{ "model": { "rank": 1138, "code": "thing-protein", "model_id": "vr.tr.protein", "name": "protein", "purpose": "any of a large group of nitrogenous organic compounds that are essential constituents of living cells; consist of polymers of amino acids; essential in the diet of animals for growth and for repair of tissues; can be obtained from meat and eggs and milk and legumes", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/protein/", "tier": 2, "score": 178, "payload": { "layer": "wordnet", "aliases": [ "capsid", "collagen", "elastin", "gluten", "corn gluten", "wheat gluten", "rheumatoid factor", "endonuclease", "exonuclease", "glutathione peroxidase", "horseradish peroxidase", "caspase", "ricin", "ricin toxin", "adenosine deaminase", "ADA", "recombinant protein", "actomyosin", "aleurone", "amyloid", "apoenzyme", "gelatin", "gelatine", "chondrin", "mucin", "conjugated protein", "compound protein", "actin", "albumin", "albumen", "lactalbumin", "serum albumin", "alpha globulin", "serum globulin", "keratin", "ceratin", "enzyme", "fibrin", "filaggrin", "growth factor" ], "aliasCount": 271, "merged": 178, "knownIn": 0, "facets": { "substance": "material", "origin": "natural", "agency": "inert", "mobility": "varies", "scale": "not-applicable", "affordances": [ "observable" ] }, "markers": [], "lexicalClass": "noun.substance", "senseRank": 0, "alsoRegisteredAs": null, "source": { "dataset": "oewn:2024", "synset": "oewn-14752903-n", "ili": "i114399", "license": "CC BY 4.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-07T10:09:15Z", "providers": [ "Codex", "Grok" ], "missingProviders": [], "pass": 2, "cost": { "grok": { "usd": 0.004845, "turns": 1, "seconds": 59.6, "error": null }, "codex": { "seconds": 82, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.3\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: 01a07b56-afea-79b3-92d8-d690be65d0e3\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: protein\nRegistry id: vr.tr.protein\nPlane / domain: PHY / PHY.MAT\nRegistry definition: any of a large group of nitrogenous organic compounds that are " } } }, "metaModel": { "id": "THING-PROTEIN", "registryId": "vr.tr.protein", "name": "protein", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/protein/", "model": { "registry_id": "vr.tr.protein", "name": "protein", "purpose": "Enable an agent to recognise a protein, assess its molecular and preparation state, and determine whether it is suitable for an intended biological, analytical, industrial or nutritional use.", "definition": "Proteins are linear heteropolymers of L-α-amino acids linked by peptide bonds, folding into one or more polypeptide chains whose sequence and three-dimensional structure confer catalytic, structural, transport, signalling, and nutritional functions in living organisms.", "scope_statement": "This model covers protein as a class of amino-acid-based biological macromolecules and as identified molecular forms or characterised preparations, distinguishing molecular protein identity from dietary protein quantities and products containing protein.", "in_scope": [ "Amino-acid sequence, chain composition, biological origin and molecular identity", "Maturation, sequence variants, covalent modifications and conjugated components", "Folding, assembly, aggregation and condition-dependent stability", "Biological function, interactions and measured activity", "Protein preparation identity, concentration, purity and contaminants", "Evidence supporting intended use, including nutritional suitability and protein-specific hazards" ], "out_of_scope": [ "Whole foods, supplements, medicines and other formulated products containing protein", "Complete diets, individual dietary prescriptions and nutritional requirements", "Genes, RNA and the full cellular machinery of protein synthesis", "Source organisms, tissues and diseases as independently modelled entities", "Manufacturing processes and laboratory instruments beyond their effects on protein state", "Free amino acids and non-protein nitrogen compounds" ], "distinguishing_features": [ "Establish that the entity contains amino-acid residues joined in polypeptide chains; nitrogen content alone does not establish protein identity.", "Distinguish a specified molecular protein from a mixed preparation or a reported dietary protein quantity.", "Record the convention used at the peptide-protein boundary rather than imposing a universal chain-length cutoff.", "Distinguish sequence and covalent molecular form from folding state: a denatured protein can retain its sequence identity.", "Separate the protein component from attached carbohydrates, lipids, cofactors and formulation ingredients while retaining their relationships." ], "characteristics": [ { "name": "Identity resolution", "kind": "category", "unit_or_values": "protein class | family | specified sequence | specified molecular form | mixed preparation", "why_it_matters": "Controls which claims can legitimately be attached to the represented entity." }, { "name": "Sequence and chain composition", "kind": "relation", "unit_or_values": "amino-acid sequences, sequence version, chain lengths in residues and chain stoichiometry", "why_it_matters": "Distinguishes related proteins, constructs and multichain entities." }, { "name": "Biological and production origin", "kind": "relation", "unit_or_values": "source organism, tissue or compartment; expression host or synthetic origin", "why_it_matters": "Separates natural origin from production history and supports interpretation of modifications and impurities." }, { "name": "Covalent molecular form", "kind": "category", "unit_or_values": "sequence variants, cleavage boundaries, modification sites and occupancies, crosslinks and conjugates", "why_it_matters": "Proteins sharing a reference sequence can differ in activity, mass and recognition." }, { "name": "Molecular mass", "kind": "measurement", "unit_or_values": "Da or kDa, with calculated or measured basis and