{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:52:06Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 20.0, "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: 01a094cf-c149-7ed0-bb09-44beb2ea8257\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: coproporphyrinogen I\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043:", "usd": 0.0, "recall": true }, "codex": { "seconds": 87.9, "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: 01a094cf-c140-7263-820c-cf22ccc3de81\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: coproporphyrinogen I\nRegistry id: vr.tr.coproporphyrinogen-i\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into thi" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:53:40+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:29+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q2468963", "registryId": "vr.tr.coproporphyrinogen-i", "name": "coproporphyrinogen I", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q2468963/", "model": { "registry_id": "vr.tr.coproporphyrinogen-i", "name": "coproporphyrinogen I", "purpose": "Enable an agent to identify coproporphyrinogen I, assess whether a sample still represents that substance, and judge its suitability for biochemical measurement or use.", "definition": "Coproporphyrinogen I is a reduced cyclic tetrapyrrole with four methyl and four propionate side chains in the type-I arrangement, formed by decarboxylation of uroporphyrinogen I and unable to proceed through the normal heme biosynthetic pathway.", "scope_statement": "This model owns the chemical identity, sample state, analytical evidence and biochemical relationships of coproporphyrinogen I under registry id vr.tr.coproporphyrinogen-i in PHY / PHY.MAT.", "in_scope": [ "Type-I substitution pattern and reduced porphyrinogen identity", "Protonation, counterions, concentration and sample composition", "Distinction from coproporphyrinogen III and coproporphyrin I", "Formation from uroporphyrinogen I and evidence about subsequent transformations", "Sample preservation, analytical recovery and fitness for experimental use" ], "out_of_scope": [ "Independent models of coproporphyrinogen III or coproporphyrin I", "The complete heme biosynthesis pathway", "Uroporphyrinogen decarboxylase structure and enzyme engineering", "Diagnosis and treatment of porphyrias", "Commercial reagent formulations and analytical instruments as products" ], "distinguishing_features": [ "Establish the type-I side-chain arrangement: repeating methyl-propionate pairs around the macrocycle, rather than the type-III arrangement with one reversed pair.", "Establish the reduced porphyrinogen state independently of isomer identity; coproporphyrin I is the corresponding oxidized porphyrin.", "Confirm four methyl and four propionate side chains, distinguishing it from uroporphyrinogen I and incompletely decarboxylated intermediates.", "Require isomer-resolving evidence: molecular mass alone cannot distinguish coproporphyrinogen I from coproporphyrinogen III." ], "characteristics": [ { "name": "Constitutional isomer assignment", "kind": "category", "unit_or_values": "Type I confirmed; mixed isomers; unresolved", "why_it_matters": "The I and III forms require different biochemical interpretations despite sharing composition." }, { "name": "Porphyrinogen integrity", "kind": "state", "unit_or_values": "Reduced form confirmed; partially oxidized; oxidized; unresolved", "why_it_matters": "Oxidation changes the analyte and can invalidate a nominal coproporphyrinogen I concentration." }, { "name": "Chemical form", "kind": "category", "unit_or_values": "Free acid or specified ionic form, counterions and solvation", "why_it_matters": "Mass-based preparation and solution behavior depend on the actual form supplied." }, { "name": "Coproporphyrinogen I concentration", "kind": "measurement", "unit_or_values": "mol/L with method, uncertainty and measurement time", "why_it_matters": "Experimental dosing requires the concentration of intact target material." }, { "name": "Isomeric and redox purity", "kind": "measurement", "unit_or_values": "mol% or mass%, with denominator and resolved impurity identities", "why_it_matters": "A total porphyrin-related signal can conceal III-isomer contamination or oxidation products." }, { "name": "Sample environment", "kind": "state", "unit_or_values": "Solvent or matrix, pH, temperature in °C, atmosphere, light exposure and elapsed time", "why_it_matters": "Preservation and measurement claims must be tied to the conditions experienced by the sample." }, { "name": "Formation relationship", "kind": "relation", "unit_or_values": "Precursor, enzyme, organism and supporting reaction evidence", "why_it_matters": "Formation from uroporphyrinogen I is documented through uroporphyrinogen decarboxylase, but experimental provenance still needs recording. [UniProt UROD](https://www.uniprot.org/uniprotkb/Q5T446/entry)" } ], "affordances": [ "Match a proposed identity to a structure-resolved chemical record.", "Assess whether a preparation contains intact coproporphyrinogen I at the required purity.", "Select an assay that resolves type-I identity and accounts for oxidation during measurement.", "Track preparation, storage and handling against an experimentally established stability window.", "Relate measured material to precursor conversion or enzyme-binding experiments.", "Accept, remeasure or reject a sample using use-specific integrity and uncertainty criteria." ], "agent_conduct": { "may": [ "Describe coproporphyrinogen I and its role in heme pathway disorders from biochemical sources.", "Explain in general terms why type I isomers build up in certain porphyrias." ], "must_not": [ "Diagnose a person with a porphyria from symptoms or a single result.", "Interpret a patient's porphyrin tests outside a qualified laboratory or clinician.", "Share a person's test results or diagnosis beyond those entitled to them." ], "requires_human": [ "Any diagnostic or treatment decision for a suspected porphyria." ] }, "ethics": { "considerations": [ "Porphyrias are rare and often misdiagnosed, causing long suffering.", "Genetic diagnoses affect whole families and must stay private." ], "affected_parties": [ "Patients with porphyria", "Their families" ] }, "owners": { "steward": "Nobody owns the molecule; clinical laboratories answer for its measurement.", "master_systems": [ "Metabolic pathway and compound databases" ] }, "visual_identification": [ "Not visible; measured as its oxidized porphyrin in urine or stool by laboratory tests." ], "failure_modes_and_hazards": [ "Wrong interpretation of porphyrin results leads to misdiagnosis." ], "what_it_is_for": [ "Coproporphyrinogen I is encountered in research on porphyrin metabolism and biochemical pathways associated with heme production.", "It may be studied in biological samples or reference preparations where distinguishing the reduced compound from its oxidation products is essential." ], "standards_and_regulation": [ "The Globally Harmonized System of Classification and Labelling of Chemicals, issued by the United Nations, provides the framework for assessing and communicating chemical hazards where implemented." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q2468963: coproporphyrinogen I", "url": "https://www.wikidata.org/wiki/Q2468963", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Coproporphyrinogen I", "url": "https://en.wikipedia.org/wiki/Coproporphyrinogen_I", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "chemical-identity", "name": "Chemical identity", "description": "Define which molecular entity the registry entry denotes.", "rationale": "Confusing isomer identity with oxidation state would merge distinct substances.", "layers": [ { "id": "macrocycle-and-substituents", "name": "Macrocycle and substituents", "description": "Specify the structural features that establish the I isomer.", "findings": [ { "id": "type-i-structure", "name": "Type-I structure", "description": "Require a numbered structure connecting porphyrinogen reduction state with the repeating type-I side-chain arrangement.", "questions": [ { "text": "Which atom-numbered structure and structure identifier establish coproporphyrinogen I?", "kind": "definition", "id": "type-i-structure-q01" }, { "text": "Which structural observations distinguish this material from coproporphyrinogen III and coproporphyrin I?", "kind": "boundary", "id": "type-i-structure-q02" } ] } ] }, { "id": "identifier-and-form-mapping", "name": "Identifier and form mapping", "description": "Connect registry identity to external records without conflating chemical forms.", "findings": [ { "id": "verified-record-equivalence", "name": "Verified record equivalence", "description": "Reconcile names and database identifiers against structures; KEGG lists coproporphyrinogen I as C05768. [KEGG pathway](https://www.genome.jp/dbget-bin/www_bget?pathway%3Ahsa00860=)", "questions": [ { "text": "Which CAS, PubChem, ChEBI and EC identifiers can be verified for this exact structure, and which remain unavailable?", "kind": "provenance", "id": "verified-record-equivalence-q01" }, { "text": "Does each linked record describe the parent acid, an ionic form, a salt or an oxidized derivative?", "kind": "boundary", "id": "verified-record-equivalence-q02" } ] } ] } ] }, { "id": "preparation-composition", "name": "Preparation composition", "description": "Describe how much intact target substance a preparation contains.", "rationale": "A label or total tetrapyrrole measurement does not establish usable coproporphyrinogen I content.", "layers": [ { "id": "chemical-form-and-medium", "name": "Chemical form and medium", "description": "Record the material form and conditions underlying concentration claims.", "findings": [ { "id": "form-dependent-quantity", "name": "Form-dependent quantity", "description": "Tie amounts to the stated