Discrepancies between GWAS diagram trait categories in download and API

[JalMacArthur]

There are discrepancies between the parent term in the download file, which should be the category the EFO trait is mapped to on the diagram, and the parent tern provided by the rest API. Each EFO only maps to one category on the diagram so each data source should only display one parent term and these should be the same.

This was reported by user (Laurent Gil) see email thread "GWAS diagram trait categories [EXT]"

Hi Jackie,

It looks like that there are some discrepancies between the data in the file and the REST API calls: e.g.:

• EFO_0004715 (MRI defined brain infarct) has "Cardiovascular disease" as parent term, but on the REST API it says ' Neurological disorder' https://www.ebi.ac.uk/gwas/rest/api/parentMapping/EFO_0004715
• EFO_0004746 (lipoprotein-associated phospholipase A(2) measurement) has " Lipid or lipoprotein measurement" as parent term, but on the REST API it says ' Cardiovascular measurement'.

I believe this is due to the multiple parents on the ontologies and possibly different algorithms for the export file and the REST API.

I will see how it works with our PGS traits.

Thanks,

Laurent

[ens-lgil]

As a side note, it seems that the discrepancy only occurs for the high level traits, e.g.:

• EFO_0000319
• EFO_0000405
• EFO_0000540
• EFO_0004298
• EFO_0004324
• EFO_0004503
• EFO_0004872
• EFO_0005105

The REST API seems to return the same trait instead of the "generic" parent, which is more informative than the reported parent: e.g. for EFO_0000319 (cardiovascular disease)

• REST API:

  • parent: cardiovascular disease
  • colourLabel: Cardiovascular disease

• Download file:

  • parent: Other disease