chain or assembly designation", "why_it_matters": "Supports identity and assembly assessment without conflating theoretical and experimental values." }, { "name": "Conformational and assembly state", "kind": "state", "unit_or_values": "folded, intrinsically disordered, unfolded, partially folded or mixed; assembly stoichiometry and aggregate fraction", "why_it_matters": "Sequence identity alone does not establish the physical state required for use." }, { "name": "Protein concentration", "kind": "measurement", "unit_or_values": "mg/mL or mol/L, with assay method and molecular basis", "why_it_matters": "Enables reproducible dosing and comparison while exposing method-dependent estimates." }, { "name": "Preparation purity", "kind": "measurement", "unit_or_values": "percentage with mass, molar or analytical-signal basis; named impurity measurements", "why_it_matters": "Purity is meaningful only relative to the target form and measurement method." }, { "name": "Functional performance", "kind": "measurement", "unit_or_values": "role-specific assay endpoint and units, assay conditions, controls and reference material", "why_it_matters": "Distinguishes demonstrated activity from identity-based expectations." }, { "name": "Stability conditions", "kind": "relation", "unit_or_values": "temperature in °C, pH, buffer composition, concentration, storage duration and handling history", "why_it_matters": "Connects observed degradation or retained activity to the conditions under which it was assessed." }, { "name": "Nutritional characterisation", "kind": "measurement", "unit_or_values": "amino-acid composition in mg/g protein and digestibility or quality measures with named methods", "why_it_matters": "Protein quantity alone does not establish nutritional suitability." }, { "name": "Use-specific hazard status", "kind": "category", "unit_or_values": "documented, suspected, assessed without detection or unassessed; hazard, exposure route and evidence specified", "why_it_matters": "Prevents broad safety conclusions from being inferred from protein identity alone." } ], "affordances": [ "Match a preparation to a reference protein and identify unresolved sequence or molecular-form differences.", "Select identity, purity, folding and activity assays appropriate to the intended use.", "Compare preparations using compatible measurement methods and explicitly stated conditions.", "Assess whether storage, formulation or handling conditions preserve required protein properties.", "Evaluate nutritional claims using composition and digestibility evidence.", "Accept, restrict or reject a proposed use against documented performance and hazard criteria." ] }, "sources": [ { "id": "iupac-gold-book-protein", "title": "IUPAC Gold Book: protein", "url": "https://goldbook.iupac.org/terms/view/P04898", "what_it_supports": "Specialist chemical definition: naturally occurring and synthetic polypeptides of amino acids, typically of higher molecular mass than peptides.", "url_status": "blocked" }, { "id": "uniprot-what-is-a-protein", "title": "What is a protein?", "url": "https://www.uniprot.org/help/proteins", "what_it_supports": "UniProt operational definition: gene products as amino-acid sequences, isoforms, and functional annotations used as the primary protein identity layer in biology.", "url_status": "live" }, { "id": "pdb-about-proteins", "title": "Introduction to Proteins", "url": "", "what_it_supports": "Structural classification (primary through quaternary structure) and the distinction between sequence, fold, and biological assembly.", "url_status": "dead" }, { "id": "fao-who-protein-quality", "title": "Dietary protein quality evaluation in human nutrition: Report of an FAO Expert Consultation", "url": "https://www.fao.org/ag/humannutrition/35978-02317b979a686a57aa4593304ffc17f06.pdf", "what_it_supports": "Nutritional sense of protein as a dietary constituent: indispensable amino acids, digestibility, DIAAS/PDCAAS, and food sources (meat, eggs, milk, legumes).", "url_status": "live" } ], "structure": { "bundles": [ { "id": "protein-identity", "name": "Protein identity", "description": "Establish what protein entity is represented and how precisely it is identified.", "rationale": "The name protein can denote a molecular species, a family, a mixture or a nutritional quantity.", "layers": [ { "id": "entity-boundary", "name": "Entity boundary", "description": "Resolve the chemical sense and level of identity.", "findings": [ { "id": "protein-sense-and-resolution", "name": "Protein sense and resolution", "description": "Record whether the subject is a protein class, specified molecule or preparation, including the peptide boundary convention.", "questions": [ { "text": "Does this record represent a molecular protein, a protein family, a mixture or only a dietary protein measurement?", "kind": "definition", "id": "protein-sense-and-resolution-q01" }, { "text": "What convention distinguishes this entity from a peptide, and does another registry record already own the same sense?", "kind": "boundary", "id": "protein-sense-and-resolution-q02" } ] } ] }, { "id": "sequence-and-origin", "name": "Sequence and origin", "description": "Connect the molecular identity to sequence evidence and biological or synthetic origin.", "findings": [ { "id": "reference-sequence-and-chain-set", "name": "Reference sequence and chain set", "description": "Identify constituent chains, reference versions and the distinction between source organism and production host.", "questions": [ { "text": "Which sequences, chain boundaries and identifiers define the protein, and which were experimentally verified?", "kind": "provenance", "id": "reference-sequence-and-chain-set-q01" }, { "text": "What is its biological source, and was this preparation isolated, recombinantly expressed or chemically synthesised?", "kind": "provenance", "id": "reference-sequence-and-chain-set-q02" } ] } ] } ] }, { "id": "molecular-form-and-structure", "name": "Molecular