protonation, counterions, solvent and concentration basis.", "questions": [ { "text": "What chemical form, solvent composition and pH describe the preparation?", "kind": "definition", "id": "form-dependent-quantity-q01" }, { "text": "How was intact coproporphyrinogen I concentration determined, including corrections for counterions, solvent and impurities?", "kind": "measurement", "id": "form-dependent-quantity-q02" } ] } ] }, { "id": "impurity-profile", "name": "Impurity profile", "description": "Separate target material from related tetrapyrroles and preparation residues.", "findings": [ { "id": "resolved-purity", "name": "Resolved purity", "description": "Assess isomeric contamination, oxidation products, residual precursor and incompletely decarboxylated material separately.", "questions": [ { "text": "What fractions are coproporphyrinogen III, coproporphyrin I, uroporphyrinogen I or partially decarboxylated intermediates?", "kind": "measurement", "id": "resolved-purity-q01" }, { "text": "Which impurity and residual-reagent limits are required for the intended enzyme or analytical experiment?", "kind": "action", "id": "resolved-purity-q02" } ] } ] } ] }, { "id": "redox-integrity-and-preservation", "name": "Redox integrity and preservation", "description": "Determine whether preparation and handling preserve the intended analyte.", "rationale": "Conversion between porphyrinogen and porphyrin must be distinguished from loss or gain of total tetrapyrrole material.", "layers": [ { "id": "conversion-history", "name": "Conversion history", "description": "Track possible chemical change from preparation through measurement.", "findings": [ { "id": "oxidation-accounting", "name": "Oxidation accounting", "description": "Require evidence about conversion to coproporphyrin I and other products during the sample's history.", "questions": [ { "text": "How much intact porphyrinogen remains at preparation, assay start and assay completion?", "kind": "measurement", "id": "oxidation-accounting-q01" }, { "text": "Which observed products arose before sampling, during extraction or during intentional analytical conversion?", "kind": "provenance", "id": "oxidation-accounting-q02" } ] } ] }, { "id": "validated-handling-window", "name": "Validated handling window", "description": "Connect storage and handling choices to measured integrity.", "findings": [ { "id": "condition-specific-stability", "name": "Condition-specific stability", "description": "Treat acceptable temperature, atmosphere, light exposure and holding time as conditions requiring validation.", "questions": [ { "text": "What stability and recovery measurements support the chosen container, atmosphere, light protection and temperature?", "kind": "measurement", "id": "condition-specific-stability-q01" }, { "text": "What elapsed time or integrity threshold triggers remeasurement, repreparation or rejection?", "kind": "action", "id": "condition-specific-stability-q02" } ] } ] } ] }, { "id": "analytical-recognition", "name": "Analytical recognition", "description": "Establish what an analytical result actually identifies and quantifies.", "rationale": "Isomer separation and control of redox conversion are both necessary to interpret a coproporphyrinogen I result.", "layers": [ { "id": "isomer-specific-identification", "name": "Isomer-specific identification", "description": "Evaluate evidence capable of separating I from III.", "findings": [ { "id": "orthogonal-identity-evidence", "name": "Orthogonal identity evidence", "description": "Combine structure-sensitive or separation-based evidence with composition measurements.", "questions": [ { "text": "Which validated separation or structural method distinguishes the I and III isomers in this matrix?", "kind": "measurement", "id": "orthogonal-identity-evidence-q01" }, { "text": "What independently characterized reference material supports the peak or structure assignment?", "kind": "provenance", "id": "orthogonal-identity-evidence-q02" } ] } ] }, { "id": "measurement-basis", "name": "Measurement basis", "description": "Separate direct analyte measurements from measurements made after chemical conversion.", "findings": [ { "id": "direct-versus-converted-signal", "name": "Direct versus converted signal", "description": "Make explicit whether the reported result measures intact porphyrinogen or a derivative used to infer its amount.", "questions": [ { "text": "Does the method measure intact coproporphyrinogen I, coproporphyrin I after oxidation, or a combined pool?", "kind": "boundary", "id": "direct-versus-converted-signal-q01" }, { "text": "How are pre-existing coproporphyrin I, conversion yield, extraction recovery and measurement uncertainty accounted for?", "kind": "measurement", "id": "direct-versus-converted-signal-q02" } ] } ] } ] }, { "id": "biochemical-context-and-use", "name": "Biochemical context and use", "description": "Connect this substance to evidenced reactions and