Consider annotation prop to distinguish disease grouping class vs disease entity

[kshefchek]

It would be useful if MONDO included a way to distinguish between a disease entity and a disease grouping. Currently the only way to do this is to check for subclasses/types of a disease; however, this results in missing valid diseases (see Huntington disease and Cystic Fibrosis). We regularly add a check that all diseases with an OMIM equivalent are disease entities, but a more formal way to determine this would be useful for analyses and application views.

[cmungall]

Not sure there is an agreed upon 'level'. E.g. ORDO calls juvenile Huntigton a disease entity

But we are doing something like this anyway for the mondo-analysis

I think the CF subclass is an error can you make ann efo ticket @nicolevasilevsky

[monicacecilia]

Dear @nicolevasilevsky - did you hear back from EFO about this?

[nicolevasilevsky]

@monicacecilia I don't think I ever did this! Thanks for the nudge

[nicolevasilevsky]

per @paolaroncaglia's comments on EBISPOT/efo#553 (comment), I revised the subclass for MONDO_0005413 cystic fibrosis associated meconium ileum

[paolaroncaglia]

@nicolevasilevsky
MONDO:0009061 'cystic fibrosis' needs fixing too please, see
EBISPOT/efo#553 (comment)
Thanks!

[nicolevasilevsky]

Got it - thanks @paolaroncaglia.
I did one PR #882
I will work on the rest of this once @cmungall approves the PR.

• Narrow down its disease location to 'intestine'

Note to self, these are the action items from EBISPOT/efo#553

• Remove the mapping between EFO:0004608 'cystic fibrosis associated meconium ileum' and its counterpart MONDO:0005413, and remove MONDO:0005413 from the Mondo list of terms, until Mondo approves the pull request in Consider annotation prop to distinguish disease grouping class vs disease entity #685, or we'll get the wrong parent back.

• Then add the Mondo mapping and the Mondo term back in their respective files:
  http://purl.obolibrary.org/obo/MONDO_0005413 http://www.ebi.ac.uk/efo/EFO_0004608 cystic fibrosis associated meconium ileum cystic fibrosis associated meconium ileum
  http://purl.obolibrary.org/obo/MONDO_0005413

• Add missing period at end of second-last sentence in definition

• When a term is created for 'perinatal disease' or similar (see Open Targets therapeutic area: Pregnancy, puerperium and perinatal conditions EBISPOT/efo#490), add it as a parent of 'cystic fibrosis associated meconium ileum'.

• Remove all current parents of EFO Orphanet:586 'Cystic fibrosis' except for 'autosomal recessive disease'

• Add database cross reference Wikipedia:Cystic_fibrosis

• Consider capturing the other superclasses of EFO Orphanet:586 'Cystic fibrosis' as features/symptoms/phenotypes. Currently they are:

pancreas disease
Rare genetic respiratory disease
rare male fertility disorder with obstructive azoospermia
Rare genetic disorder with obstructive azoospermia
rare pulmonary disease
Genetic biliary tract disease
Genetic pancreatic disease

• Remove the mapping between EFO:0004608 'cystic fibrosis' and its counterpart MONDO:0009061, and remove MONDO:0009061 from the Mondo list of terms, until Mondo fixes the same issue (see Consider annotation prop to distinguish disease grouping class vs disease entity #685 (comment)), or we'll get the wrong parents back.

[kshefchek]

Is the original request in scope or feasible to be included in mondo, or should we look for a workaround?

[paolaroncaglia]

Going back to MONDO:0005413 'cystic fibrosis associated meconium ileum', I'm afraid there's a typo in the label that you inherited from EFO, it should be "ileus" not "ileum". (See e.g.
https://www.cysticfibrosisjournal.com/article/S1569-1993(17)30809-3/fulltext
https://www.chop.edu/conditions-diseases/meconium-ileus
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3085752/)

And based on the above, I'd also suggest to make 'cystic fibrosis associated meconium ileus' a subclass of MONDO:0054868 'meconium ileus'

Thanks,
Paola

[paolaroncaglia]

Hi @nicolevasilevsky ,
I'm afraid that part of this ticket got a bit side-tracked due to technical issues ;-)
It would be great if you could please, before your next release, complete the edits agreed upon for 'cystic fibrosis', so EFO can resume mapping to Mondo for this term. Summing up:

• Edits (as applicable to Mondo) listed in Consider annotation prop to distinguish disease grouping class vs disease entity #685 (comment)
• Edits suggested in Consider annotation prop to distinguish disease grouping class vs disease entity #685 (comment)
  Thank you very much.
  Paola

[cmungall]

Would use of github milestones help with prioritizing tickets for releases? Kent can you say more about the negative consequence of classifying CF as non leaf? I thought the distinction purely drove the kind of table displayed, to minimize repetition with leaf terms

…

On Wed, Nov 13, 2019, 05:28 paolaroncaglia ***@***.***> wrote: Hi @nicolevasilevsky <https://github.com/nicolevasilevsky> , I'm afraid that part of this ticket got a bit side-tracked due to technical issues ;-) It would be great if you could please, before your next release, complete the edits agreed upon for 'cystic fibrosis', so EFO can resume mapping to Mondo. Summing up: - Edits (as applicable to Mondo) listed in #685 (comment) <#685 (comment)> - Edits suggested in #685 (comment) <#685 (comment)> Thank you very much. Paola — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#685?email_source=notifications&email_token=AAAMMOICF7EOHZKAJ4M2IALQTP6H7A5CNFSM4HJNXBMKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOED6ENSI#issuecomment-553404105>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOO5W2ODPBRRGKABQLLQTP6H7ANCNFSM4HJNXBMA> .

[nicolevasilevsky]

@kshefchek - see comment above

@cmungall yes- let's use GitHub milestones, great idea

[nicolevasilevsky]

@paolaroncaglia, I assigned this ticket to the December release milestone (which I just created).

Are you able to assign milestones too? Feel free to assign and help prioritize. (If not, I think I can adjust your permissions so you can do so)