form and structure", "description": "Describe covalent form, conformation and assembly.", "rationale": "Proteins with the same reference sequence can occupy materially different molecular and structural states.", "layers": [ { "id": "maturation-and-modification", "name": "Maturation and modification", "description": "Resolve changes between the reference sequence and the material under assessment.", "findings": [ { "id": "observed-covalent-form", "name": "Observed covalent form", "description": "Record processing, mutations, tags, disulfides and other modifications without assuming uniform occupancy.", "questions": [ { "text": "Which cleavage events, sequence changes, tags, crosslinks or covalent modifications distinguish the observed form from the reference?", "kind": "definition", "id": "observed-covalent-form-q01" }, { "text": "Which modification sites and occupancies are measured, and does the observed mass support the assigned form?", "kind": "measurement", "id": "observed-covalent-form-q02" } ] } ] }, { "id": "conformation-and-assembly", "name": "Conformation and assembly", "description": "Describe structural populations under specified conditions.", "findings": [ { "id": "folding-and-association-state", "name": "Folding and association state", "description": "Distinguish functional disorder or assembly from unfolding, unwanted association and aggregation.", "questions": [ { "text": "What evidence establishes folded, disordered, unfolded or mixed conformations under the stated conditions?", "kind": "measurement", "id": "folding-and-association-state-q01" }, { "text": "What chain stoichiometry, partner association and aggregate fraction are observed, and which states are expected for its function?", "kind": "measurement", "id": "folding-and-association-state-q02" } ] } ] } ] }, { "id": "protein-function", "name": "Protein function", "description": "Connect proposed biological roles to interactions and demonstrated performance.", "rationale": "Protein identity does not establish activity, and protein function extends beyond catalysis.", "layers": [ { "id": "roles-and-partners", "name": "Roles and partners", "description": "Specify context-dependent roles and dependencies.", "findings": [ { "id": "functional-role-evidence", "name": "Functional role evidence", "description": "Separate experimentally supported roles from predictions based on sequence or family membership.", "questions": [ { "text": "Which catalytic, structural, transport, signalling, binding or other roles are supported, and in what biological context?", "kind": "definition", "id": "functional-role-evidence-q01" }, { "text": "Which partners, cofactors, membranes or cellular locations are required, and what evidence supports those dependencies?", "kind": "provenance", "id": "functional-role-evidence-q02" } ] } ] }, { "id": "activity-and-acceptance", "name": "Activity and acceptance", "description": "Define measurements that establish suitability for a particular function.", "findings": [ { "id": "assayed-functional-performance", "name": "Assayed functional performance", "description": "Record performance with assay conditions, controls and acceptance criteria.", "questions": [ { "text": "Which assay endpoint, units, controls and conditions demonstrate the required function for this protein?", "kind": "measurement", "id": "assayed-functional-performance-q01" }, { "text": "What performance threshold must this preparation meet before the intended use can proceed?", "kind": "action", "id": "assayed-functional-performance-q02" } ] } ] } ] }, { "id": "preparation-quality-and-stability", "name": "Preparation quality and stability", "description": "Assess the actual material, including its composition and changes during handling.", "rationale": "A correct molecular label does not guarantee a pure, intact or usable preparation.", "layers": [ { "id": "content-and-impurities", "name": "Content and impurities", "description": "Establish how much target protein is present and what accompanies it.", "findings": [ { "id": "quantified-preparation-composition", "name": "Quantified preparation composition", "description": "Record concentration, purity basis, formulation components and relevant contaminants.", "questions": [ { "text": "How were protein concentration and target-form purity measured, and how do assay interferences affect the reported values?", "kind": "measurement", "id": "quantified-preparation-composition-q01" }, { "text": "Which other proteins, nucleic acids, host-derived contaminants, residual reagents or formulation ingredients remain in the preparation?", "kind": "measurement", "id": "quantified-preparation-composition-q02" } ] } ] }, { "id": "condition-dependent-integrity", "name": "Condition-dependent integrity", "description": "Relate storage and handling to molecular integrity and retained function.", "findings": [ { "id": "stability-and-handling-window", "name": "Stability and handling window", "description": "Track proteolysis, chemical alteration, precipitation, aggregation and activity loss over time.", "questions": [ { "text": "Under which temperature, pH, buffer, concentration and time conditions were integrity and activity retained?", "kind": "measurement", "id": "stability-and-handling-window-q01" }, { "text": "What evidence determines acceptable storage, freeze-thaw exposure, reconstitution and criteria for retesting or disposal?", "kind": "action", "id": "stability-and-handling-window-q02" } ] } ] } ] }, { "id": "nutrition-hazards-and-use", "name": "Nutrition, hazards and use", "description": "Evaluate nutritional relevance and constraints specific to the proposed exposure and application.", "rationale": "The registry includes a dietary sense, but nutritional value and safety require evidence beyond classification as a protein.", "layers": [ { "id": "nutritional-interpretation", "name": "Nutritional interpretation", "description": "Connect dietary protein measurements to