Error with "rare" subset annotation for Hematologic Diseases that may also be propagating into 'inferred rare' assignments

[ericsid]

Mondo term (ID Label)
MONDO:0005570

Bug/Typo/Error description
MONDO:0005570 Hematologic Disease has a subset annotation of "rare" when it should not. Consequently, this may also be leading to subset annotations for "Inferred Rare" being applied to descendants that are not rare.

This likely comes from MONDO:0005570 Hematologic Disease (which should include both rare and common hematologic diseases) being currently set as equivalentTo Orpha:97992 Rare Hematologic Diseases (which should only include rare hematologic diseases).

Here are two good examples of hematologic diseases that are not rare and have "inferred rare" subset annotations:
MONDO:0002280 anemia - CDC has multiple datasets that can substantiate this is not rare (e.g., https://www.cdc.gov/nchs/fastats/anemia.htm)
MONDO:0001356 iron deficiency anemia - CDC's NHANES survey covers this so there's plenty of citations to suggest this is not rare (e.g., here's one from a quick search - https://jamanetwork.com/journals/jama/fullarticle/2806540)

The problem is widespread enough that this may be an issue in the axiom used for assigning "inferred rare" to entities in the 'Hematologic Disease' branch.

Last example, MONDO:0003785 Leukopenia is another common finding that should not be rare. It seems to have received "inferred rare" from Hematologic Disease branch, since its other parent branch (MONDO:0005046 Immune System Disorder) does not have a rare subset annotation.

Your nano-attribution (ORCID)
0000-0001-7697-3026
-Eric

[ericsid]

@sabrinatoro - if this is helpful, attached is a brief analysis of inferred rare concepts under this branch. I extracted all descendants of 'hematologic diseases', filtered for inferred rare, and eyeballed the results.

Identified 13 concepts (including the two above) as examples that are likely not rare - see sheet 'manual analysis'. Most of these can be classified as clinical lab findings (e.g., leukopenia, normocytic anemia, etc.) so it depends on whether these are interpreted as an acute finding (incidence rates are unlikely to be rare) or limited to chronic finding (this may make it rare...but would require much more in-depth manual curation...).

Please let me know what (if any) details may be helpful for you so that I can better structure how we report on other future information.

Incorrect-InferredRare_HematologicDiseases-2024.04.05.xlsx

[sabrinatoro]

Hi @ericsid.
A lot of work has been done about the rare disease subset since you submitted this issue. I am finally able to get back to it and review the list you reported above.

The diseases on the list you shared are not "inferred rare" anymore. However, the following terms are still reported as rare because they came from the GARD rare disease list. We should update this list.

• MONDO:0003785
• MONDO:0001475
• MONDO:0001529
• MONDO:0002901
• MONDO:0003783
• MONDO:0003785
• MONDO:0044348

I am closing this issue. Let's connect and update the GARD rare disease list soon.