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Queried BioSamples for Gallus gallus, Danio rerio and Anolis carolinensis with the pre-registered organism-part values, and took the value with the largest total. Trachemys scripta is reported and is not required for the verdict. One hit refutes the universal; no hit is inconclusive." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: 4 sources or species with a kidney record (n = 14). Interpretation: Feathered animals are represented by the chicken, scaled fishes by the zebrafish, and scaly reptiles that are not tortoises by the green anole. Aristotle allows flattened kidney-like bodies in some birds and still says the kidney is wanting; a structure named kidney, or a pronephros, mesonephros or metanephros, counts as the organ. Tortoises are the stated exception and are queried only as a description. 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An ontology or sample index that does not mention an organ is not evidence of absence." } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "claim-test/0.1.0" } ], "https://w3id.org/delphi/ontology/dataKind": [ { "@value": "biological" } ], "https://w3id.org/delphi/ontology/disconfirmingObservation": [ { "@value": "A curated zebrafish anatomy term naming a kidney, or at least one public biosample of kidney from a chicken, a zebrafish or a green anole." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "A biosample of kidney shows that the organ was taken from that species. It is not a survey of every bird and every fish." }, { "@value": "Aristotle's flattened kidney-like bodies in birds are counted as kidneys when the source names them as a kidney or a nephros." }, { "@value": "No kidney record in these two sources would not establish that kidneys are absent, so that outcome stays inconclusive." }, { "@value": "ZFIN is the anatomy of the zebrafish, a scaled bony fish, not of every scaled animal." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "No confirming observation is defined. The universal would require coded absence across feathered and scaled animals, which these sources do not provide." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Pre-registered. The claim is refuted if the ZFIN zebrafish anatomy list contains a term whose name is kidney, metanephros, mesonephros or pronephros, or if EBI BioSamples reports at least one sample of Gallus gallus, Danio rerio or Anolis carolinensis whose organism-part value is one of kidney, Kidney, adult kidney or kidney tissue. A tortoise sample is reported and is not required. If both sources are fetched and neither records such a kidney, the verdict is inconclusive with reason other. If both sources fail to return a readable file or response, the verdict is inconclusive with reason data-unavailable." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.85", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/aristotle-pa03-23--claim-test--pr-169--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/aristotle-pa03-23--claim-test--pr-169--dataset-2" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "refutes" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "If kidneys are absent from every feathered or scaled animal except tortoises, public anatomy records do not list a kidney for a bird, a bony fish or a lizard." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "Exact, case-sensitive match of organism-part values in the pre-registered list, and a case-insensitive exact match of ZFIN term names to the four kidney names. One hit refutes the universal. Zero hits, with the sources readable, is inconclusive." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Pre-registered. The test cannot support the universal absence. Failure to find a kidney record in the two sources is not evidence that the organ is absent. 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