amino-acid availability while preserving the food-product boundary.", "findings": [ { "id": "protein-quantity-and-quality", "name": "Protein quantity and quality", "description": "Distinguish measured protein content from nitrogen-based estimates and assess composition and digestibility.", "questions": [ { "text": "Is reported protein content directly measured or inferred from nitrogen, and which conversion factor and non-protein nitrogen correction were used?", "kind": "measurement", "id": "protein-quantity-and-quality-q01" }, { "text": "What amino-acid composition and digestibility evidence applies to this preparation, processing state and intended consumer population?", "kind": "measurement", "id": "protein-quantity-and-quality-q02" } ] } ] }, { "id": "exposure-and-use-constraints", "name": "Exposure and use constraints", "description": "Determine which hazards, identifiers and use restrictions apply to the specific protein or preparation.", "findings": [ { "id": "evidence-based-use-disposition", "name": "Evidence-based use disposition", "description": "Record allergenic, toxic, immunogenic or other relevant hazards and applicable use requirements without assigning universal properties to all proteins.", "questions": [ { "text": "What evidence addresses hazards of this protein and its contaminants for the intended exposure route, dose and population?", "kind": "provenance", "id": "evidence-based-use-disposition-q01" }, { "text": "Which substance identifiers, hazard classifications and grade or jurisdiction requirements apply to this exact preparation and intended use?", "kind": "action", "id": "evidence-based-use-disposition-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-kinds", "name": "Kinds and varieties", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "globular proteins (enzymes, antibodies, transport proteins)", "fibrous proteins (collagen, keratin, elastin, fibroin)", "membrane proteins (receptors, channels, transporters)", "intrinsically disordered proteins", "conjugated proteins (glycoproteins, lipoproteins, metalloproteins, nucleoproteins)", "dietary/food proteins (complete vs incomplete; animal vs plant)", "recombinant/therapeutic proteins (biologics, enzymes, monoclonal antibodies)", "denatured, hydrolysed, or aggregated protein (peptides, isolates, hydrolysates)" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of protein this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ { "scheme": "Wikidata", "value_or_pattern": "Q8054 (protein as class of biomolecule)", "note": "This sense is the biomolecule/chemical class, not a sports protein supplement brand or a food-label protein claim as a nutrient quantity." }, { "scheme": "UniProt accession", "value_or_pattern": "[OPQ][0-9][A-Z0-9]{3}[0-9] (Swiss-Prot/TrEMBL canonical form, e.g. P04637)", "note": "Names a specific protein sequence (gene product), not the class 'protein'." }, { "scheme": "Protein Data Bank ID", "value_or_pattern": "4-character PDB ID (e.g. 1AKE)", "note": "Names a deposited three-dimensional structure of a protein (or complex), not the substance class." }, { "scheme": "CAS Registry Number", "value_or_pattern": "assigned per isolated protein, isolate, or hydrolysate (no single CAS for 'protein')", "note": "The class has no unique CAS; commercial casein, whey, collagen, etc. each have their own numbers." }, { "scheme": "EC number (IUBMB Enzyme Commission)", "value_or_pattern": "n.n.n.n for enzymes (e.g. 3.4.21.4 trypsin)", "note": "Classifies catalytic function of enzyme proteins only." }, { "scheme": "ChEBI", "value_or_pattern": "CHEBI:36080 (protein)", "note": "Ontology class for proteins as molecular entities." }, { "scheme": "HGNC / gene symbol", "value_or_pattern": "approved gene symbol mapping to the encoded protein (e.g. TP53 → cellular tumor antigen p53)", "note": "Gene identity is not protein identity when isoforms, PTMs, or proteolytic products differ." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of protein this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-standards-and-regulation", "name": "Standards and regulation", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "IUPAC Recommendations on amino-acid and peptide nomenclature (IUPAC/IUBMB Joint Commission on Biochemical Nomenclature)", "IUBMB Enzyme Nomenclature (NC-IUBMB) for catalytic proteins", "Codex Alimentarius / FAO-WHO protein quality methods: PDCAAS and DIAAS for food labelling and nutrition evaluation", "AOAC Official Methods for crude protein (Kjeldahl, Dumas/combustion nitrogen) in foods and feeds", "ISO 1871 and related ISO methods for determination of nitrogen and protein in foodstuffs", "ICH Q6B (Specifications: Test Procedures and Acceptance Criteria for Biotechnological/Biological Products) for therapeutic proteins", "WHO/INN and pharmacopoeial monographs (Ph. Eur., USP) for named protein drugs and blood products", "GHS/CLP: many purified proteins are not classified as hazardous as a class; specific toxins, allergens, and enzymes may carry H-statements (e.g. respiratory sensitisation)" ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of protein this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Structural and catalytic macromolecules in every living cell (enzymes, cytoskeleton, membrane receptors)", "Human diet: indispensable amino-acid supply from meat, eggs, milk, fish, legumes, and cereals; labelled as 'protein' on food packaging", "Food ingredients: whey and casein isolates, soy protein isolate, collagen peptides, gluten, egg albumen", "Biopharmaceuticals: monoclonal antibodies, insulin, coagulation factors, enzymes, vaccines (antigen proteins)", "Laboratory reagents and diagnostics: antibodies, recombinant enzymes, protein standards, ELISA antigens", "Industrial enzymes: proteases, amylases, lipases in detergents, food processing, and biofuel", "Materials: silk fibroin, wool keratin, leather collagen, protein-based adhesives and films" ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of