Improved measurement and biomarker representation in EFO

[zoependlington]

Measurements and clinical attributes representation (UK biobank and GWAS representation) (OTAR, GWAS). The EFO measurement hierarchy is used to annotate a number of gwas traits. Often the link to the primary trait (diagnosis or phenotype) is missing in the ontology. We need to review the EFO design pattern and how annotations are created in GWAS to reflect better what, how, then e.g. what was the trait of interest, how was it being measured, and what was the finding.

[paolaroncaglia]

Note for self: this ticket used to be an Epic in the ebispot.github.io tracker. As it collected EFO-only tickets, we've moved it to the EFO tracker so it's more visible. We'll collect tickets about biomarkers here, too.

[paolaroncaglia]

Note for self: there are several tickets in this Epic that we need to look into; this said, at a meeting with @smnorthen and @zoependlington today, we summarised the following points:

• Current structure of measurement and biomarker branches is too flat (and may contain errors)
• Need to look into how to axiomatise terms to make them more useful, but make the axioms generally valid, i.e. don't restrict them by linking measurements to diseases because those inferences may not always hold true (e.g. you may want to measure glucose levels in non-diabetes patients too)
• Grouping terms may be created if useful.
• Also, @smnorthen wrote: "Here are a few examples of categorising biomarkers in EFO. I have removed some columns which were specific to the GWAS catalog. I have only done a few (quite a while back!), but hopefully it will give you some suggestions/ideas on re-structuring the measurement branch.". I'll attach her draft file here. EFO_Measurements_revised.xlsx

[kallia-p]

@rays22 Biomarkers ticket for handover