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mp_term assigned for "Not significant" classification_tag #100

@marinak-ebi

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@marinak-ebi

mp_term assigned for "Not significant" classification_tag which leads to incorrect display on the website.

  1. Page with a bug:
    https://www.mousephenotype.org/data/supporting-data?mgiGeneAccessionId=MGI:2150037&mpTermId=MP:0004647

Two significant p-values are shown. However, when we scroll down, the classification is "Not significant," and there is no p-value displayed. The Statistical Method tab also shows N/A values.

  1. Solr query for the data from the page:
    https://www.ebi.ac.uk/mi/impc/solr/statistical-result/select?q=colony_id:EPD0002_2_B07%20AND%20parameter_name:%22Number%20of%20lumbar%20vertebrae%22
  • Both datasets have the same p-value on the website as in the Solr core.
  • The classification_tag is "Not significant" in the Solr core as we see on the website.
  • The mp_term was assigned by the annotation pipeline, which means that these p-values were considered significant. Otherwise, the mp_term wouldn't have been assigned.
  1. classification_tag is generated by OpenStats R package.

mainAgeing function runs VectorOutput0 function that use classificationTag function from OpenStats:

p1$`Classification tag` = OpenStats:::classificationTag(c.ww0$NormalObj)

Website use classification_tag field from statpacket to generate pages. Issue appears in the statistical pipeline.

  1. Search for classification_tag:"Not significant" AND significant:true.
    Five data points for legacy EuroPhenome were found:
    https://www.ebi.ac.uk/mi/impc/solr/statistical-result/select?fl=classification_tag,significant,resource_name,parameter_stable_id&q=classification_tag:%22Not%20significant%22%20AND%20significant:true

To debug this as a first step we need to investigate classificationTag function from OpenStats.

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