{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:13:30Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 19.9, "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: 01a09551-6f49-7ec3-834c-b8a47d0c9d61\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: medullary sponge kidney\nSense to describe: (none recorded)\nDomain code: XCT.STA\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 0", "usd": 0.0, "recall": true }, "codex": { "seconds": 73.3, "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: 01a09551-6f3e-7340-b917-3e6323435724\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: medullary sponge kidney\nRegistry id: vr.tr.medullary-sponge-kidney\nPlane / domain: XCT / XCT.STA\nRegistry definition: (none recorded)\nNames folded in" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:42:16+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:25+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q119280", "registryId": "vr.tr.medullary-sponge-kidney", "name": "medullary sponge kidney", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "XCT.STA" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q119280/", "model": { "registry_id": "vr.tr.medullary-sponge-kidney", "name": "medullary sponge kidney", "purpose": "Enable an agent to recognize medullary sponge kidney, record the evidence and complication burden, and support clinician-directed evaluation and follow-up.", "definition": "Medullary sponge kidney is a developmental renal malformation characterized by cystic dilatation of collecting ducts in the renal papillae and medulla, predisposing to nephrocalcinosis, kidney stones and urinary tract infections.", "scope_statement": "This model owns the characterization of medullary sponge kidney as a developmental abnormality of medullary and papillary collecting ducts, including diagnostic confidence, anatomical distribution, associated urinary abnormalities, and complication-linked care needs for registry entry vr.tr.medullary-sponge-kidney.", "in_scope": [ "Evidence of collecting-duct ectasia and its distribution within and between kidneys", "Diagnostic confidence and distinction from other causes of medullary calcification", "Associated stones, urinary infections, hematuria, and pain", "Measured urinary stone-risk factors and renal function", "Condition-specific follow-up needs and links to complication management" ], "out_of_scope": [ "General kidney anatomy and normal collecting-duct physiology", "Full diagnostic and treatment models for urinary stones and urinary tract infections", "Autosomal dominant tubulointerstitial kidney disease and polycystic kidney diseases", "Independent models of hyperparathyroidism and renal tubular acidosis", "Detailed prescribing, procedural technique, and emergency treatment protocols" ], "distinguishing_features": [ "Require evidence addressing medullary or papillary collecting-duct dilatation; renal calcification alone does not establish the defining abnormality. [NLM MeSH](https://www.ncbi.nlm.nih.gov/mesh/68007691)", "Record whether excretory imaging demonstrates contrast within dilated collecting ducts, producing a characteristic paintbrush pattern. [Differential diagnosis study](https://pubmed.ncbi.nlm.nih.gov/6729542/)", "Distinguish stones or nephrocalcinosis accompanying collecting-duct ectasia from stones or nephrocalcinosis without demonstrated ectasia. [Biopsy-confirmed study](https://pubmed.ncbi.nlm.nih.gov/25615853/)", "Check the anatomical distribution of cystic change before equating the diagnosis with a broader cystic kidney disorder. [Imaging case report](https://pubmed.ncbi.nlm.nih.gov/6740360/)" ], "characteristics": [ { "name": "Diagnostic confidence", "kind": "state", "unit_or_values": "suspected | supported | clinician-confirmed | disputed; evidence and date required", "why_it_matters": "Prevents an incidental calcification report from becoming an unsupported permanent diagnosis." }, { "name": "Collecting-duct abnormality", "kind": "category", "unit_or_values": "ectasia demonstrated | suggestive appearance | not demonstrated | not assessable", "why_it_matters": "Records evidence for the defining anatomical feature." }, { "name": "Anatomical extent", "kind": "category", "unit_or_values": "left | right | bilateral | unknown; affected papillae or segments where reported", "why_it_matters": "Preserves distribution without assuming every papilla or both kidneys are affected." }, { "name": "Imaging evidence", "kind": "relation", "unit_or_values": "study, modality, protocol, date, report, and interpreting clinician", "why_it_matters": "Makes diagnostic confidence traceable to what the examination could assess." }, { "name": "Stone and calcification burden", "kind": "measurement", "unit_or_values": "stone count, maximum diameter in mm, location; nephrocalcinosis recorded separately", "why_it_matters": "Separates discrete calculi from diffuse calcification and supports comparison over time." }, { "name": "Symptomatic complication burden", "kind": "measurement", "unit_or_values": "dated stone and infection episodes; hematuria and pain frequency; observation interval", "why_it_matters": "Distinguishes incidental anatomy from recurrent clinical impact." }, { "name": "Urinary metabolic profile", "kind": "measurement", "unit_or_values": "24-hour volume in L/day, calcium and citrate in laboratory-reported units, urine pH", "why_it_matters": "Records measured contributors to stone risk without assuming a uniform metabolic phenotype." }, { "name": "Renal function trajectory", "kind": "measurement", "unit_or_values": "serum creatinine in µmol/L or mg/dL; eGFR in mL/min/1.73 m²; dates", "why_it_matters": "Identifies change requiring assessment of complications or additional kidney disease." }, { "name": "Complication attribution", "kind": "relation", "unit_or_values": "manifestation linked to supporting evidence, alternative explanations, and clinician assessment", "why_it_matters": "Prevents every urinary symptom or renal abnormality from being attributed to this condition." } ], "affordances": [ "Assemble an evidence-linked diagnostic summary and identify missing anatomical confirmation.", "Compare imaging reports for changes in stones, calcification, and obstruction.", "Link recurrent stone episodes to available composition and urine studies.", "Identify documented acute complications requiring clinician triage.", "Prepare a follow-up agenda based on symptoms, renal function, and unresolved diagnostic questions." ], "agent_conduct": { "may": [ "Explain the condition in general terms from reputable medical sources.", "Advise a person with severe flank pain, fever or blood in the urine to seek care." ], "must_not": [ "Diagnose the condition from symptoms or scans.", "Recommend diet changes or medicines to a specific person for stone prevention.", "Disclose a person's kidney health records without consent.", "Promote unproven stone-dissolving products." ], "requires_human": [ "Any treatment or procedure to remove stones." ] }, "ethics": { "considerations": [ "Recurrent stones cause severe pain and lost work, often with little recognition.", "Accurate information prevents both alarm and neglect." ], "affected_parties": [ "Patients", "Their families", "Employers of affected workers" ] }, "owners": { "steward": "Nobody owns the condition; patients and their clinicians answer for care.", "master_systems": [] }, "visual_identification": [ "On imaging, small calcium deposits and widened ducts in the inner parts of the kidney, sometimes described as a paintbrush pattern." ], "failure_modes_and_hazards": [ "Recurrent kidney stones and urinary infections.", "Calcium deposits in the kidney can affect its function." ], "what_it_is_for": [ "Medullary sponge kidney is encountered in renal imaging and in clinical evaluation of kidney stones, urinary tract infections or blood in the urine.", "It may also be identified incidentally in someone without symptoms.", "Documenting the malformation helps clinicians interpret collecting duct changes and assess associated complications over time." ], "standards_and_regulation": [ "The International Classification of Diseases ICD-10, issued by the World Health Organization, includes medullary sponge kidney under Q61.5 for medullary cystic kidney." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q119280: medullary sponge kidney", "url": "https://www.wikidata.org/wiki/Q119280", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Medullary sponge kidney", "url": "https://en.wikipedia.org/wiki/Medullary_sponge_kidney", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "identity-and-anatomical-boundary", "name": "Identity and anatomical boundary", "description": "Define the collecting-duct abnormality represented by this registry entry.", "rationale": "Recognition depends on anatomical specificity rather than the name or the presence of kidney stones.", "layers": [ { "id": "defining-lesion", "name": "Defining lesion", "description": "Capture the anatomical evidence underlying the condition label.", "findings": [ { "id": "medullary-papillary-duct-ectasia", "name": "Medullary and papillary duct ectasia", "description": "The defining abnormality involves dilatation of collecting ducts in medullary and inner papillary regions. [NLM MeSH](https://www.ncbi.nlm.nih.gov/mesh/68007691)", "questions": [ { "text": "What evidence identifies dilated collecting ducts in the medullary or papillary region?", "kind": "definition", "id": "medullary-papillary-duct-ectasia-q01" }, { "text": "Which report or clinician established that the abnormality belongs to the collecting ducts?", "kind": "provenance", "id": "medullary-papillary-duct-ectasia-q02" } ] } ] }, { "id": "extent-and-neighbouring-conditions", "name": "Extent and neighbouring conditions", "description": "Map involved anatomy and preserve boundaries with other renal disorders.", "findings": [ { "id": "distribution-without-diagnostic-conflation", "name": "Distribution without diagnostic conflation", "description": "Record the reported distribution and distinguish the diagnosis from other cystic disorders or causes of medullary nephrocalcinosis.", "questions": [ { "text": "Which kidney, segments, or papillae are reported as involved?", "kind": "measurement", "id": "distribution-without-diagnostic-conflation-q01" }, { "text": "What supports collecting-duct ectasia rather than a different cystic disorder or calcification without ectasia?", "kind": "boundary", "id": "distribution-without-diagnostic-conflation-q02" } ] } ] } ] }, { "id": "diagnostic-evidence-and-confidence", "name": "Diagnostic evidence and confidence", "description": "Connect the diagnosis to interpretable observations and their limitations.", "rationale": "A historical label, suggestive calcification, and demonstrated duct ectasia carry different evidential weight.", "layers": [ { "id": "imaging-observations", "name": "Imaging observations", "description": "Record findings together with the protocol that produced them.", "findings": [ { "id": "contrast-demonstrated-duct-pattern", "name": "Contrast-demonstrated duct pattern", "description": "Contrast within dilated collecting ducts can produce the characteristic paintbrush appearance described in diagnostic literature. [Differential diagnosis study](https://pubmed.ncbi.nlm.nih.gov/6729542/)", "questions": [ { "text": "Did the study include an excretory phase capable of showing contrast within collecting ducts?", "kind": "provenance", "id": "contrast-demonstrated-duct-pattern-q01" }, { "text": "Did the report describe duct ectasia or a paintbrush pattern, or only stones and medullary calcification?", "kind": "boundary", "id": "contrast-demonstrated-duct-pattern-q02" } ] } ] }, { "id": "evidence-reconciliation", "name": "Evidence reconciliation", "description": "Resolve differences between diagnostic labels and underlying evidence.", "findings": [ { "id": "confidence-and-discordance", "name": "Confidence and discordance", "description": "Preserve original wording, subsequent interpretations, and unresolved disagreement rather than silently upgrading suggestive evidence.", "questions": [ { "text": "Is the diagnosis suspected, supported, confirmed by a clinician, or disputed, and on what basis?", "kind": "provenance", "id": "confidence-and-discordance-q01" }, { "text": "Would expert review of existing imaging resolve uncertainty before considering another examination?", "kind": "action", "id": "confidence-and-discordance-q02" } ] } ] } ] }, { "id": "stones-and-urinary-phenotype", "name": "Stones and urinary phenotype", "description": "Characterize stone formation and measured urinary contributors.", "rationale": "The anatomical diagnosis alone does not specify an individual's stone burden or prevention needs.", "layers": [ { "id": "stone-localization-and-history", "name": "Stone localization and history", "description": "Distinguish imaging burden from clinically active stone episodes.", "findings": [ { "id": "ductal-and-urinary-stone-burden", "name": "Ductal and urinary stone burden", "description": "A biopsy-confirmed study found enlarged inner medullary collecting ducts containing small stones; record stone location when demonstrated rather than assuming all calcification represents freely passing calculi. [Biopsy-confirmed study](https://pubmed.ncbi.nlm.nih.gov/25615853/)", "questions": [ { "text": "Where are discrete stones, ductal deposits, and nephrocalcinosis reported, and which locations remain uncertain?", "kind": "measurement", "id": "ductal-and-urinary-stone-burden-q01" }, { "text": "Which dated episodes involved stone passage, obstruction, intervention, or recovered stone analysis?", "kind": "provenance", "id": "ductal-and-urinary-stone-burden-q02" } ] } ] }, { "id": "measured-metabolic-contributors", "name": "Measured metabolic