Issue 391 - Updates to EFO feedback processing

[apriltuesday]

Closes #391 . Some notes:

• Updated spreadsheet template here. I've left the sample data in there but will remove once this is merged.
• Updated code and SOPs - done in this PR.
• Automating retrieval of MedGen/OMIM terms: Decided to do this properly in a separate issue, by extracting xrefs from ClinVar and including them in the curation spreadsheet so they're available for all traits, not just new ones. See Include ClinVar xrefs in manual curation spreadsheet #429.
• QC of new terms (parent is present in EFO): This would require an extra manual step of exporting not just the main curation worksheet but also the new terms worksheet. I wasn't sure if this would be worth the effort given that it's created manually and checked manually by SPOT, so I left it out for now.
• QC of import terms (term not present in EFO): This is doable since these URIs are present in the main worksheet, but I'm not sure of the value as it's only useful for mappings not already in the spreadsheet (those in the spreadsheet have already been checked for EFO containment). If we want to improve this further we could do it as part of Better processing of exact MONDO/HP mappings not in EFO #414.

Let me know if you think we should add the QC as part of this PR...

[apriltuesday]

BioMart is not working, apparently due to the recent release of Ensembl 112... I've emailed them but meanwhile the tests won't pass.

[tcezard]

Changes looks good.
Tests are failing due to changes in Ensembl 112

[apriltuesday]

Tests are failing due to changes in Ensembl 112

It's a problem with BioMart, Ensembl is working on it... there are probably E2E tests to fix as well though. Sorry BioMart was already fixed, have updated the tests now.