Scoping FE for Adding "direction of effect" data

[carcruz]

We need to scope DoE results visualisation for the following 8 data widgets:

"ot_genetics_portal",
"gene_burden",
"eva",
"eva_somatic",
"gene2phenotype",
"orphanet",
"impc",
"chembl"

See this ticket for BE details.

Relevant API field/responses are:

1)variantEffect (values= LoF/GoF/Null)
2)directionOnTrait (values=Risk/Protective/Null)

Preliminary visualisation suggestions here- now with hovering text

[buniello]

Proposed names for the two new columns (happy to her different opinions): 1) DoE (variant) 2) DoE (trait) also discussed second option, having one single column with both icons - named DoE (variant and trait)

They both should have a tooltip with following text: See here for more info on our assessment method - with link to the doc page that will describe assessment method (from @Juanmaria-rr)

[buniello]

Proposed positions of the two new columns within each widget (as discussed today with FE team @chinmehta ): 1) OT Genetics: the two new columns should be added between Variant consequence and Associations p-value 2) Gene Burden: columns between beta and p-value 3) ClinVar: columns between Variant Consequence and Clinical significance 4) ClinVar somatic: between Clinical Significance and Allele origin 5) Gene2phenotype: columns between Functional consequence and Allelic requirement 6) Orphanet: columns between Functional consequence and Allele origin 7) IMPC: columns between Mouse phenotypes and Mouse model allelic composition 8) chEMBL: columns between MoA and Phase

I tried to keep position as consistent as possible within different data table

[buniello]

Just an update for the team: @chinmehta has prepared a slide deck with different visualisation options and will present them at the AOTF meeting tomorrow.

[prashantuniyal02]

• Header:

  • Direction of Effect (heading) - combined columns makes sense
  • No variant / trait subheader (i.e. no subheader) as Variant is not a good header

• Icons

  • trend arrows for variants
  • GoF up,
  • LoF down
  • exclamation - risk
  • half shield - protect

• Also, we have to keep in mind the icons for version 2 as they will be probably moving next in the AOTF column

• Also, we should ensure the icons are easier to change / abstraction - i.e. we should not have to change icons on every widget.

[prashantuniyal02]

Links for the tooltip for the direction of effect column: @chinmehta

1) OT Genetics: https://platform-docs.opentargets.org/evidence#open-targets-genetics 2) Gene Burden: https://platform-docs.opentargets.org/evidence#gene-burden 3) ClinVar: https://platform-docs.opentargets.org/evidence#clinvar 4) ClinVar somatic: https://platform-docs.opentargets.org/evidence#clinvar-somatic 5) Gene2phenotype: https://platform-docs.opentargets.org/evidence#gene2phenotype 6) Orphanet: https://platform-docs.opentargets.org/evidence#orphanet 7) IMPC: https://platform-docs.opentargets.org/evidence#impc 8) chEMBL: https://platform-docs.opentargets.org/evidence#chembl