{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:46:50Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 23.2, "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: 01a094cb-25a8-7f02-9c94-4e2ad91cdc4f\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: collagen type I trimer\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 04", "usd": 0.0, "recall": true }, "codex": { "seconds": 75.0, "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: 01a094cb-25b4-7932-a7b5-e2fd1c6d2699\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: collagen type I trimer\nRegistry id: vr.tr.collagen-type-i-trimer\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:57:13+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "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-Q14881714", "registryId": "vr.tr.collagen-type-i-trimer", "name": "collagen type I trimer", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q14881714/", "model": { "registry_id": "vr.tr.collagen-type-i-trimer", "name": "collagen type I trimer", "purpose": "Enable an agent to recognise a collagen type I trimer, assess its molecular integrity and processing state, and determine which characterisation or assembly actions its evidence supports.", "definition": "A collagen type I trimer is a three-chain, triple-helical protein assembly, usually composed of two α1(I) chains and one α2(I) chain, that forms the molecular building block of type I collagen fibrils in vertebrate extracellular matrices.", "scope_statement": "This model owns the molecular complex identified as vr.tr.collagen-type-i-trimer in PHY / PHY.MAT: its constituent chains, triple-helical organisation, molecular modifications, maturation and experimentally observed behaviour; precursor forms and alternative chain compositions require explicit qualification.", "in_scope": [ "Type I collagen chain identities, sequences, species and trimer stoichiometry", "Triple-helix integrity and molecular damage", "Propeptide processing and telopeptide retention", "Hydroxylation, glycosylation and molecular cross-link participation", "Condition-dependent solubility, stability and capacity to participate in fibril assembly", "Evidence connecting a characterised preparation to the registered molecular entity" ], "out_of_scope": [ "COL1A1 and COL1A2 genes as independently modelled genetic entities", "Isolated collagen alpha chains as standalone proteins", "Collagen fibrils, fibres and tissue-scale mechanical properties", "Gelatin and collagen hydrolysates as separate material classes", "Collagen-containing implants, scaffolds, supplements and other formulated products", "Whole-cell collagen biosynthesis pathways and collagen-associated diseases" ], "distinguishing_features": [ "Establish type I chain identity using sequence-specific evidence; a collagen-like triple helix alone does not distinguish type I from other collagen types.", "Resolve chain stoichiometry: the usual type I complex contains two alpha1(I) chains and one alpha2(I) chain; alpha1(I) homotrimers must be identified explicitly. [UniProt COL1A1](https://www.uniprot.org/uniprotkb/P02452/entry)", "Demonstrate association of three chains and triple-helical conformation using complementary evidence; observing constituent chains after denaturing electrophoresis is insufficient by itself.", "Identify retained N- and C-propeptides to distinguish precursor or partially processed forms from mature collagen, and record telopeptide removal separately.", "Distinguish an intact molecular trimer from a fibrillar assembly, unfolded gelatin or hydrolysed fragments; collagen content alone does not establish trimer identity." ], "characteristics": [ { "name": "Chain composition", "kind": "category", "unit_or_values": "alpha1(I)2-alpha2(I); alpha1(I)3; mixed preparation; unresolved", "why_it_matters": "Separates the usual heterotrimer from alternative compositions and prevents bulk ratios from being mistaken for individual-complex identity." }, { "name": "Biological and sequence origin", "kind": "relation", "unit_or_values": "Source organism, chain sequence accessions, variants and native or recombinant origin", "why_it_matters": "Defines which molecular sequences are present and limits transfer of evidence between preparations." }, { "name": "Terminal processing state", "kind": "state", "unit_or_values": "N- and C-propeptides independently present, absent, partial or unknown; telopeptides independently retained, removed or unknown", "why_it_matters": "Distinguishes maturation from extraction-induced trimming." }, { "name": "Triple-helix integrity", "kind": "measurement", "unit_or_values": "Method-specific circular dichroism signal, calibrated helical fraction where justified, or controlled protease-resistance result", "why_it_matters": "Tests whether the preparation retains the defining folded structure." }, { "name": "Post-translational modification profile", "kind": "measurement", "unit_or_values": "Site occupancy (%) for measured hydroxylation and glycosylation sites, with chain and residue mapping", "why_it_matters": "Distinguishes molecular forms that may differ in folding, stability and assembly behaviour." }, { "name": "Molecular mass distribution", "kind": "measurement", "unit_or_values": "kDa, with method, processing state and distribution", "why_it_matters": "Helps detect retained propeptides, fragments or associated species without assuming one invariant mass." }, { "name": "Denaturation transition", "kind": "measurement", "unit_or_values": "Degrees Celsius, with