{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T10:38:14Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 20.1, "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: 01a09531-066f-7bf3-9c09-a8892852e61d\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway\nSense to describe: (none recorded)\nDomain code: ACT.PRC\nAlso known as", "usd": 0.0, "recall": true }, "codex": { "seconds": 81.8, "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: 01a09531-0678-7320-b793-95ff94ff0c31\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway\nRegistry id: vr.tr.isopentenyl-diphosphate-biosynthetic-process-me" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T11:00:00Z", "ingestedAt": "2026-10-06T08:13:40+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:28+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q21198649", "registryId": "vr.tr.isopentenyl-diphosphate-biosynthetic-process-methylerythrito", "name": "isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q21198649/", "model": { "registry_id": "vr.tr.isopentenyl-diphosphate-biosynthetic-process-methylerythrito", "name": "isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway", "purpose": "Enable an agent to recognize MEP-pathway production of isopentenyl diphosphate, assess its activity in a specified biological system, and identify justified measurements or interventions.", "definition": "The methylerythritol 4-phosphate (MEP) pathway is a sequence of enzymatic reactions that converts pyruvate and glyceraldehyde 3-phosphate into the isoprenoid precursors isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), operating in many bacteria and in the plastids of plants and various algae.", "scope_statement": "This ACT.PRC model owns the pathway-specific specialization of isopentenyl diphosphate biosynthesis registered as vr.tr.isopentenyl-diphosphate-biosynthetic-process-methylerythrito: reaction continuity through methylerythritol phosphate intermediates, biological realization, pathway-attributed output, and responses to perturbation.", "in_scope": [ "Reaction continuity from precursor entry through MEP intermediates to IPP production.", "Enzyme-function assignments and evidence for missing or alternative implementations.", "Organism, compartment, physiological condition, and observation interval defining an instance.", "Intermediate pools, pathway-specific flux, and associated DMAPP output.", "Resource dependencies, competing precursor sources, and experimentally supported perturbation responses." ], "out_of_scope": [ "The broader class of IPP biosynthetic processes and its shared properties.", "Mevalonate-pathway chemistry, except as an alternative source requiring attribution.", "Standalone models of IPP, MEP, enzymes, genes, or organisms.", "Downstream prenyl-chain elongation and synthesis of individual terpenoids.", "General central-carbon metabolism and organelle transport mechanisms beyond their pathway interfaces." ], "distinguishing_features": [ "Require evidence for a route through MEP intermediates; IPP detection alone cannot distinguish the MEP and mevalonate routes. [KEGG terpenoid backbone biosynthesis](https://www.genome.jp/pathway/map00900)", "Check continuity through DXP reductoisomerase, the intervening MEP reactions, and HMBPP synthesis and reduction. [KEGG M00096](https://www.kegg.jp/entry/M00096)", "Distinguish terminal HMBPP conversion from IPP-DMAPP isomerization, which KEGG also includes in its broader C5 module. [KEGG M00096](https://www.kegg.jp/entry/M00096)", "Treat gene annotation as evidence of potential capacity; require condition-specific biochemical evidence before classifying an instance as actively producing IPP.", "Keep production of the C5 precursor distinct from downstream incorporation into larger isoprenoids. [KEGG terpenoid backbone biosynthesis](https://www.genome.jp/pathway/map00900)" ], "characteristics": [ { "name": "Biological realization", "kind": "relation", "unit_or_values": "Organism or strain, tissue or cell type, compartment, and native or engineered context", "why_it_matters": "Defines where evidence applies and prevents combining reactions from incompatible biological locations." }, { "name": "Reaction coverage", "kind": "state", "unit_or_values": "Each required conversion: experimentally supported, predicted, unresolved, or demonstrated unavailable", "why_it_matters": "Distinguishes a continuous pathway from a collection of annotated enzymes." }, { "name": "Activity assessment", "kind": "state", "unit_or_values": "Capacity