{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T09:13:19Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 19.2, "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: 01a094e3-5439-7e51-9362-db4896e06ce1\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: discodermolide\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: 1001 ", "usd": 0.0, "recall": true }, "codex": { "seconds": 78.7, "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: 01a094e3-5444-7682-9d66-0d55a7eec131\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: discodermolide\nRegistry id: vr.tr.discodermolide\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (no" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:56:03+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "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-Q2920456", "registryId": "vr.tr.discodermolide", "name": "discodermolide", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q2920456/", "model": { "registry_id": "vr.tr.discodermolide", "name": "discodermolide", "purpose": "Enable an agent to recognize discodermolide, assess the identity and fitness of a particular sample, and determine which research or handling actions its evidence supports.", "definition": "Discodermolide is a polyhydroxylated polyketide lactone originally isolated from the marine sponge Discodermia dissoluta that stabilizes microtubules and exhibits potent antiproliferative activity.", "scope_statement": "This model owns vr.tr.discodermolide in PHY / PHY.MAT: the stereochemically defined substance conventionally identified as naturally occurring (+)-discodermolide, together with sample composition, condition, provenance, biological evidence and handling constraints.", "in_scope": [ "Molecular connectivity, absolute stereochemistry and distinction from the opposite enantiomer", "Sample purity, concentration, impurities and analytical identity evidence", "Isolated-material and solution state, stability and storage history", "Evidence for tubulin binding, microtubule stabilization and cellular effects", "Source provenance and documented restrictions on handling and use" ], "out_of_scope": [ "The source sponge as an organism or ecological population", "Synthetic routes and extraction operations as independently modeled processes", "Discodermolide analogues, derivatives and molecular hybrids as separate substances", "Finished formulations and delivery systems as products", "Clinical treatment protocols and patient-specific decisions" ], "distinguishing_features": [ "Require connectivity and stereochemical agreement with natural (+)-discodermolide; the opposite enantiomer and individual epimers do not satisfy that identity merely because their mass matches.", "Check the characteristic polypropionate framework, δ-lactone, carbamate, hydroxyl substitution and unsaturation pattern against an authenticated structure. Structural context: [synthesis and biological evaluation](https://pmc.ncbi.nlm.nih.gov/articles/PMC2991168/).", "Distinguish discodermolide from paclitaxel and other microtubule stabilizers by molecular structure; a shared biological endpoint is insufficient identification.", "Require the unmodified parent structure when distinguishing discodermolide from simplified analogues or discodermolide-paclitaxel hybrids." ], "characteristics": [ { "name": "Stereochemical identity", "kind": "category", "unit_or_values": "Natural (+) configuration confirmed; opposite enantiomer; stereoisomeric mixture; unresolved", "why_it_matters": "Connectivity or mass alone cannot establish that a sample is the intended stereoisomer." }, { "name": "Registry identifier concordance", "kind": "relation", "unit_or_values": "Structure-linked CAS, PubChem and EC records, each with source and verification date or explicit unresolved status", "why_it_matters": "External identifiers must refer to the same stereochemically defined substance." }, { "name": "Parent-compound content", "kind": "measurement", "unit_or_values": "Mass fraction or molar fraction; chromatographic area percentage recorded separately with method", "why_it_matters": "Assay concentration and sample suitability depend on actual parent content." }, { "name": "Stereoisomeric composition", "kind": "measurement", "unit_or_values": "Enantiomeric excess and diastereomer proportions, with method and uncertainty", "why_it_matters": "A chemically clean sample may still contain the wrong stereoisomer." }, { "name": "Material presentation", "kind": "state", "unit_or_values": "Isolated solid; dissolved stock; suspension; formulated mixture; unknown", "why_it_matters": "Presentation changes how concentration, transfer and stability can be assessed." }, { "name": "Dissolved parent concentration", "kind": "measurement", "unit_or_values": "µmol/L or mmol/L, with solvent, temperature, preparation date and measurement basis", "why_it_matters": "Nominal loading may differ from dissolved, intact discodermolide." }, { "name": "Condition-dependent stability", "kind": "measurement", "unit_or_values": "Parent remaining as percentage over hours or days under specified conditions", "why_it_matters": "Storage and preparation decisions require evidence that the parent compound persists." }, { "name": "Microtubule-stabilizing activity", "kind": "measurement", "unit_or_values": "Assay-specific polymerization, depolymerization or binding endpoint with concentration and experimental conditions", "why_it_matters": "Activity is conditional on the tubulin system and assay design." }, { "name": "Cellular response", "kind": "measurement", "unit_or_values": "Endpoint-specific potency in nmol/L or µmol/L, with cell model, exposure time and uncertainty", "why_it_matters": "Growth inhibition, mitotic arrest and cell death are distinct observations." }, { "name": "Handling and use status", "kind": "category", "unit_or_values": "Documented supplier and institutional controls, jurisdiction-specific classification, permitted use or unresolved", "why_it_matters": "Biological activity alone does not establish formal hazard classification or authorized use." } ], "affordances": [ "Compare a candidate sample with an authenticated discodermolide structure and analytical reference.", "Qualify or reject a lot for a specified experiment using composition and condition evidence.", "Calculate parent-equivalent assay loading from measured content and dissolved concentration.", "Select storage and preparation conditions supported by stability and solubility evidence.", "Compare biological results only after aligning stereoisomer, exposure and assay conditions.", "Flag unresolved identity, deterioration or handling requirements before further use." ], "agent_conduct": { "may": [ "Identify discodermolide by name, source and documented properties, citing sources.", "Report the status of its clinical research accurately, including that it is not an approved medicine.", "Record the identity and storage of research samples for their keeper." ], "must_not": [ "Present it as an approved or proven cancer treatment.", "Help supply it to patients outside lawful clinical trials.", "Encourage harvesting of wild marine sponges to obtain it.", "Handle samples outside a controlled laboratory." ], "requires_human": [ "Any use in human research.", "Disposal of research samples." ] }, "ethics": { "considerations": [ "False hope for cancer patients is a real harm when experimental compounds are oversold.", "Marine natural products raise questions of fair benefit for source countries." ], "affected_parties": [ "Cancer patients and families", "Research staff", "Marine ecosystems" ] }, "owners": { "steward": "The research institution holding the samples.", "master_systems": [] }, "visual_identification": [ "Identity rests on labels and analytical data, not appearance.", "Exists mainly as small research samples." ], "failure_modes_and_hazards": [ "Potent cell toxicity to staff handling samples.", "Toxicity seen in clinical research.", "Overstated treatment claims." ], "standards_and_regulation": [ "Globally Harmonized System of Classification and Labelling of Chemicals (GHS), United Nations." ], "what_it_is_for": [ "Discodermolide is encountered in natural products chemistry, chemical synthesis and laboratory research on microtubule stabilization.", "Researchers use it to investigate cell division and antiproliferative effects, with sample identity and purity essential to interpreting results.", "Its history as an experimental anticancer compound does not establish suitability for routine clinical treatment." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q2920456: discodermolide", "url": "https://www.wikidata.org/wiki/Q2920456", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Discodermolide", "url": "https://en.wikipedia.org/wiki/Discodermolide", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "parent-identity", "name": "Parent identity", "description": "Establish which stereochemically defined molecule the registry entry denotes.", "rationale": "Discodermolide must be distinguished from its antipode, epimers and structurally related experimental compounds.", "layers": [ { "id": "connectivity-and-stereochemistry", "name": "Connectivity and stereochemistry", "description": "Represent the complete parent structure and evidence for stereochemical assignment.", "findings": [ { "id": "natural-parent-reference", "name": "Natural parent reference", "description": "The literature distinguishes natural (+)-discodermolide from its synthetic opposite enantiomer, making absolute configuration part of identity. Source: [synthesis and biological evaluation](https://pmc.ncbi.nlm.nih.gov/articles/PMC2991168/).", "questions": [ { "text": "Which authenticated structure fixes every stereocenter and alkene geometry for this entry?", "kind": "definition", "id": "natural-parent-reference-q01" }, { "text": "What evidence establishes agreement with that structure beyond molecular mass or optical rotation alone?", "kind": "measurement", "id": "natural-parent-reference-q02" } ] } ] }, { "id": "identifiers-and-neighbours", "name": "Identifiers and neighbours", "description": "Resolve external identities and separate the parent from related substances.", "findings": [ { "id": "structure-linked-identifiers", "name": "Structure-linked identifiers", "description": "Accept external identifiers only after checking their represented structure and stereochemical specificity.", "questions": [ { "text": "Which verified CAS, PubChem and EC records resolve to the intended parent, and which are unavailable or ambiguous?", "kind": "provenance", "id": "structure-linked-identifiers-q01" }, { "text": "Does a proposed synonym denote the parent, an epimer, the opposite enantiomer or a modified analogue?", "kind": "boundary", "id": "structure-linked-identifiers-q02" } ] } ] } ] }, { "id": "lot-composition-and-origin", "name": "Lot composition and origin", "description": "Determine what a supplied discodermolide sample contains and how its identity is traceable.", "rationale": "Neither a