experimental decisions.", "rationale": "The I isomer must not inherit pathway behavior or experimental suitability from the III isomer.", "layers": [ { "id": "formation-and-fate", "name": "Formation and fate", "description": "Record organism-specific precursor and transformation relationships.", "findings": [ { "id": "isomer-specific-pathway-role", "name": "Isomer-specific pathway role", "description": "UROD annotations distinguish formation of the I isomer from the III-isomer route that can proceed to heme. [UniProt UROD](https://www.uniprot.org/uniprotkb/Q5T446/entry)", "questions": [ { "text": "Which organism, enzyme and experimental evidence establish formation from uroporphyrinogen I?", "kind": "provenance", "id": "isomer-specific-pathway-role-q01" }, { "text": "Which downstream reactions are demonstrated or excluded for the I isomer in the biological system being modeled?", "kind": "boundary", "id": "isomer-specific-pathway-role-q02" } ] } ] }, { "id": "experimental-fitness", "name": "Experimental fitness", "description": "Determine whether a preparation supports a specified biochemical use.", "findings": [ { "id": "use-specific-acceptance", "name": "Use-specific acceptance", "description": "Separate evidence of binding from evidence of catalytic conversion; a UROD complex with coproporphyrinogen I is recorded as 1R3Q. [NCBI structure](https://www.ncbi.nlm.nih.gov/Structure/pdb/1R3Q)", "questions": [ { "text": "Does the intended experiment require a ligand, reaction product, analytical standard or demonstrated enzyme substrate?", "kind": "action", "id": "use-specific-acceptance-q01" }, { "text": "Which controls establish that the observed effect comes from intact coproporphyrinogen I rather than oxidation products, other isomers or preparation reagents?", "kind": "measurement", "id": "use-specific-acceptance-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, without source consultation.", "Confirm database identifiers, protonation state, and any salt form before assigning a definitive substance record.", "Physical constants, stability conditions, and hazard classifications require verification." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of coproporphyrinogen I 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": "Molecular formula", "value_or_pattern": "C36H44N4O8", "note": "Formula of the neutral free acid; ionization changes the hydrogen count and charge." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of coproporphyrinogen I 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": [ "Research on porphyrin metabolism and the formation of type-I porphyrin byproducts.", "Substrate in biochemical studies of porphyrinogen oxidation." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of coproporphyrinogen I 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": "Molar mass of the neutral free acid", "typical_range": "Approximately 660.76", "unit": "g/mol" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of coproporphyrinogen I 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": [ "Oxidation during handling can convert it to coproporphyrin I, changing the chemical identity and analytical response.", "Confusing the type-I and type-III isomers leads to incorrect interpretation of their roles in heme biosynthesis.", "Toxicological and handling classifications should be established from substance-specific documentation rather than inferred from other porphyrins." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of coproporphyrinogen I 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": "Coproporphyrinogen III", "difference": "Has the type-III side-chain arrangement and is an intermediate in normal heme biosynthesis." }, { "name": "Coproporphyrin I", "difference": "Is the oxidized, conjugated porphyrin corresponding to coproporphyrinogen I." }, { "name": "Uroporphyrinogen I", "difference": "Has four acetate side chains where coproporphyrinogen I has four methyl groups; decarboxylation connects the two." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of coproporphyrinogen I this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which CAS, PubChem, ChEBI and EC records unambiguously identify the parent substance and its separately indexed ionic forms?", "What experimentally supported solubility, acid-base and thermal data exist for defined forms, and are melting or boiling measurements meaningful before decomposition?", "What preservation conditions and maximum holding times retain quantified porphyrinogen integrity in relevant matrices?", "Which validated assays distinguish native coproporphyrinogen I from pre-existing coproporphyrin I and oxidation introduced during preparation?", "What substance-specific hazard classifications, exposure limits and handling evidence are available, separately from solvent hazards and evidence about oxidized porphyrins?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 16, "questions": 26 } }