protein this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ { "quantity": "relative molecular mass (Mr) of a typical polypeptide chain", "typical_range": "about 5 000-500 000 (peptides below ~5 kDa are usually not called proteins; some complexes exceed 1 MDa)", "unit": "dalton (Da) or kilodalton (kDa)" }, { "quantity": "dietary protein reference intake (adult)", "typical_range": "0.8-1.6 g per kg body mass per day depending on activity, age, and clinical state; FAO/WHO safe level historically ~0.83 g·kg⁻¹·d⁻¹ of high-quality protein", "unit": "g·kg⁻¹·d⁻¹" }, { "quantity": "nitrogen-to-protein conversion (Kjeldahl/Dumas)", "typical_range": "Jones factor 5.7 (wheat) to 6.38 (milk); default 6.25 still widely used", "unit": "dimensionless (g protein per g nitrogen)" }, { "quantity": "isoelectric point (pI)", "typical_range": "typically pH 4-11 depending on amino-acid composition", "unit": "pH units" }, { "quantity": "protein concentration in human plasma (total)", "typical_range": "60-80", "unit": "g·L⁻¹" }, { "quantity": "thermal denaturation / melting temperature (Tm) of globular proteins", "typical_range": "often 40-90 under physiological buffer; highly variable", "unit": "°C" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of protein this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Denaturation: loss of native fold (heat, pH, urea, SDS, mechanical shear) with loss of function; may be reversible or irreversible", "Aggregation and amyloid formation: insoluble deposits; associated with neurodegenerative disease and with manufacturing failure of biologics", "Proteolysis: unwanted cleavage by proteases during storage, digestion, or bioprocess", "Chemical degradation: oxidation (Met, Cys, Trp), deamidation (Asn, Gln), glycation - common in therapeutic protein stability", "Allergenicity: IgE-mediated food and occupational allergy (e.g. peanut, milk, egg, wheat, latex, industrial enzymes)", "Toxicity of specific proteins: bacterial toxins, plant lectins, prion proteins (infectious misfolded conformers)", "Nutritional failure: insufficient indispensable amino acids or digestibility (low DIAAS) despite adequate crude-protein nitrogen", "Analytical artefact: 'protein' by N × 6.25 overestimates true protein when non-protein nitrogen is present" ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of protein this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-regional-variation", "name": "Regional variation", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Food labelling: US FDA and EU both declare protein (g) but quality scoring (PDCAAS vs DIAAS) and health-claim rules differ; EU Nutrition and Health Claims Regulation vs US Nutrition Facts", "Nitrogen conversion factors vary by commodity and jurisdiction (Codex vs national food tables)", "Dietary emphasis: dairy and meat proteins dominate some food cultures; legumes, soy, and cereals dominate others; religious dietary laws restrict some animal proteins", "Therapeutic protein naming: USAN vs INN vs JAN (Japan) suffixes and glycosylation qualifiers", "The English word 'protein' also names a nutrient panel line and, in sport, a powdered supplement - a different registry sense from the biomolecule class" ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of protein this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ { "name": "peptide / oligopeptide", "difference": "Same chemistry (amide-linked amino acids) but conventionally shorter (often <20-50 residues or <5 kDa) and usually lacking a stable tertiary fold; IUPAC treats the boundary as conventional, not sharp." }, { "name": "amino acid", "difference": "Monomer vs polymer: free amino acids are the residues from which proteins are polymerised and to which they are hydrolysed; a protein assay is not an amino-acid profile." }, { "name": "protein (dietary nutrient / food-label quantity)", "difference": "The nutrient 'protein' is a mass estimated from nitrogen or amino acids in a food; it is a compositional claim, not a single molecular species. Same English name, different registry sense (this batch also lists protein twice)." }, { "name": "meat", "difference": "Meat is a tissue/food that contains protein plus water, fat, minerals, and connective matrix; protein is the polymer class, not the food." }, { "name": "deoxyribonucleic acid (DNA)", "difference": "DNA encodes protein sequence but is a nucleic acid polymer of nucleotides, not amino acids; proteins are the translation products." }, { "name": "glycoprotein vs glycan", "difference": "A glycoprotein is a protein with covalently attached carbohydrate; the glycan moiety is not itself a protein." }, { "name": "prion / amyloid", "difference": "A conformational (misfolded) state of a protein, not a separate chemical class; infectivity or pathology comes from fold, not from a different polymer chemistry." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of protein this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the other protein entry represent the same chemical sense, a dietary aggregate or a different scope, and is there an existing world model that should own this concept?", "Which peptide-protein boundary convention should the registry adopt for short chains and borderline entities?", "How should heterogeneous proteoforms and protein mixtures be represented without implying a single verified molecular identity?", "Which assay and acceptance criteria should be required for each intended use, especially when sequence identity is known but activity or structural state is unassessed?", "Which nutritional methods, hazard evidence and regulatory identifiers are applicable to the specific proteins or preparations that will instantiate this model?