natural-source label nor a synthetic-source label establishes usable parent content.", "layers": [ { "id": "content-and-impurities", "name": "Content and impurities", "description": "Separate parent amount, stereochemical composition and other constituents.", "findings": [ { "id": "usable-parent-content", "name": "Usable parent content", "description": "Record quantitative parent content separately from chromatographic purity and identify limits in resolving closely related impurities.", "questions": [ { "text": "What method measures parent content, and does its reported percentage represent mass fraction or detector area?", "kind": "measurement", "id": "usable-parent-content-q01" }, { "text": "Can the analytical evidence distinguish epimers, residual solvents and degradation products from intact discodermolide?", "kind": "measurement", "id": "usable-parent-content-q02" } ] } ] }, { "id": "material-lineage", "name": "Material lineage", "description": "Connect the lot to isolation or synthesis records and reference standards.", "findings": [ { "id": "traceable-lot", "name": "Traceable lot", "description": "Keep origin and chain of custody attached to the sample without turning the substance model into a manufacturing procedure.", "questions": [ { "text": "Which supplier, isolation record or synthesis record identifies this lot and its analytical release evidence?", "kind": "provenance", "id": "traceable-lot-q01" }, { "text": "Which authenticated reference material supports its assignment as (+)-discodermolide?", "kind": "provenance", "id": "traceable-lot-q02" } ] } ] } ] }, { "id": "physical-state-and-integrity", "name": "Physical state and integrity", "description": "Assess the physical presentation and persistence of intact discodermolide during storage and preparation.", "rationale": "A correct label does not establish that an aged solid or diluted stock supplies the intended dissolved parent concentration.", "layers": [ { "id": "solid-and-solution-behaviour", "name": "Solid and solution behaviour", "description": "Attach measured physical properties to the actual material and conditions.", "findings": [ { "id": "available-dissolved-parent", "name": "Available dissolved parent", "description": "Distinguish isolated-material properties, stock-solvent solubility and behavior after dilution into an assay medium.", "questions": [ { "text": "What solid-state and thermal measurements are available, and do observed transitions represent melting or decomposition?", "kind": "measurement", "id": "available-dissolved-parent-q01" }, { "text": "What concentration remains dissolved after dilution into the intended medium at the stated temperature and solvent fraction?", "kind": "measurement", "id": "available-dissolved-parent-q02" } ] } ] }, { "id": "storage-and-degradation", "name": "Storage and degradation", "description": "Evaluate whether storage and preparation preserve the specified parent structure.", "findings": [ { "id": "integrity-over-time", "name": "Integrity over time", "description": "Treat possible changes involving the lactone or unsaturated framework as analytical questions until demonstrated for the actual conditions.", "questions": [ { "text": "How much intact parent remains after the recorded temperature, light, solvent and freeze-thaw exposure?", "kind": "measurement", "id": "integrity-over-time-q01" }, { "text": "Which measured acceptance criteria justify continued use, reanalysis or rejection of this stock?", "kind": "action", "id": "integrity-over-time-q02" } ] } ] } ] }, { "id": "biological-action-and-evidence", "name": "Biological action and evidence", "description": "Represent discodermolide's experimentally supported molecular and cellular effects.", "rationale": "Its characteristic biological action is useful for research qualification but cannot substitute for chemical identity or clinical evidence.", "layers": [ { "id": "tubulin-interaction", "name": "Tubulin interaction", "description": "Connect binding evidence to effects on microtubule assembly and stability.", "findings": [ { "id": "taxane-site-stabilization", "name": "Taxane-site stabilization", "description": "Structural research places discodermolide at the taxane site of β-tubulin and relates its binding to microtubule stabilization. Source: [structural basis of stabilization](https://pmc.ncbi.nlm.nih.gov/articles/PMC5559732/).", "questions": [ { "text": "Which direct binding or structural evidence supports the claimed interaction in the relevant tubulin system?", "kind": "provenance", "id": "taxane-site-stabilization-q01" }, { "text": "Under which tubulin concentration, nucleotide conditions and temperature was stabilization measured?", "kind": "measurement", "id": "taxane-site-stabilization-q02" } ] } ] }, { "id": "cellular-response-boundaries", "name": "Cellular response boundaries", "description": "Keep cellular endpoints and experimental contexts distinct.", "findings": [ { "id": "endpoint-specific-response", "name": "Endpoint-specific response", "description": "Experimental work reports mitotic arrest in MG63 cells; this remains a specified cellular observation rather than a universal response or therapeutic conclusion. Source: [binding and mitotic-arrest study](https://pubmed.ncbi.nlm.nih.gov/8807856/).", "questions": [ { "text": "Which endpoint was measured: proliferation inhibition, mitotic arrest, senescence, apoptosis or another response?", "kind": "definition", "id": "endpoint-specific-response-q01" }, { "text": "What cell model, exposure