only, activity demonstrated, activity below detection, or unresolved; qualified by conditions", "why_it_matters": "Separates biosynthetic potential from observed operation." }, { "name": "MEP-attributed IPP production rate", "kind": "measurement", "unit_or_values": "nmol IPP per mg protein per minute, or another explicitly stated normalization; uncertainty required", "why_it_matters": "Measures output attributable to this route rather than total cellular IPP." }, { "name": "Intermediate abundance", "kind": "measurement", "unit_or_values": "Concentration or normalized amount for identified DXP, MEP, downstream intermediates, and HMBPP", "why_it_matters": "Helps localize pathway changes when interpreted alongside turnover and sampling conditions." }, { "name": "IPP-to-DMAPP output ratio", "kind": "measurement", "unit_or_values": "Molar ratio, with terminal-reaction output distinguished from the subsequent cellular pool ratio", "why_it_matters": "Prevents interconversion and downstream consumption from being mistaken for terminal enzyme behavior." }, { "name": "Route attribution evidence", "kind": "category", "unit_or_values": "Annotation, enzyme assay, metabolite identification, isotope tracing, perturbation, or convergent evidence", "why_it_matters": "Determines which conclusions about pathway operation are justified." }, { "name": "Perturbation response", "kind": "measurement", "unit_or_values": "Change in pathway-attributed flux or intermediate abundance relative to a matched control, with exposure and duration", "why_it_matters": "Supports context-specific decisions about pathway control." } ], "affordances": [ "Classify evidence as supporting MEP-pathway capacity, observed activity, or an unresolved assignment.", "Identify gaps in the reaction chain and select evidence needed to resolve them.", "Compare pathway-attributed IPP production across matched conditions.", "Distinguish changed intermediate pools from changed biosynthetic flux.", "Evaluate proposed perturbations against target engagement, resource dependencies, and alternative precursor supply.", "Link the registered process to neighboring models of enzymes, metabolites, transport, and downstream synthesis." ], "agent_conduct": { "may": [ "Describe the MEP pathway's steps and enzymes from scientific sources.", "Annotate genes and organisms as having the pathway when evidence supports it." ], "must_not": [ "Annotate an organism as having the pathway without evidence.", "Confuse it with the mevalonate pathway that makes the same precursors.", "Overstate early research on pathway inhibitors as proven medicines or herbicides." ], "requires_human": [ "Releasing engineered organisms that carry modified versions of the pathway." ] }, "ethics": { "considerations": [ "The pathway is a target for antimalarial drugs and herbicides, whose claims need honest evidence." ], "affected_parties": [ "Researchers", "Patients awaiting new drugs" ] }, "owners": { "steward": "Nobody owns the process; biological databases curate its annotations.", "master_systems": [ "Gene and pathway annotation databases" ] }, "visual_identification": [ "Drawn as a sequence of enzyme steps from pyruvate and glyceraldehyde 3-phosphate to isoprenoid precursors.", "Found in most bacteria, plant plastids and malaria parasites, not in animals." ], "failure_modes_and_hazards": [ "Wrong annotations propagate across genome databases." ], "what_it_is_for": [ "This pathway occurs in many bacteria and in the plastids of plants and various algae, where it supplies precursors for isoprenoid synthesis.", "It is studied in microbial physiology, plant metabolism and biotechnology to understand precursor production and its contribution to downstream compounds." ], "standards_and_regulation": [ "The Gene Ontology Consortium provides the biological process classification for isopentenyl diphosphate biosynthesis through the methylerythritol 4-phosphate pathway." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q21198649: isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway", "url": "https://www.wikidata.org/wiki/Q21198649", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Non-mevalonate pathway", "url": "https://en.wikipedia.org/wiki/Non-mevalonate_pathway", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "mep-route-identity", "name": "MEP route identity", "description": "Criteria for recognizing this specific route and delimiting its output.", "rationale": "The shared IPP endpoint does not establish which biosynthetic route produced it.", "layers": [ { "id": "route-membership", "name": "Route membership", "description": "Evidence connecting the observed process to MEP chemistry.", "findings": [ { "id": "mep-specific-continuity", "name": "MEP-specific continuity", "description": "Record the conversions supporting route identity and explicitly mark unobserved links.", "questions": [ { "text": "Which observed reactions or labeled intermediates establish passage through MEP?", "kind": "definition", "id": "mep-specific-continuity-q01" }, { "text": "Which experiment supports this assignment beyond detecting IPP or predicting homologous genes?", "kind": "provenance", "id": "mep-specific-continuity-q02" } ] } ] }, { "id": "precursor-output-boundary", "name": "Precursor output boundary", "description": "Separate IPP formation from associated C5 interconversion and downstream use.", "findings": [ { "id": "terminal-output-accounting", "name": "Terminal output accounting", "description": "Represent terminal production and subsequent IPP-DMAPP interconversion separately so pathway boundaries remain explicit.", "questions": [ { "text": "Does the reported endpoint measure terminal-reaction IPP production, net IPP accumulation, or incorporation into downstream products?", "kind": "boundary", "id": "terminal-output-accounting-q01" }, { "text": "How are associated DMAPP production and later isomerization accounted for?", "kind": "measurement", "id": "terminal-output-accounting-q02" } ] } ] } ] }, { "id": "reaction-chain-realization", "name": "Reaction chain realization", "description": "Organism-specific implementation of the reference reaction sequence.", "rationale": "Completeness depends on demonstrated conversions rather than a fixed count of gene names.", "layers": [ { "id": "dxp-to-mep-entry", "name": "DXP to MEP entry", "description": "Define precursor supply and entry into MEP chemistry.", "findings": [ { "id": "entry-reaction-assignment", "name": "Entry reaction assignment", "description": "The reference module includes DXP synthase and DXP reductoisomerase; record their local implementation and precursor interfaces. [KEGG M00096](https://www.kegg.jp/entry/M00096)", "questions": [ { "text": "Which evidence establishes precursor delivery to DXP formation in this system?", "kind": "provenance", "id": "entry-reaction-assignment-q01" }, { "text": "Which enzyme or demonstrated alternative carries out DXP-to-MEP conversion?", "kind": "definition", "id": "entry-reaction-assignment-q02" } ] } ] }, { "id": "mep-to-hmbpp-continuity", "name": "MEP to HMBPP continuity", "description": "Assess the intervening conversions that connect MEP to the terminal substrate.", "findings": [ { "id": "intermediate-conversion-coverage", "name": "Intermediate conversion coverage", "description": "Map cytidylyltransferase, kinase, cyclodiphosphate synthase, and HMBPP synthase activities to local evidence. [KEGG M00096](https://www.kegg.jp/entry/M00096)", "questions": [ { "text": "Which intervening activities are demonstrated, predicted, or unresolved?", "kind": "provenance", "id": "intermediate-conversion-coverage-q01" }, { "text": "Do fused proteins, alternative enzymes, or incomplete annotations explain apparent gaps?", "kind": "boundary", "id": "intermediate-conversion-coverage-q02" } ] } ] }, { "id": "hmbpp-conversion", "name": "HMBPP conversion", "description": "Assess the terminal reaction and its measured products.", "findings": [ { "id": "terminal-reductase-evidence", "name": "Terminal reductase evidence", "description": "Record HMBPP reductase assignment and direct evidence for terminal product formation. [KEGG M00096](https://www.kegg.jp/entry/M00096)", "questions": [ { "text": "What supports catalytic activity of the assigned terminal reductase under the stated conditions?", "kind": "provenance", "id": "terminal-reductase-evidence-q01" }, { "text": "Were IPP and DMAPP resolved and quantified separately in the terminal-reaction assay?", "kind": "measurement", "id": "terminal-reductase-evidence-q02" } ] } ] } ] }, { "id": "cellular-context-and-resources", "name": "Cellular context and resources", "description": "Location and enabling conditions for the pathway instance.", "rationale": "Reaction annotations do not establish that substrates, catalysts, and required resources meet in an operating system.", "layers": [ { "id": "compartmental-realization", "name": "Compartmental realization", "description": "Anchor the pathway to a specific biological location.", "findings": [ { "id": "colocation-and-exchange", "name": "Colocation and exchange", "description": "Record enzyme localization, metabolite accessibility, and any transport assumptions connecting reactions.", "questions": [ { "text": "Which organism, cell type, and compartment contain the claimed pathway instance?", "kind": "definition", "id": "colocation-and-exchange-q01" }, { "text": "Which reaction connections require transport, and what evidence supports that exchange?", "kind": "boundary", "id": "colocation-and-exchange-q02" } ] } ] }, { "id": "catalytic-resource-support", "name": "Catalytic resource support", "description": "Track the resources needed by the locally implemented reactions.", "findings": [ { "id": "resource-dependency-assessment", "name": "Resource dependency assessment", "description": "Record reaction-specific nucleotide, reducing-equivalent, cofactor, and electron-delivery requirements without assuming identical implementations across organisms.", "questions": [ { "text": "Which resource and cofactor requirements are experimentally established for the local enzymes?", "kind": "provenance", "id": "resource-dependency-assessment-q01" }, { "text": "What measurements distinguish resource limitation from insufficient catalytic capacity?", "kind": "measurement", "id": "resource-dependency-assessment-q02" } ] } ] } ] }, { "id": "flux-and-route-attribution", "name": "Flux and route attribution", "description": "Evidence that this route contributes to IPP production and the size of that contribution.", "rationale": "Pool abundance and total isoprenoid production are insufficient measures of MEP-specific flux.", "layers": [ { "id": "pool-versus-throughput", "name": "Pool versus throughput", "description": "Separate metabolite abundance from production rate.", "findings": [ { "id": "flux-measurement-validity", "name": "Flux measurement validity", "description": "Require a time basis, normalization, analytical specificity, and stated assumptions for inferred MEP throughput.", "questions": [ { "text": "Does the experiment measure a metabolite pool, turnover, or pathway-attributed production rate?", "kind": "measurement", "id": "flux-measurement-validity-q01" }, { "text": "How do sampling, detection limits, and uncertainty affect the inferred flux?", "kind": "measurement", "id": "flux-measurement-validity-q02" } ] } ] }, { "id": "alternative-source-separation", "name": "Alternative source separation", "description": "Resolve MEP contributions where other routes or imported precursors may contribute.", "findings": [ { "id": "ipp-origin-discrimination", "name": "IPP origin discrimination", "description": "Record evidence separating local MEP synthesis from mevalonate-derived or externally supplied precursor contributions.", "questions": [ { "text": "What tracing or perturbation evidence distinguishes MEP-derived IPP from other sources?", "kind": "provenance", "id": "ipp-origin-discrimination-q01" }, { "text": "Could precursor exchange or mixed cell populations explain the apparent pathway contribution?", "kind": "boundary", "id": "ipp-origin-discrimination-q02" } ] } ] } ] }, { "id": "pathway-control-and-perturbation", "name": "Pathway control and perturbation", "description": "Context-specific evidence for altering MEP output and interpreting the consequences.", "rationale": "An agent needs causal evidence before selecting a pathway intervention or assigning a bottleneck.", "layers": [ { "id": "control-point-assessment", "name": "Control point assessment", "description": "Connect changes in particular reactions to changes in pathway output.", "findings": [ { "id": "conditional-flux-control", "name": "Conditional flux control", "description": "Treat control by an entry, intermediate, or terminal reaction as a condition-specific hypothesis requiring perturbation evidence.", "questions": [ { "text": "Which targeted change altered MEP-attributed flux under matched conditions?", "kind": "provenance", "id": "conditional-flux-control-q01" }, { "text": "What additional measurement would distinguish a catalytic bottleneck from altered substrate supply or product consumption?", "kind": "action", "id": "conditional-flux-control-q02" } ] } ] }, { "id": "response-and-compensation", "name": "Response and compensation", "description": "Evaluate pathway-specific effects and possible compensation after intervention.", "findings": [ { "id": "perturbation-causal-assessment", "name": "Perturbation causal assessment", "description": "Link target engagement, intermediate changes, precursor