assay, heating rate, solvent, pH and concentration", "why_it_matters": "Supports condition-specific handling decisions rather than assigning a universal melting point." }, { "name": "Association state", "kind": "state", "unit_or_values": "Dispersed trimers; oligomers; fibril-associated; nonspecific aggregates; mixed; unresolved", "why_it_matters": "Separates molecular identity from higher-order organisation." }, { "name": "Cross-link participation", "kind": "relation", "unit_or_values": "Mapped linkage chemistry, residues, linked partners and endogenous or introduced origin", "why_it_matters": "Clarifies whether a trimer remains independently recoverable or is incorporated into a covalent assembly." }, { "name": "Preparation composition", "kind": "measurement", "unit_or_values": "Type I collagen fraction (% with stated basis), concentration (mg/mL), other collagen types and detected fragments", "why_it_matters": "Prevents preparation-level measurements from being attributed to a pure intact trimer without evidence." } ], "affordances": [ "Classify an observed complex by chain identity, stoichiometry and terminal processing evidence.", "Select complementary assays to resolve uncertain trimer association or triple-helix integrity.", "Compare preparations while accounting for species, sequence, modifications and extraction history.", "Choose storage or assay conditions within experimentally supported stability limits.", "Evaluate whether a characterised preparation can enter a specified fibril-assembly experiment.", "Trace cleavage, unfolding or cross-linking outcomes and reclassify products when they cease to be intact trimers." ], "agent_conduct": { "may": [ "Describe the type I collagen trimer, its chain makeup and role in fibrils, citing sources.", "Report the source species, purity and form of a collagen sample." ], "must_not": [ "Present a collagen product as medically effective without evidence.", "Label animal-derived collagen without stating its source species where buyers rely on that.", "Present a collagen implant material as safe without approved testing.", "Interpret a person's genetic collagen variant as a diagnosis." ], "requires_human": [ "Using collagen materials in implants or wound care for people.", "Interpreting collagen gene results for a patient." ] }, "ethics": { "considerations": [ "Animal sourcing matters to people with religious, ethical or allergy concerns.", "Cosmetic collagen claims often go beyond evidence." ], "affected_parties": [ "Consumers and patients", "People with brittle bone or connective tissue disorders", "Animals used as sources" ] }, "owners": { "steward": "The producer or laboratory that holds the material.", "master_systems": [] }, "visual_identification": [ "As purified material, a white fibrous or spongy solid or a viscous solution.", "The triple helix is seen only by structural methods; source and type are settled by analysis." ], "failure_modes_and_hazards": [ "Allergic or immune reactions to animal-derived collagen.", "Disease transmission risk from poorly sourced animal material." ], "what_it_is_for": [ "Collagen type I trimers occur in vertebrate extracellular matrices, including those of bone, skin and tendon.", "They are studied in structural biology and tissue research to understand triple helix integrity, molecular processing and fibril assembly.", "Characterization of collagen materials uses their chain composition and assembly state to interpret material quality and biological function." ], "standards_and_regulation": [ "The Gene Ontology Consortium maintains the cellular component classification collagen type I trimer for annotating this molecular complex." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q14881714: collagen type I trimer", "url": "https://www.wikidata.org/wiki/Q14881714", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Type I collagen", "url": "https://en.wikipedia.org/wiki/Type_I_collagen", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "type-i-molecular-identity", "name": "Type I molecular identity", "description": "Establish which chains form the complex and how confidently it maps to the registered thing.", "rationale": "Neither generic collagen detection nor a triple-helical signal establishes type I trimer identity.", "layers": [ { "id": "chain-identity-and-stoichiometry", "name": "Chain identity and stoichiometry", "description": "Resolve constituent proteins and their association within individual complexes.", "findings": [ { "id": "heterotrimer-and-homotrimer-discrimination", "name": "Heterotrimer and homotrimer discrimination", "description": "Record the usual alpha1(I)2-alpha2(I) composition separately from alpha1(I)3 complexes; both forms are discussed in experimental work on collagen I assembly. [Structural basis of homo- and heterotrimerization of collagen I](https://pmc.ncbi.nlm.nih.gov/articles/PMC5353611/)", "questions": [ { "text": "Which chain-specific measurements establish alpha1(I) and alpha2(I) identity and their stoichiometry?", "kind": "measurement", "id": "heterotrimer-and-homotrimer-discrimination-q01" }, { "text": "Does the evidence resolve individual trimer compositions, or only an average chain ratio across a mixture?", "kind": "boundary", "id": "heterotrimer-and-homotrimer-discrimination-q02" } ] } ] }, { "id": "sequence-and-preparation-lineage", "name": "Sequence and preparation lineage", "description": "Connect the observed complex to its biological source and molecular sequence.", "findings": [ { "id": "source-qualified-identity", "name": "Source-qualified