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monarch-initiative / mondo

Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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Mass Obsoletion: focus on branch 'immune system disorder' (MONDO:0005046) #6747

Closed sabrinatoro closed 7 months ago

sabrinatoro commented 1 year ago

branch: 'immune system disorder' (MONDO:0005046)

terms to obsolete: obsoletion candidate ID obsoletion candidate label
http://purl.obolibrary.org/obo/MONDO_0015822 acquired neutropenia
http://purl.obolibrary.org/obo/MONDO_0015818 aggressive primary cutaneous B-cell lymphoma
http://purl.obolibrary.org/obo/MONDO_0016599 autosomal dominant secondary polycythemia
http://purl.obolibrary.org/obo/MONDO_0016536 autosomal recessive lymphoproliferative disease
http://purl.obolibrary.org/obo/MONDO_0018720 common cystic lymphatic malformation
http://purl.obolibrary.org/obo/MONDO_0016495 functional variant of Guillain-Barre syndrome
http://purl.obolibrary.org/obo/MONDO_0015975 hyper-IgM syndrome with susceptibility to opportunistic infections
http://purl.obolibrary.org/obo/MONDO_0015976 hyper-IgM syndrome without susceptibility to opportunistic infections
http://purl.obolibrary.org/obo/MONDO_0015132 immunodeficiency predominantly affecting antibody production
http://purl.obolibrary.org/obo/MONDO_0017036 Langerhans cell histiocytosis in childhood and adulthood
http://purl.obolibrary.org/obo/MONDO_0020537 occupational allergic alveolitis
http://purl.obolibrary.org/obo/MONDO_0015823 primary immunodeficiency due to a defect in adaptive immunity
http://purl.obolibrary.org/obo/MONDO_0015135 primary immunodeficiency due to a genetic defect in innate immunity
http://purl.obolibrary.org/obo/MONDO_0015133 quantitative and/or qualitative congenital phagocyte defect
http://purl.obolibrary.org/obo/MONDO_0016494 regional variant of Guillain-Barre syndrome
http://purl.obolibrary.org/obo/MONDO_0018745 superficial pemphigus
http://purl.obolibrary.org/obo/MONDO_0019520 syndromic lymphedema
http://purl.obolibrary.org/obo/MONDO_0016493 variant of Guillain-Barre syndrome
nicolevasilevsky commented 1 year ago

Spreadsheet is here

LCCarmody commented 1 year ago

@nicolevasilevsky @sabrinatoro Please review

nicolevasilevsky commented 1 year ago

Hi @LCCarmody - I review the orphaned classes and it looks good. I made one comment.

Do you want to proceed with reviewing the 'leaves the branch' terms?

LCCarmody commented 12 months ago

Sorry, I missed this message. And I'm not sure what 'reviewing the 'leaves the branch' terms' means, exactly... Same process just see if it is correct?

nicolevasilevsky commented 12 months ago

Yes - similar process. Your spreadsheet is filtered on terms that leave the branch. This means that when we obsolete their parent(s), they will no longer be a type of immune system disorder. The goal is to review the terms, definitions, etc. and decide if they should be a type of immune system disorder (either a child of that parent class or something more specific in that branch) or if it is okay if they leave the branch. You can look at the other parents the term has in columns F-I or you can look at it in the ontology.

If you think it should have a new parent that is in the immune system disorder branch, please add the new parent like before.

If you think it's okay to leave the branch, just leave columns K-N blank but assign your curator confidence, so we know you looked at it.

Thanks @LCCarmody !

LCCarmody commented 12 months ago

Sure, but I don't think I can get to it until Wed afternoon.

nicolevasilevsky commented 12 months ago

no problem, @LCCarmody! Thanks for doing this!

LCCarmody commented 11 months ago

just finished. Have a few uncertainties.

nicolevasilevsky commented 11 months ago

Thanks @LCCarmody! I'll review this

nicolevasilevsky commented 11 months ago

@LCCarmody I am done reviewing, do you want to review my comments and let me know if you have any questions?

LCCarmody commented 11 months ago

Sorry, if i wasn't clear I am done reviewing. I agreed with Nicole's review--just had some questions about what is a feature. I added in all the requests. @sabrinatoro @nicolevasilevsky

sabrinatoro commented 10 months ago

expert reviewer spreadsheet is here: https://docs.google.com/spreadsheets/d/1TU7pMnQn_-y7SHVp_6c7hYRDYgrOV4l9/edit#gid=12697062

To DO:

After this to do list is done, 7 terms will remain for which reviewers were unsure.

sabrinatoro commented 7 months ago

There are some comments from the community that should be reviewed, but this is future work. This issue can be closed for now.