output, and downstream effects while recording possible alternative explanations.", "questions": [ { "text": "What establishes that the intervention affected the intended MEP reaction?", "kind": "provenance", "id": "perturbation-causal-assessment-q01" }, { "text": "Could alternative IPP supply, altered uptake, or general physiological impairment explain the response?", "kind": "boundary", "id": "perturbation-causal-assessment-q02" }, { "text": "Which control or rescue observation would most directly test the proposed causal explanation?", "kind": "action", "id": "perturbation-causal-assessment-q03" } ] } ] } ] }, { "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, not a source-checked account; verify the exact GO accession and current term definition.", "MEP pathway, DOXP/DXP pathway and non-mevalonate pathway are commonly used related names; descriptions can differ in whether they include the upstream DXP-forming reaction.", "Pathway presence, compartmentation and dependence require organism-specific verification; taxonomic distribution should not be treated as geographic variation." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "scheme": "Gene Ontology (GO), Biological Process", "value_or_pattern": "GO: followed by seven digits", "note": "The supplied name is a GO-style biological process label; the exact accession is not asserted from recall." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway 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": [ "Supplies precursors for the biosynthesis of numerous isoprenoids, including carotenoids and the side chains of chlorophylls and quinones.", "Provides metabolic engineering targets for microbial production of terpenes and other isoprenoids.", "Provides targets for antimicrobial and antiparasitic research because humans lack this pathway." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway 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": "Carbon atoms per IPP or DMAPP molecule", "typical_range": "5", "unit": "carbon atoms per molecule" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway 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": [ "Inhibition or loss of essential pathway enzymes can deprive an organism of isoprenoid precursors when no adequate alternative supply exists.", "The iron-sulfur enzymes IspG and IspH require suitable cluster assembly and electron delivery; disruption can limit pathway activity.", "In metabolic engineering, increasing an upstream reaction alone may cause intermediate accumulation without increasing final isoprenoid production." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway 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": "Mevalonate pathway", "difference": "Produces isoprenoid precursors through mevalonate from acetyl-CoA, rather than through MEP from pyruvate and glyceraldehyde 3-phosphate." }, { "name": "Isopentenyl diphosphate biosynthetic process", "difference": "The broader process includes IPP formation by either the MEP pathway or other routes." }, { "name": "Dimethylallyl diphosphate biosynthetic process", "difference": "Names formation of the allylic isomer DMAPP; the terminal MEP pathway reaction produces both DMAPP and IPP." }, { "name": "Isoprenoid biosynthetic process", "difference": "Includes downstream assembly and modification of isoprenoid products beyond production of their five-carbon precursors." }, { "name": "1-Deoxy-D-xylulose 5-phosphate biosynthetic process", "difference": "Produces the upstream intermediate DXP; in some organisms DXP also feeds pathways other than isoprenoid biosynthesis." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should the registry boundary include precursor formation through DXP synthase, and how should it align with reference modules that also include IPP-DMAPP isomerization?", "Which organism-specific alternative enzymes or fused activities must be supported before reaction coverage can be judged reliably?", "Which compartments exchange intermediates or C5 precursors in the intended biological systems, and how much does that exchange affect route attribution?", "Which resource dependencies and control points are experimentally established for each intended context rather than extrapolated from another organism?", "What minimum combination of tracing, analytical resolution, and perturbation evidence should qualify an instance as actively producing IPP through the MEP pathway?" ], "statistics": { "bundles": 6, "layers": 12, "findings": 17, "questions": 29 } }