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 18, "questions": 28 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "chemical substance or material", "method": "Written from the archetype playbook - what this kind of thing needs beyond identity and provenance - and from the structure that recurred across 6,333 models already researched by two engines. Applied to this entry by rule. No source was read for this thing and no claim here is researched.", "facetsInferred": false, "nextPass": "A researcher replaces this draft with a sourced specification. Treat every sentence below as a proposal to argue with.", "purpose": "Give an agent a durable, checkable way to recognise a protein, record what state it is in, and decide what may be done with it.", "whatItIs": "any of a large group of nitrogenous organic compounds that are essential constituents of living cells; consist of polymers of amino acids; essential in the diet of animals for growth and for repair of tissues; can be obtained from meat and eggs and milk and legumes", "characteristics": { "substance": "material", "origin": "natural", "agency": "inert", "mobility": "varies" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: capsid, collagen, elastin, gluten, corn gluten, wheat gluten, rheumatoid factor, endonuclease, exonuclease, glutathione peroxidase, horseradish peroxidase, caspase.", "178 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it." ], "openQuestionsForResearch": [ "Which of the bundles below does a real task actually need, and which are ceremony?", "What does this thing have that the facets do not capture at all?", "Which neighbouring kind is most often confused with a protein, and on what evidence are they told apart?" ], "whatItIsMadeOf": "matter you can touch", "physicalCharacter": [ "Mobility varies between examples.", "Does nothing on its own; everything it does, something else did to it." ], "whatCanBeDoneWithIt": [ "observe it, measure it, record its state" ], "howItIsRecognised": [ "Not recognisable by sight in any reliable way. Appearance varies with grade, form and additives; identification is by label, by documentation, or by assay." ], "relatedModels": [ { "relation": "covers", "note": "Finer kinds folded into this entry because telling them apart needs a task that asks for it. Each is a model waiting to be split out when one does.", "targets": [ "capsid", "collagen", "elastin", "gluten", "corn gluten", "wheat gluten", "rheumatoid factor", "endonuclease", "exonuclease", "glutathione peroxidase", "horseradish peroxidase", "caspase" ] } ], "standing": "178 finer distinctions are held inside this entry as names rather than as separate models.", "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one protein from another, and a protein from things that resemble it.", "rationale": "Recognition comes before every other claim. Without stable identity nothing else in the model can be trusted to be about the same thing twice.", "layers": [ { "id": "naming-and-identifiers", "name": "Names and identifiers", "description": "The names this thing goes by and the identifiers that survive translation and time.", "findings": [ { "id": "preferred-name-and-aliases", "name": "Preferred name, aliases and local names", "description": "Which name to use, which names mean the same thing, and which merely sound similar.", "questions": [ { "id": "preferred-name-and-aliases-q01", "text": "What identifies and describes the name of a protein, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "preferred-name-and-aliases-q02", "text": "Who or what asserted this about the name of a protein, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "preferred-name-and-aliases-q03", "text": "What may an agent decide or do once the name of a protein is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "stable-identifiers", "name": "Stable identifiers and external keys", "description": "Identifiers that keep pointing at this kind of thing across systems and languages.", "questions": [ { "id": "stable-identifiers-q01", "text": "What identifies and describes an identifier for a protein, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stable-identifiers-q02", "text": "Who or what asserted this about an identifier for a protein, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stable-identifiers-q03", "text": "What may an agent decide or do once an identifier for a protein is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "classification-and-granularity", "name": "Classification and granularity", "description": "Where a protein sits among kinds, and how finely a task needs to cut it.", "findings": [ { "id": "kind-and-parents", "name": "Kind, parents and neighbouring kinds", "description": "The classes this thing belongs to and the ones it is next to.", "questions": [ { "id": "kind-and-parents-q01", "text": "What identifies and describes the kind of a protein, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "kind-and-parents-q02", "text": "Who or what asserted this about the kind of a protein, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "kind-and-parents-q03", "text": "What may an agent decide or do once the kind of a protein is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "distinguishing-features", "name": "Distinguishing features", "description": "What separates a protein from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a protein, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "distinguishing-features-q02", "text": "Who or what asserted this about what distinguishes a protein, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "distinguishing-features-q03", "text": "What may an agent decide or do once what distinguishes a protein is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "form-and-composition", "name": "Form, composition and condition", "description": "What a protein is made of, what shape and size it takes, and what state it is in.", "rationale": "A physical thing can be measured, and a model that cannot record its measurements cannot support any decision that depends on them.", "layers": [ { "id": "form-and-dimensions", "name": "Form and dimensions", "description": "Shape, size, mass