https://w3id.org/np/RAhx-Dba6QUDfeoq71hoC1VBOqJSCkRZb73JslrPnBkMw
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
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dc:description "fetch.py downloads go-basic.obo and the MGI GAF. analysis.py drops NOT-qualified and obsolete-term lines, builds each gene's set of experimental BP terms and their is_a/part_of ancestors, removes 612 genes annotated to ion channel, gap junction or neurotransmission terms, and tests overlap of GO:0007611 and GO:0009653 in the remaining 10,243 genes with a one-sided Fisher exact test. Annotation depth is controlled by a Mantel-Haenszel odds ratio over ten equal-sized strata of genes ranked by their number of distinct experimental BP terms. Specificity is the percentile of the odds ratio among the 327 BP terms of 128-286 genes that are neither ancestors nor descendants of either term.";
<http://www.w3.org/2000/01/rdf-schema#comment> "Measured: 2.6573 odds ratio, learning-or-memory vs anatomical-structure-morphogenesis gene sets (mouse, experimental BP annotations, channel/synaptic genes excluded) (n = 10243, one-sided Fisher exact p = 1.140e-09). 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.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of levin-2022-tame-19: refutes, confidence 0.7";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2022-tame-19/result.json>;
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<https://w3id.org/delphi/ontology/admissibleDatasets> "Planned datasets: go-basic-obo, mgi-gaf";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "biological";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "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).";
<https://w3id.org/delphi/ontology/evidenceAgainst> "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.",
"Mouse only and experimental evidence only. TAME frames the prediction across animals; other species or inclusion of inferred annotations could differ.",
"Only the first half of the claim is tested. Whether memory genes appear in cancer, regeneration and embryogenesis screens is not addressed.",
"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.",
"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.",
"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). The control comparison (64.5th percentile) fails pass criterion (c) but does not by itself meet the fail rule, since 2.66 is above the control median of 1.87.";
<https://w3id.org/delphi/ontology/expectedObservation> "Pre-registered: after exclusions, (a) the one-sided Fisher exact test of overlap between the learning-or-memory set (GO:0007611 and is_a/part_of descendants) and the morphogenesis set (GO:0009653 and descendants) gives odds ratio > 1.5 and p < 0.001; (b) the Mantel-Haenszel odds ratio stratified by deciles of each gene's number of experimental BP annotations is > 1.5; (c) the unstratified odds ratio is above the 75th percentile of odds ratios between the morphogenesis set and every control BP term whose post-exclusion gene count is within a factor of 1.5 of the learning-or-memory set's and which is neither an ancestor nor a descendant of GO:0007611 or GO:0009653.";
<https://w3id.org/delphi/ontology/failCriterion> "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).";
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<https://w3id.org/delphi/resource/evidence/levin-2022-tame-19--claim-test--dataset-2>;
<https://w3id.org/delphi/ontology/hasVerdict> "refutes";
<https://w3id.org/delphi/ontology/hypothesis> "Among mouse genes with experimental Gene Ontology biological-process annotations, genes annotated to learning or memory are over-represented among genes annotated to anatomical structure morphogenesis, even after removing ion channels, gap-junction channels and neurotransmission genes, and this overlap is larger than the overlap of morphogenesis with other biological-process terms of similar size.";
<https://w3id.org/delphi/ontology/inferenceMethod> "fetch.py downloads go-basic.obo and the MGI GAF. analysis.py drops NOT-qualified and obsolete-term lines, builds each gene's set of experimental BP terms and their is_a/part_of ancestors, removes 612 genes annotated to ion channel, gap junction or neurotransmission terms, and tests overlap of GO:0007611 and GO:0009653 in the remaining 10,243 genes with a one-sided Fisher exact test. Annotation depth is controlled by a Mantel-Haenszel odds ratio over ten equal-sized strata of genes ranked by their number of distinct experimental BP terms. Specificity is the percentile of the odds ratio among the 327 BP terms of 128-286 genes that are neither ancestors nor descendants of either term.";
<https://w3id.org/delphi/ontology/passCriterion> "Pre-registered: after exclusions, (a) the one-sided Fisher exact test of overlap between the learning-or-memory set (GO:0007611 and is_a/part_of descendants) and the morphogenesis set (GO:0009653 and descendants) gives odds ratio > 1.5 and p < 0.001; (b) the Mantel-Haenszel odds ratio stratified by deciles of each gene's number of experimental BP annotations is > 1.5; (c) the unstratified odds ratio is above the 75th percentile of odds ratios between the morphogenesis set and every control BP term whose post-exclusion gene count is within a factor of 1.5 of the learning-or-memory set's and which is neither an ancestor nor a descendant of GO:0007611 or GO:0009653.";
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dc:license "CC BY 4.0";
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