duration, vehicle control and verified parent concentration support the reported potency?", "kind": "measurement", "id": "endpoint-specific-response-q02" }, { "text": "What additional evidence is required before extending this result to another cell system or an organism?", "kind": "boundary", "id": "endpoint-specific-response-q03" } ] } ] } ] }, { "id": "handling-and-use-constraints", "name": "Handling and use constraints", "description": "Connect the actual material presentation to documented containment and permitted-use decisions.", "rationale": "Discodermolide's experimentally observed cellular activity requires explicit handling evidence, while formal classifications must be verified independently.", "layers": [ { "id": "exposure-and-classification", "name": "Exposure and classification", "description": "Distinguish biological hazard evidence from supplier and jurisdiction-specific classifications.", "findings": [ { "id": "documented-handling-basis", "name": "Documented handling basis", "description": "Record the applicable safety documentation without inventing a GHS category or an occupational exposure limit.", "questions": [ { "text": "Which current safety data sheet and institutional assessment cover this lot, concentration and physical form?", "kind": "provenance", "id": "documented-handling-basis-q01" }, { "text": "Are GHS classifications and exposure limits documented, absent from the checked sources or still unverified?", "kind": "definition", "id": "documented-handling-basis-q02" } ] } ] }, { "id": "allowed-actions", "name": "Allowed actions", "description": "Identify conditions governing transfer, experimentation and disposal.", "findings": [ { "id": "evidence-bounded-use", "name": "Evidence-bounded use", "description": "Determine permitted actions from the intended experiment and applicable documentation; substance identity alone does not authorize administration.", "questions": [ { "text": "Which documented controls govern weighing, dissolving, transferring and disposing of this discodermolide material?", "kind": "action", "id": "evidence-bounded-use-q01" }, { "text": "What approvals and material qualifications are required for the proposed research use?", "kind": "action", "id": "evidence-bounded-use-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 account is recalled knowledge; no sources were consulted.", "Verify exact registry identifiers, stereochemical identity, purity and measured physical properties before creating a substance record.", "Clinical development outcomes, current regulatory status and formal hazard classifications require verification; research activity does not establish an approved therapeutic use." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of discodermolide 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": "C33H55NO8", "note": "Specifies elemental composition but does not distinguish stereoisomers." }, { "scheme": "CAS Registry Number", "value_or_pattern": "Two to seven digits, a hyphen, two digits, a hyphen, one check digit", "note": "The exact identifier should be verified for the natural stereoisomer." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of discodermolide 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 microtubule stabilization and inhibition of cell proliferation.", "Investigational anticancer drug development.", "A target for total synthesis and development of stereoselective synthetic methods." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of discodermolide 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", "typical_range": "Approximately 593.8", "unit": "g/mol" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of discodermolide 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": [ "Its cytotoxic activity presents a potential hazard during handling.", "Microtubule stabilization can disrupt normal cell division as well as cancer-cell proliferation.", "Incorrect stereochemistry or insufficient purity can change measured biological activity." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of discodermolide 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": "Paclitaxel", "difference": "Both stabilize microtubules, but paclitaxel has a taxane skeleton whereas discodermolide is a structurally distinct polyketide lactone." }, { "name": "Discodermia dissoluta", "difference": "The sponge is the organism from which discodermolide was originally isolated; discodermolide is an individual chemical compound." }, { "name": "Discodermolide analogues", "difference": "Analogues alter the parent compound's structure or stereochemistry and should be identified separately." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of discodermolide this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which authoritative CAS, PubChem and EC records match natural (+)-discodermolide with explicit stereochemistry?", "Which authenticated reference and analytical methods reliably resolve the parent from its antipode, epimers and relevant degradation products?", "What measured solubility, solid-state and thermal data apply to characterized discodermolide, and is boiling behavior measurable before decomposition?", "What storage conditions, solution lifetimes and degradation pathways are supported by direct stability measurements?", "What current jurisdiction-specific classifications, exposure limits and use restrictions apply to the intended material and research setting?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 16, "questions": 27 } }