identity", "description": "Identify species, chain accessions, variants and preparation history before transferring evidence from another type I collagen preparation.", "questions": [ { "text": "Which organism, tissue or expression system supplied the chains, and which sequence records describe them?", "kind": "provenance", "id": "source-qualified-identity-q01" }, { "text": "Were mutations, tags, sequence truncations or chemical modifications introduced during production?", "kind": "provenance", "id": "source-qualified-identity-q02" } ] } ] } ] }, { "id": "maturation-and-molecular-chemistry", "name": "Maturation and molecular chemistry", "description": "Describe processing and modifications that distinguish molecular forms of type I collagen.", "rationale": "A label of type I collagen does not disclose whether propeptides, telopeptides or relevant modifications remain.", "layers": [ { "id": "terminal-processing", "name": "Terminal processing", "description": "Resolve precursor removal separately from telopeptide trimming.", "findings": [ { "id": "propeptide-and-telopeptide-status", "name": "Propeptide and telopeptide status", "description": "Track N- and C-propeptides and telopeptides independently to distinguish maturation intermediates from extraction-derived forms.", "questions": [ { "text": "What terminal peptide or cleavage-site evidence establishes the processing state of each constituent chain?", "kind": "measurement", "id": "propeptide-and-telopeptide-status-q01" }, { "text": "Should this observed form be represented as mature collagen, a qualified precursor or an extraction-modified derivative?", "kind": "boundary", "id": "propeptide-and-telopeptide-status-q02" } ] } ] }, { "id": "residue-modifications-and-linkages", "name": "Residue modifications and linkages", "description": "Record measured residue chemistry and covalent connections.", "findings": [ { "id": "mapped-modification-profile", "name": "Mapped modification profile", "description": "Keep site-specific hydroxylation, glycosylation and cross-link evidence distinct from bulk amino-acid composition or inferred native chemistry.", "questions": [ { "text": "Which modification sites and occupancies were measured, and which remain unresolved?", "kind": "measurement", "id": "mapped-modification-profile-q01" }, { "text": "Which detected covalent links connect chains within this complex or connect it to other molecules?", "kind": "boundary", "id": "mapped-modification-profile-q02" } ] } ] } ] }, { "id": "triple-helix-integrity-and-stability", "name": "Triple-helix integrity and stability", "description": "Assess folded structure, cleavage and condition-dependent loss of molecular integrity.", "rationale": "An intact sequence, a three-chain association and a correctly folded triple helix are different claims requiring evidence.", "layers": [ { "id": "fold-and-chain-integrity", "name": "Fold and chain integrity", "description": "Distinguish helical trimers from associated but unfolded chains and fragmented material.", "findings": [ { "id": "orthogonal-integrity-evidence", "name": "Orthogonal integrity evidence", "description": "Combine conformation-sensitive observations with chain-integrity and association measurements, recording what each method can establish.", "questions": [ { "text": "Which complementary assays support triple-helical conformation, three-chain association and intact chain lengths?", "kind": "measurement", "id": "orthogonal-integrity-evidence-q01" }, { "text": "What detection limits leave partial unfolding, cleavage or mixed intact and damaged populations unresolved?", "kind": "measurement", "id": "orthogonal-integrity-evidence-q02" } ] } ] }, { "id": "environment-dependent-stability", "name": "Environment-dependent stability", "description": "Relate structural persistence to temperature, solution conditions and handling history.", "findings": [ { "id": "qualified-denaturation-and-storage-limits", "name": "Qualified denaturation and storage limits", "description": "Treat stability limits as preparation- and protocol-dependent measurements, including exposure time and reversibility.", "questions": [ { "text": "Under which pH, solvent, temperature, concentration and exposure time was structural stability measured?", "kind": "measurement", "id": "qualified-denaturation-and-storage-limits-q01" }, { "text": "Which storage, heating or freeze-thaw actions are supported by integrity measurements for this preparation?", "kind": "action", "id": "qualified-denaturation-and-storage-limits-q02" } ] } ] } ] }, { "id": "assembly-participation-and-use", "name": "Assembly participation and use", "description": "Connect molecular state to fibril participation and justified experimental use.", "rationale": "Fibril formation and preparation suitability cannot be inferred from the type I label alone.", "layers": [ { "id": "molecule-to-fibril-boundary", "name": "Molecule-to-fibril boundary", "description": "Track whether trimers are dispersed, aggregated or incorporated into an ordered assembly.", "findings": [ { "id": "assembly-state-and-competence", "name": "Assembly state and competence", "description": "Separate the current association state from demonstrated ability to form fibrils under a specified protocol.", "questions": [ { "text": "What evidence distinguishes dispersed trimers, nonspecific aggregates and ordered fibrils in this preparation?", "kind": "measurement", "id": "assembly-state-and-competence-q01" }, { "text": "Under what tested conditions does