and the ranges these take across examples.", "findings": [ { "id": "measurable-dimensions", "name": "Measurable dimensions and their units", "description": "The quantities worth recording and the units they are recorded in.", "questions": [ { "id": "measurable-dimensions-q01", "text": "What identifies and describes the dimensions of a protein, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "measurable-dimensions-q02", "text": "Who or what asserted this about the dimensions of a protein, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "measurable-dimensions-q03", "text": "What may an agent decide or do once the dimensions of a protein is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "material-and-composition", "name": "Material and composition", "description": "Materials, parts and how they are put together.", "findings": [ { "id": "parts-and-materials", "name": "Parts and materials", "description": "What a protein is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a protein, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "parts-and-materials-q02", "text": "Who or what asserted this about the composition of a protein, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "parts-and-materials-q03", "text": "What may an agent decide or do once the composition of a protein is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "condition-and-integrity", "name": "Condition and integrity", "description": "Wear, damage, health and the difference between working and broken.", "findings": [ { "id": "condition-assessment", "name": "Condition, damage and health", "description": "How the condition of a protein is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a protein, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "condition-assessment-q02", "text": "Who or what asserted this about the condition of a protein, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "condition-assessment-q03", "text": "What may an agent decide or do once the condition of a protein is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "place-and-movement", "name": "Place and movement", "description": "Where a protein is, how it got there and where it may go (varies).", "rationale": "A thing that can move needs its position recorded with a time, or every later claim about it is about a place it has left.", "layers": [ { "id": "location-and-placement", "name": "Location and placement", "description": "Position, containment and the reference frame the position is given in.", "findings": [ { "id": "position-and-frame", "name": "Position, container and reference frame", "description": "Where a protein is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a protein, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "position-and-frame-q02", "text": "Who or what asserted this about the location of a protein, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "position-and-frame-q03", "text": "What may an agent decide or do once the location of a protein is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "movement-and-transfer", "name": "Movement and transfer", "description": "How a protein is carried, installed or relocated.", "findings": [ { "id": "movement-events", "name": "Movement events and constraints", "description": "What counts as a movement, what records it and what limits it.", "questions": [ { "id": "movement-events-q01", "text": "What identifies and describes the movement of a protein, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "movement-events-q02", "text": "Who or what asserted this about the movement of a protein, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "movement-events-q03", "text": "What may an agent decide or do once the movement of a protein is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "state-and-lifecycle", "name": "State and lifecycle", "description": "The states a protein passes through and the events that move it between them.", "rationale": "Most decisions about a thing depend on what state it is in now, which is a claim with a time on it, not a property.", "layers": [ { "id": "lifecycle-stages", "name": "Lifecycle stages", "description": "From coming into existence to ceasing to be one of these.", "findings": [ { "id": "stages-and-transitions", "name": "Stages and transitions", "description": "The stages worth naming and what moves a protein between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a protein, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stages-and-transitions-q02", "text": "Who or what asserted this about the lifecycle of a protein, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stages-and-transitions-q03", "text": "What may an agent decide or do once the lifecycle of a protein is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "observations-and-status", "name": "Observations and current status", "description": "What is observed about a protein, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a protein is recorded so that it can be superseded rather than overwritten.", "questions": [ { "id": "observation-record-q01", "text": "What identifies and describes an observation of a protein, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "observation-record-q02", "text": "Who or what asserted this about an observation of a protein, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "observation-record-q03", "text": "What may an agent decide or do once an observation of a protein is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "composition-and-identity", "name": "Composition, grade and chemical identity", "description": "What protein is made of and how pure the thing in hand is.", "rationale": "Grade decides what a substance may be used for, so a model that records only the name cannot support any decision about use.", "layers": [ { "id": "chemical-identity", "name": "Chemical identity", "description": "Formula, structure and the registry numbers that name it