contributors", "description": "Document individual urine chemistry and any separate acidification assessment.", "findings": [ { "id": "urine-chemistry-with-context", "name": "Urine chemistry with context", "description": "Record measured calcium, citrate, volume, and pH with collection quality, treatment exposure, and laboratory interpretation; do not infer abnormalities from the diagnosis.", "questions": [ { "text": "What do available 24-hour urine studies show, with units and evidence of collection completeness?", "kind": "measurement", "id": "urine-chemistry-with-context-q01" }, { "text": "If an acidification disorder is suspected, what independent assessment supports it beyond a single urine pH?", "kind": "boundary", "id": "urine-chemistry-with-context-q02" }, { "text": "Which documented abnormality is the clinician's prevention plan intended to address?", "kind": "action", "id": "urine-chemistry-with-context-q03" } ] } ] } ] }, { "id": "clinical-manifestations-and-complications", "name": "Clinical manifestations and complications", "description": "Track symptoms and acute events without treating them as diagnostic proof.", "rationale": "Medullary sponge kidney can be associated with stones and urinary infections, but each episode needs its own evidence. [NIDDK overview](https://www.niddk.nih.gov/health-information/kidney-disease/children/medullary-sponge-kidney)", "layers": [ { "id": "symptoms-and-attribution", "name": "Symptoms and attribution", "description": "Connect symptoms to contemporaneous investigations.", "findings": [ { "id": "hematuria-and-pain-context", "name": "Hematuria and pain context", "description": "Record hematuria and pain separately from the structural diagnosis, including alternative explanations and unresolved attribution.", "questions": [ { "text": "When do pain or hematuria occur relative to documented stones, infection, or obstruction?", "kind": "measurement", "id": "hematuria-and-pain-context-q01" }, { "text": "What other causes have been considered when symptoms lack a matching urinary finding?", "kind": "boundary", "id": "hematuria-and-pain-context-q02" } ] } ] }, { "id": "infection-and-obstruction", "name": "Infection and obstruction", "description": "Represent acute urinary events that change the care priority.", "findings": [ { "id": "acute-complication-evidence", "name": "Acute complication evidence", "description": "Capture symptoms, cultures, imaging, renal function changes, and the clinician's assessment of urgency.", "questions": [ { "text": "What evidence supports symptomatic infection, obstruction, or their coexistence in this episode?", "kind": "provenance", "id": "acute-complication-evidence-q01" }, { "text": "Has the episode received clinician triage, and what escalation or follow-up was specified?", "kind": "action", "id": "acute-complication-evidence-q02" } ] } ] } ] }, { "id": "renal-course-and-care-response", "name": "Renal course and care response", "description": "Track functional outcomes and the response to complication-focused care.", "rationale": "Follow-up should reflect observed clinical burden, renal trajectory, and treatment effects rather than the anatomical label alone.", "layers": [ { "id": "functional-course", "name": "Functional course", "description": "Assess kidney function over time and investigate unexplained change.", "findings": [ { "id": "renal-function-and-additional-disease", "name": "Renal function and additional disease", "description": "Maintain dated renal function measurements and distinguish documented complications from possible additional renal disease.", "questions": [ { "text": "What is the creatinine and eGFR trajectory, including measurements during and after acute episodes?", "kind": "measurement", "id": "renal-function-and-additional-disease-q01" }, { "text": "If function declines, what evidence addresses obstruction, infection, medication effects, or an additional kidney disorder?", "kind": "boundary", "id": "renal-function-and-additional-disease-q02" } ] } ] }, { "id": "care-targets-and-review", "name": "Care targets and review", "description": "Make clinician-directed prevention and follow-up assessable.", "findings": [ { "id": "complication-focused-care-response", "name": "Complication-focused care response", "description": "Link each intervention to its intended complication or measured risk factor and record response, tolerability, and review criteria.", "questions": [ { "text": "Which intervention targets recurrent stones, infection, symptoms, or a documented urinary abnormality?", "kind": "action", "id": "complication-focused-care-response-q01" }, { "text": "Have