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Interpretation: TAME\'s prediction is phrased across animals; the test uses the mouse because MGI curation gives the deepest experimental annotation of both developmental and behavioural phenotypes in a single species. \'Genes involved in morphogenesis\' is GO:0009653 anatomical structure morphogenesis and \'memory and learning categories\' is GO:0007611 learning or memory, each with is_a and part_of descendants. Only experimental evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, HTP, HDA, HMP, HGI, HEP) are used, so electronic or sequence-similarity annotations cannot create the overlap. The universe is every gene with at least one such BP annotation, after removing NOT-qualified lines. \'Beyond the known shared ion channels, connexins and neurotransmitter machinery\' is implemented by excluding from the universe every gene annotated (any evidence) to GO:0005216 ion channel activity, GO:0005243 gap junction channel activity, GO:0005921 gap junction, GO:0007268 chemical synaptic transmission, GO:0001505 regulation of neurotransmitter levels or GO:0030594 neurotransmitter receptor activity, with descendants. Only the first part of the claim is tested; its second part (memory genes appearing in cancer, regeneration and embryogenesis screens) is out of scope here." } } } rows { name { value: "label" } } rows { quad { p_iri { } o_literal { lex: "Claim test of levin-2022-tame-19: refutes, confidence 0.7" } } } rows { name { value: "seeAlso" } } rows { prefix { value: "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2022-tame-19/" } } rows { name { value: "result.json" } } rows { quad { p_iri { } o_iri { prefix_id: 12 } } } rows { name { value: "wasAttributedTo" } } rows { prefix { value: "https://w3id.org/delphi/resource/agent/" } } rows { name { value: "delphisci-claim-tester-claude-opus-5-5" } } rows { quad { p_iri { prefix_id: 5 } o_iri { prefix_id: 13 } } } rows { name { value: "admissibleDatasets" } } rows { quad { p_iri { prefix_id: 10 } o_literal { lex: "Planned datasets: go-basic-obo, mgi-gaf" } } } rows { name { value: "assessmentType" } } rows { quad { p_iri { } o_literal { lex: "claim-test/0.1.0" } } } rows { name { value: "dataKind" } } rows { quad { p_iri { } o_literal { lex: "biological" } } } rows { name { value: "disconfirmingObservation" } } rows { quad { p_iri { } o_literal { lex: "Pre-registered: unstratified odds ratio <= 1.2 or p >= 0.05, or Mantel-Haenszel odds ratio <= 1.2, or the odds ratio at or below the median of the size-matched control terms. Outcomes meeting neither criterion are pre-registered as \'mixed\' (overlap present but not specific, or explained by annotation depth)." } } } rows { name { value: "evidenceAgainst" } } rows { quad { p_iri { } o_literal { lex: "GO annotations reflect what has been studied: genes are annotated to learning or memory largely because they were knocked out and tested behaviourally, which happens mostly to genes already well studied in development. Annotation-depth stratification addresses this only approximately." } } } rows { quad { o_literal { lex: "Mouse only and experimental evidence only. TAME frames the prediction across animals; other species or inclusion of inferred annotations could differ." } } } rows { quad { o_literal { lex: "Only the first half of the claim is tested. Whether memory genes appear in cancer, regeneration and embryogenesis screens is not addressed." } } } rows { quad { o_literal { lex: "Size-matched control terms include developmental processes adjacent to morphogenesis (axon, limb, cardiac chamber, neural tube development) with very high odds ratios, which raises the 75th-percentile bar; the depth-stratified result does not depend on this choice." } } } rows { quad { o_literal { lex: "The GO release is \'current\' at retrieval time and is not versioned in the URL; re-running later will fetch a newer release, so exact numbers will drift. The SHA-256 above identifies the files used." } } } rows { quad { o_literal { lex: "The crude overlap is real: 69 genes against 34 expected (odds ratio 2.66, p = 1.1e-9), and removing channel, gap-junction and neurotransmission genes barely changes it (2.64 before exclusion). It does not survive control for annotation depth: learning-or-memory genes sit almost entirely in the most-annotated strata, and within the top decile (13-167 BP terms) 43 of 63 of them (68%) are morphogenesis genes against 621 of 961 other genes (65%). The pre-registered fail rule is met by the Mantel-Haenszel odds ratio (0.94 <= 1.2). 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