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IDR / idr-gallery

https://pypi.org/project/idr-gallery/
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Genes starting with spaces #12

Closed pwalczysko closed 2 years ago

pwalczysko commented 2 years ago

Some genes seem to have a leading space in their name. This must be an IDR/mapr/search_engine issue, as I cannot imagine this is a real name in biological sense. Or maybe it is a typo of a submitter ?

Workflow

  1. go to a mapr-governed search interface, such as idr.openmicroscopy.org or select the "Gene" as key from the list on idr-testing
  2. go to the Value box, and click spacebar (ie. type in a space)
  3. observe a list of genes appear in autocomplete suggestion

Screenshot 2022-09-01 at 15 02 00

pwalczysko commented 2 years ago

cc @francesw especially the Ciz1 seems to perform very strange behaviour when inside mapr in webclient.

  1. type in " ciz1" under Genes tab (note the leading space)
  2. get 1 study with 1048 images
  3. expand the containers inside the study, select one image
  4. find the Gene section in RHP
  5. click on the Gene symbol "Ciz1"
  6. get in a new mapr search 53 images from 6 studies
pwalczysko commented 2 years ago

@jburel @francesw I think we should check this short list of Genes as per screenshot, possibly the search_engine will behave better than mapr, but maybe it is also a candidate for IDR metadata correction ?

pwalczysko commented 2 years ago

It turns out that the leading space is most probably only in 2 genes in 1 study

Gene    Study           Images
Ciz1    idr0110A        1048
Spen    idr0110A        1919

cc @francesw @dominikl

pwalczysko commented 2 years ago

This is a curation problem, so closing it here.