strategic refinement questions

[nicolevasilevsky]

Discussion board to ask questions about mass obsoletion.

[nicolevasilevsky]

What should we do about terms that will be obsoleted, like MONDO:0016495 - TO_BE_OBSOLETED in this spreadsheet?

[nicolevasilevsky]

assign them to the top level parent, ie MONDO:0005046. They will need a temporary parent, otherwise the QC build will fail when we create the PR. They will be obsoleted when all the spreadsheets are reviewed and the mass obsoletion is done.

these terms will be obsoleted in the mass obsoletion pipeline, so they can be ignored.

@katiermullen FYI 👀

[nicolevasilevsky]

Why are some terms targeted for obsoletion and some are not (when they probably should be)? for example, why is term not in the list to be obsoleted: http://purl.obolibrary.org/obo/MONDO_0017026 ('interstitial lung disease specific to adulthood')? There are other "...interstitial lung disease..." terms that are being obsoleted?

[nicolevasilevsky]

Sabrina and I reviewed this list of potential obsoletion candidates, and some were marked as 'rescue', which means we'll go back and revisit them later. We'll do another round of review and mass obsoletion after this first round.

See more details here:
https://mondo.readthedocs.io/en/latest/editors-guide/mass-obsoletion/#review-ordo-grouping-classes-for-obsoletion

[LCCarmody]

I have a more specific, nuanced question: Term to be obsoleted: common cystic lymphatic malformation which is child of MONDO:0002013->lymphangioma

So:
MONDO:0002013->lymphangioma

MONDO:0018720 common cystic lymphatic malformation
Terms to be orphaned:
>> MONDO:0018717 | mixed cystic lymphatic malformation
>>MONDO:0019329 | microcystic lymphatic malformation
>> MONDO:0019328 | macrocystic lymphatic malformation

However, according to NORD explicitly (and other papers, implicitly), "Several different terms were once used to describe conditions now grouped under the umbrella term “lymphatic malformations.” Such terms include cystic hygroma, lymphangioma, cavernous lymphangioma, cystic lymphangioma and lymphangioma circumscriptum. These terms have been abandoned because some of the outdated terms imply a relationship to cancer. Lymphatic malformations are not cancerous and there is no known risk of malignant transformation."

Therefore, there should be a new term 'lymphatic malformation' and it is ONLY child of MONDO:0005833 lymphatic system disorder.

I believe lymphangioma should also be obsoleted.

Not sure how to do that in spreadsheet form...

[nicolevasilevsky]

Creating a new ticket to obsolete this term is best. The term lymphangioma is in NCIT, so we can ask them about it as well.

[nicolevasilevsky]

Thanks @LCCarmody!

[LCCarmody]

It would also be a NTR, but NCIT can comment on that, too

[nicolevasilevsky]

ah yes. Feel free to create one ticket for both requests (and label it New term request and Obsolete)

[LCCarmody]

Another: What should you do if the orphaned term should also be obsoleted?

Example:
MONDO:0015823 - TO_BE_OBSOLETED->primary immunodeficiency due to a defect in adaptive immunity
Term to be orphaned:

MONDO:0010123 | absent thumb-short stature-immunodeficiency syndrome

Text definition is accurate: "An exceedingly rare, autosomal recessive immune disease characterized by thumb aplasia, short stature with skeletal abnormalities, and combined immunodeficiency described in three sibships from two possibly related families. The skeletal abnormalities included unfused olecranon and the immunodeficiency manifested with severe chickenpox and chronic candidiasis. No new cases have been reported since 1978."

[nicolevasilevsky]

I'm not sure I understand the question. Are you referring to row 39?

[nicolevasilevsky]

and you think this term should be obsoleted? (MONDO:0010123 absent thumb-short stature-immunodeficiency syndrome)

Please create an obsoletion ticket and we can revisit it later.

[LCCarmody]

Yes, row 39. Assume that's a standard MONDO ticket? I can do that.

[nicolevasilevsky]

there are a lot of examples of Orphanet terms like this- historic diseases that may not actually be diseases. I feel like we've discussed this before but I don't remember if we decided we'd try to obsolete them all or do something else. I'll create a new label called historic disease, can you label the new ticket as such and we can discuss these at some point.

[nicolevasilevsky]

yep- use the obsolete term template. Thank you!

[sabrinatoro]

syndromes

How have we been dealing with "syndromes"?
Should syndromes be reclassified as "syndromic diseases", or should they be more specific?
for example: we have said that "syndromic retinitis pigmentosa" is not a "retinitis pigmentosa", it is a syndrome that have a major phenotype of retinitis pigmentosa.
What have you been doing?

[nicolevasilevsky]

Discussed with @sabrinatoro and @twhetzel:
For any syndromic disease, we should classify these as syndromic diseases, regardless if the syndrome has features of all the same type, like a cataract-glaucoma should be a syndromic disease, not an eye disease.

We will have a workshop in the new year to discuss this.

cc @katiermullen @LCCarmody @monicacecilia

[katiermullen]

I think that I am now confused by what constitutes a syndromic disease. Can we discuss on the curation call tomorrow?

[nicolevasilevsky]

yes, we'll discuss tomorrow!

[LCCarmody]

I'm not sure I will make it to the call, but I do have an issue with the classification of 'autoinflammatory syndrome'. It should be classified as a syndromic disease (and it is!), but it should NOT be classified as rheumatic disease...or rheumatic disease needs a new definition. Honestly, I think both. I assume I should write a ticket.

[monicacecilia]

We agreed to dump all 'leaving' syndromes to their own branch.
Will reach to the community to corroborate (upvote / downvote) their new location.
Will reach out to community via Outreach Call to inform.
Plan to have updated before December release.
Will schedule workshop for late Jan'24 with community.