symptomatic episodes, procedures, or measured urinary risk factors changed over a defined follow-up interval?", "kind": "measurement", "id": "complication-focused-care-response-q02" }, { "text": "What findings trigger reassessment of the diagnosis, prevention plan, or specialist follow-up?", "kind": "action", "id": "complication-focused-care-response-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 a recall-based description; no sources were consulted.", "Anatomical distributions are descriptive varieties, not a universally standardized subtype classification.", "Prevalence, genetic contributions and diagnostic performance of different imaging methods require source verification." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of medullary sponge kidney this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Bilateral involvement", "Unilateral involvement", "Segmental involvement confined to some renal papillae" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of medullary sponge kidney 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": "ICD-10", "value_or_pattern": "Q61.5", "note": "The World Health Organization category 'Medullary cystic kidney' includes medullary sponge kidney; the category title is broader than this specific condition." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of medullary sponge kidney 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": [ "A diagnostic consideration in recurrent calcium kidney stones or medullary nephrocalcinosis.", "Identification of characteristic papillary collecting-duct abnormalities on excretory imaging.", "A reason to investigate associated urinary abnormalities that contribute to stone formation." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of medullary sponge kidney 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": "Urinary calcium, citrate, pH and volume", "typical_range": "Variable; no single diagnostic range defines medullary sponge kidney.", "unit": "Commonly mg/24 h or mmol/24 h for calcium and citrate, pH units, and L/24 h for volume" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of medullary sponge kidney 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": [ "Recurrent calcium-containing kidney stones.", "Medullary nephrocalcinosis.", "Urinary tract infections, including pyelonephritis.", "Hematuria and renal colic, sometimes with urinary obstruction.", "Kidney function is usually preserved, but substantial impairment can occur, particularly with recurrent infection or obstruction." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of medullary sponge kidney 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": "Medullary nephrocalcinosis", "difference": "This is calcium deposition in the renal medulla from several possible causes; medullary sponge kidney specifically involves dilated papillary collecting ducts." }, { "name": "Autosomal dominant tubulointerstitial kidney disease", "difference": "Some forms were historically called medullary cystic kidney disease; they cause inherited progressive tubulointerstitial disease rather than the characteristic collecting-duct malformation of medullary sponge kidney." }, { "name": "Autosomal dominant polycystic kidney disease", "difference": "Typically produces numerous cysts throughout enlarged kidneys, rather than primarily small dilatations of medullary and papillary collecting ducts." }, { "name": "Distal renal tubular acidosis", "difference": "Defined by impaired distal urinary acidification; it can coexist with medullary sponge kidney but is a functional disorder rather than the structural malformation itself." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of medullary sponge kidney this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "What diagnostic criteria and contemporary imaging protocols most reliably distinguish collecting-duct ectasia from medullary nephrocalcinosis without ectasia?", "Which developmental or inherited mechanisms are established, and when does family history justify additional evaluation?", "How often do urinary acidification defects and other metabolic abnormalities occur in rigorously confirmed cases rather than populations selected for recurrent stones?", "What explains persistent pain when infection, obstruction, and a symptomatic stone are not demonstrated?", "Which surveillance intervals and prevention strategies improve outcomes specifically in medullary sponge kidney, beyond evidence from general stone-forming populations?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 17, "questions": 29 } }