this molecular form participate in fibril formation, and which resulting properties belong to the fibril model?", "kind": "boundary", "id": "assembly-state-and-competence-q02" } ] } ] }, { "id": "preparation-qualified-actions", "name": "Preparation-qualified actions", "description": "Determine whether the measured material supports a proposed molecular or assembly experiment.", "findings": [ { "id": "assay-suitability-and-product-reclassification", "name": "Assay suitability and product reclassification", "description": "Base action choices on composition, extraction history and integrity evidence; record transformed products under an appropriate identity.", "questions": [ { "text": "Do other collagen types, fragments, residual extraction reagents or uncertain trimer composition confound the proposed experiment?", "kind": "action", "id": "assay-suitability-and-product-reclassification-q01" }, { "text": "After proteolysis, heating or chemical cross-linking, what measurements determine whether the product remains an intact type I trimer?", "kind": "action", "id": "assay-suitability-and-product-reclassification-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 recalled knowledge; no sources were consulted.", "Check whether the registry intends mature collagen, procollagen or an ontology category encompassing precursor and mature assemblies.", "Dimensions describe mature molecules approximately; thermal properties, molecular mass and preparation hazards require species and processing context." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of collagen type I trimer 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": [ "Canonical heterotrimer, [α1(I)]2α2(I)", "α1(I) homotrimer, [α1(I)]3" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of collagen type I trimer 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 identifier", "value_or_pattern": "GO: followed by seven digits", "note": "The exact identifier for the collagen type I trimer should be checked." }, { "scheme": "HGNC human gene symbols", "value_or_pattern": "COL1A1; COL1A2", "note": "Identify the genes encoding the constituent chains, not the assembled trimer; other organisms use their own gene nomenclature." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of collagen type I trimer 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": [ "Provides tensile support in tendon, skin, bone and other connective tissues through assembly into fibrils.", "Contributes to the organic matrix within which bone mineral is deposited.", "Type I collagen preparations are used in cell-culture matrices, tissue-engineering scaffolds and wound-care materials." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of collagen type I trimer 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": "Approximate length of the mature triple-helical molecule", "typical_range": "Approximately 300", "unit": "nm" }, { "quantity": "Approximate diameter of the mature triple-helical molecule", "typical_range": "Approximately 1.5", "unit": "nm" }, { "quantity": "Polypeptide chains per trimer", "typical_range": "3", "unit": "chains" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of collagen type I trimer 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": [ "Sequence changes, particularly substitutions affecting triple-helical glycine residues, can disrupt folding, secretion or fibril function.", "Defective hydroxylation or propeptide processing can compromise collagen maturation and tissue integrity.", "Heating or unsuitable chemical conditions can denature the triple helix; stability depends on species, modification state and preparation.", "Collagenolytic proteases can cleave the molecule and promote matrix degradation.", "Animal-derived preparations can introduce immunogenicity or contamination risks that depend on sourcing and processing." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of collagen type I trimer 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": "Type I procollagen", "difference": "The biosynthetic precursor retains terminal propeptides that are removed during maturation." }, { "name": "Collagen type I fibril", "difference": "A fibril is a higher-order assembly of many collagen molecules, rather than one three-chain molecule." }, { "name": "Collagen α1(I) chain", "difference": "An individual polypeptide constituent rather than the assembled trimer." }, { "name": "Collagen type II trimer", "difference": "Composed of three α1(II) chains rather than type I collagen chains." }, { "name": "Gelatin", "difference": "A preparation of denatured and often partially hydrolysed collagen rather than intact native type I trimers." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of collagen type I trimer this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry intend this entry to include both alpha1(I)2-alpha2(I) heterotrimers and alpha1(I)3 homotrimers, or only the canonical heterotrimer?", "Does the entry own procollagen and partially processed trimers as qualified states, or should it link to separately registered precursor entities?", "Which species, sequence variants and extraction-derived forms must the initial model support?", "Which assay combinations and acceptance thresholds adequately establish intact triple-helical trimers for the intended use?", "Does an existing Vercy world model already cover this molecular complex, and which external complex identifiers map to precisely the same scope?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 15, "questions": 23 } }