unambiguously.", "findings": [ { "id": "identity-record", "name": "Identity and registry numbers", "description": "What identifies this substance across suppliers and regulators.", "questions": [ { "id": "identity-record-q01", "text": "What formula, structure and registry identifiers name protein unambiguously?", "kind": "definition" }, { "id": "identity-record-q02", "text": "Which related substances share a name in common use but not an identifier?", "kind": "boundary" } ] } ] }, { "id": "grade-and-impurities", "name": "Grade, purity and impurities", "description": "The specification a batch meets and what else is in it.", "findings": [ { "id": "specification", "name": "Specification and assay", "description": "How purity is stated and measured, and which impurities matter.", "questions": [ { "id": "specification-q01", "text": "What grades of protein exist, how is purity assayed, and which impurities are limited?", "kind": "measurement" }, { "id": "specification-q02", "text": "Which use requires which grade, and what happens when a lower grade is substituted?", "kind": "action" } ] } ] } ] }, { "id": "properties-and-behaviour", "name": "Properties and behaviour", "description": "How protein behaves under conditions an agent can measure or change.", "rationale": "Physical constants are the part of a substance model that transfers between contexts, and each needs its unit and its conditions.", "layers": [ { "id": "physical-constants", "name": "Physical constants", "description": "Values that hold for the pure substance, with their conditions.", "findings": [ { "id": "constants-record", "name": "Constants and conditions", "description": "The quantities worth recording and the state they apply in.", "questions": [ { "id": "constants-record-q01", "text": "What are the defining physical constants of protein, in what units and under what conditions?", "kind": "measurement" }, { "id": "constants-record-q02", "text": "Which of these values change with grade or form rather than being fixed?", "kind": "boundary" } ] } ] }, { "id": "stability-and-reactivity", "name": "Stability and reactivity", "description": "What it reacts with, degrades into, and how it is stored.", "findings": [ { "id": "incompatibilities", "name": "Incompatibilities and degradation", "description": "What must not meet it, and what it becomes over time.", "questions": [ { "id": "incompatibilities-q01", "text": "What is protein incompatible with, and what does it degrade into under storage?", "kind": "definition" }, { "id": "incompatibilities-q02", "text": "What storage and handling does that require, and who is competent to do it?", "kind": "action" } ] } ] } ] }, { "id": "hazard-and-regulation", "name": "Hazard classification and regulation", "description": "How protein can harm, and what the law says about holding and moving it.", "rationale": "A substance model without its hazard class and its regulatory identity is unusable in exactly the situations that matter.", "layers": [ { "id": "hazard-class", "name": "Hazard classification", "description": "Classified hazards, exposure limits and protective measures.", "findings": [ { "id": "classified-hazards", "name": "Classified hazards and limits", "description": "The classification, the scheme it belongs to, and the limits set.", "questions": [ { "id": "classified-hazards-q01", "text": "How is protein classified for hazard, under which scheme, and what exposure limits apply?", "kind": "definition" }, { "id": "classified-hazards-q02", "text": "What protection does handling require, and what must an agent refuse to do without it?", "kind": "action" } ] } ] }, { "id": "regulatory-identity", "name": "Regulatory identity and control", "description": "Registration, restriction and transport rules by jurisdiction.", "findings": [ { "id": "controls", "name": "Controls and jurisdiction", "description": "Where it is restricted and what the restriction attaches to.", "questions": [ { "id": "controls-q01", "text": "Which registrations, restrictions or transport rules cover protein, and where?", "kind": "provenance" }, { "id": "controls-q02", "text": "Does the control attach to the substance, its concentration, or its intended use?", "kind": "boundary" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a protein came from and when it held.", "rationale": "A claim without a source and a time cannot be superseded, only overwritten, and an agent that overwrites loses the ability to explain itself.", "layers": [ { "id": "source-and-authority", "name": "Source and authority", "description": "Who said it, on what evidence, and how strongly.", "findings": [ { "id": "claim-provenance", "name": "Claim provenance and confidence", "description": "The authority behind each claim about a protein and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a protein, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "claim-provenance-q02", "text": "Who or what asserted this about a claim about a protein, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "claim-provenance-q03", "text": "What may an agent decide or do once a claim about a protein is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "time-and-versions", "name": "Time, versions and supersession", "description": "When a claim was true, when it was learnt, and what replaced it.", "findings": [ { "id": "validity-and-supersession", "name": "Validity period and supersession", "description": "How an old claim about a protein is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a protein, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "validity-and-supersession-q02", "text": "Who or what asserted this about the validity of a claim about a protein, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "validity-and-supersession-q03", "text": "What may an agent decide or do once the validity of a claim about a protein is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 8, "layers": 17, "findings": 19, "questions": 51 } } } }