ribosome 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 (GO)", "value_or_pattern": "GO: followed by seven digits", "note": "Cellular Component terms distinguish the mitochondrial ribosome and its subunits; no exact accession is asserted here." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of mitochondrial ribosome 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": [ "Synthesis of mitochondrially encoded proteins required for oxidative phosphorylation.", "Investigation of mitochondrial translation disorders and respiratory-chain dysfunction.", "Assessment of drug toxicity caused by unintended inhibition of mitochondrial translation.", "Structural and evolutionary research on the divergence of mitochondrial and bacterial translation systems." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of mitochondrial ribosome 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": "Sedimentation coefficient of the assembled mammalian mitoribosome", "typical_range": "Approximately 55", "unit": "Svedberg (S)" }, { "quantity": "Sedimentation coefficient of the mammalian small subunit", "typical_range": "Approximately 28", "unit": "Svedberg (S)" }, { "quantity": "Sedimentation coefficient of the mammalian large subunit", "typical_range": "Approximately 39", "unit": "Svedberg (S)" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of mitochondrial ribosome 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": [ "Defects in mitoribosomal proteins, ribosomal RNAs or assembly factors can impair mitochondrial protein synthesis and oxidative phosphorylation.", "Certain antibiotics can inhibit mitochondrial translation because of similarities to bacterial translation machinery.", "Some mitochondrial ribosomal RNA variants increase susceptibility to aminoglycoside-associated hearing loss.", "Faulty assembly, decoding or translation termination can reduce production of functional mitochondrial proteins." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of mitochondrial ribosome 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": "Cytosolic ribosome", "difference": "Operates in the cytosol or on the endoplasmic reticulum rather than within mitochondria and translates a different pool of messenger RNAs." }, { "name": "Bacterial ribosome", "difference": "Functions in a bacterial cell; mitoribosomes are evolutionarily related but have lineage-specific changes in RNA, protein composition and architecture." }, { "name": "Chloroplast ribosome", "difference": "Translates messenger RNAs within chloroplasts rather than mitochondria." }, { "name": "Mitochondrial ribosomal subunit", "difference": "Is one component of the ribosome; translation requires cooperation between the small and large subunits." }, { "name": "Mitochondrion", "difference": "Is the organelle containing mitoribosomes and other systems, rather than the translation complex itself." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of mitochondrial ribosome this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which authoritative lineage-specific references should define expected constituent inventories and accepted mitochondrial ribosome nomenclature?", "Which architectural features can be required across mitochondrial ribosomes, and which must remain conditional on lineage?", "What evidence thresholds reliably distinguish mature but inactive particles from late assembly intermediates in each experimental system?", "How should translation measurements from different assays be normalised so that particle abundance, catalytic activity and product stability remain distinguishable?", "Which membrane contacts, assembly pathways and stalled-ribosome responses are experimentally established in each represented lineage?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 17, "questions": 27 } }