Closed apriltuesday closed 8 months ago
Hello @tcezard @M-casado, here is the curation spreadsheet for this round. Some notes on this one:
Ready for review.
112 DONE
227 IMPORT
1 NEW
4 UNSURE
Couple of extra points:
I think we could have these search precomputed before the spreadsheet is made. That would make the manual curation much faster.
@apriltuesday pointed me to the documentation on multiple mappings so I change the UNSURE curations by duplicating the rows and add terms that cover different portion of the ClinVar description. In some case that create a mixture of IMPORT and DONE terms which might be confusing
café-au-lait macules with pulmonary stenosis
is confusing, but based on that Medgen page I changed it to Watson syndrome... let me know if you disagree.
For the others I'm not really sure whether we should recreate in EFO the intermediate grouping that Mondo obsoleted (so make these NEW terms), or map to the multiple terms as you've done... Mondo seems to have a lot of exclusion rules that I don't know apply to us (or EFO, or Open Targets...). But there might be something problematic about the intermediate grouping that I'm not seeing.... Maybe should wait for @M-casado's input.
UNSURE
ClinVar labels
stickler syndrome, dominant
- I read your comment @tcezard regarding the duplicated rows to cover types 1, 2 and IIa6. Nevertheless, I also found that there are other types of the disease that are dominant (see highlighted text). Some of these are present already in Mondo and EFO, some only in EFO, and some in other ontologies.
Stickler syndrome
(MONDO:0019354)EFO_CURRENT
, but are not (e.g. http://purl.obolibrary.org/obo/MONDO_0011493|Stickler syndrome type 2|||
)antenatal bartter syndrome
- A similar case, where a parental term was made obsolete and we are mapping to subtypes.
EFO_CURRENT
issue: MONDO:0009424
is not in EFO, but has EFO_CURRENT
in its mapping.autosomal recessive stickler syndrome
- Continuation of the first UNSURE
, but with a different type of inheritance.
We could use the "stickler syndrome" term which would be correct but is not quite specific enough
I think that, based on our rubric, we either: (1) import/create a new parent term that distinguishes the inheritance mode; (2) import/create all subtypes to map them extensively; (3) recur to mapping a subtype to a parental type. My experience tells me we ought to do the last one. This is my fear regarding mappings from parent types to subtypes: unless we are extensive on the duplicated mappings, we would be incurring in a wrong and skimmed association.
I also changed severe myoclonic epilepsy in infancy
to UNSURE
, given that the associated term (MONDO_0014960) to be IMPORTED
was not related for what I could find. I added a comment regarding which EFO term we could map it to, although it's a parental type, and has a note regarding possible obsoletion.
All done for resolving the UNSURE: Thank you @M-casado @apriltuesday I've made a copy of the spreadsheet that we can use during upcoming KT session without risking modifying the one we use for submission.
Thanks all, export done and EFO issue created.
Refer to documentation for full description of steps.
Checklist: