Ensure latest available EFO mappings are applied to Finngen study index

[d0choa]

We have a curation table for finngen that goes back to FinnGen R6. This was a high-quality curation process that started from a template that I generated in this project https://github.com/opentargets/finngen2efo. Since R6 the number of traits in subsequent releases has not increased significantly.

https://docs.google.com/spreadsheets/d/1RRWfUTLy4TO9XmBzcbJ2wPRdda3qISjRS4PJmEdxE3k/edit?gid=1853278839#gid=1853278839

It would be good to ensure we are using the right set of finngen mappings in the study index.

[d0choa]

I suspect studies will not pass validation in #3359 until valid mappings are added

[ireneisdoomed]

Out of 2444 endpoints, 578 are new between the R6 and R11 releases. Out of those, I could map automatically 160, which left us with 420 terms to curate.

Notebook I used to prepare the working spreadsheet is here: https://colab.research.google.com/drive/12iRaCIShMMShpEEoYZT6CI5xrqlnDqs_?authuser=1#scrollTo=5RJQzHHc2bzs

This task is not completely finished because some mappings require importing terms from other ontologies, or requesting new terms. Once they're added, we'll update the curation table accordingly.

Therefore, I see 3 tasks here:

• [x] Update the Finngen study generation in step to bring the IDs from the curation table

• [ ] Request EFO to import 55 terms from other ontologies - @vivienho, could you help me with this one? Table of IDs to request to_import.tsv.zip

• [ ] Suggest EFO to create new terms for 11 traits Traits:

  Benign neoplasm: Pelvic bones, sacrum and coccyx
  Disorders of amino-acid transport
  Lesion of medial popliteal nerve
  Phantom limb syndrome
  Thoracic root disorders
  conjunctival scars
  Otorrhagia
  Otorrhoea
  Acquired atrophy of ovary and fallopian tube
  Feeding problems of newborn
  Tracheo-bronchomalasia

[d0choa]

any pending work here? Shall we close? @ireneisdoomed

[ireneisdoomed]

The only thing pending was asking EFO to add/import terms for studies we couldn't map. https://github.com/EBISPOT/efo/issues/2285 https://github.com/EBISPOT/efo/issues/2284 (Note: Tracheo-bronchomalasia doesn't need to be requested, it already exists MONDO_0019804)

We need to add the new terms in the curation after their inclusion in EFO.

[addramir]

What is the status of this issue?