Review request: 56 clingen preferred synonyms classified as "narrow"

[matentzn]

After our meeting with ClinGen, I am trying to put together a Mondo subset for ClinGen which we can load into Monarch OLS, and which gives the ClinGen data engineers a way to render Mondo information with the ClinGen preferred labels.

While building my draft, I noticed that current 55 synonyms preferred by ClinGen are considered "narrow" in Mondo. My questions are the following:

1. Should these 55 be really considered "narrow"
2. If so, is it not somewhat risky to "swap" them out during the subset generation process, as "narrow" implies as somewhat different conceptual extent of the Mondo class?

entity	label	clingen_preferred	synonym_property
MONDO:0011767	"autosomal recessive nonsyndromic hearing loss 31"	"autosomal recessive nonsyndromic deafness 31"	oio:hasNarrowSynonym
MONDO:0013210	"autosomal recessive nonsyndromic hearing loss 25"	"autosomal recessive nonsyndromic deafness 25"	oio:hasNarrowSynonym
MONDO:0013249	"autosomal recessive nonsyndromic hearing loss 84A"	"autosomal recessive nonsyndromic deafness 84A"	oio:hasNarrowSynonym
MONDO:0013215	"autosomal recessive nonsyndromic hearing loss 79"	"autosomal recessive nonsyndromic deafness 79"	oio:hasNarrowSynonym
MONDO:0010860	"autosomal recessive nonsyndromic hearing loss 3"	"autosomal recessive nonsyndromic deafness 3"	oio:hasNarrowSynonym
MONDO:0012273	"autosomal recessive nonsyndromic hearing loss 48"	"autosomal recessive nonsyndromic deafness 48"	oio:hasNarrowSynonym
MONDO:0013119	"autosomal recessive nonsyndromic hearing loss 77"	"autosomal recessive nonsyndromic deafness 77"	oio:hasNarrowSynonym
MONDO:0012060	"autosomal recessive nonsyndromic hearing loss 35"	"autosomal recessive nonsyndromic deafness 35"	oio:hasNarrowSynonym
MONDO:0013489	"autosomal recessive nonsyndromic hearing loss 89"	"autosomal recessive nonsyndromic deafness 89"	oio:hasNarrowSynonym
MONDO:0011160	"autosomal recessive nonsyndromic hearing loss 15"	"autosomal recessive nonsyndromic deafness 15"	oio:hasNarrowSynonym
MONDO:0013985	"autosomal recessive nonsyndromic hearing loss 18B"	"autosomal recessive nonsyndromic deafness 18B"	oio:hasNarrowSynonym
MONDO:0011102	"autosomal dominant nonsyndromic hearing loss 12"	"autosomal dominant nonsyndromic deafness 12"	oio:hasNarrowSynonym
MONDO:0010965	"autosomal recessive nonsyndromic hearing loss 6"	"autosomal recessive nonsyndromic deafness 6"	oio:hasNarrowSynonym
MONDO:0012602	"autosomal recessive nonsyndromic hearing loss 24"	"autosomal recessive nonsyndromic deafness 24"	oio:hasNarrowSynonym
MONDO:0011762	"autosomal recessive nonsyndromic hearing loss 22"	"autosomal recessive nonsyndromic deafness 22"	oio:hasNarrowSynonym
MONDO:0012485	"autosomal recessive nonsyndromic hearing loss 68"	"autosomal recessive nonsyndromic deafness 68"	oio:hasNarrowSynonym
MONDO:0012420	"autosomal recessive nonsyndromic hearing loss 49"	"autosomal recessive nonsyndromic deafness 49"	oio:hasNarrowSynonym
MONDO:0033201	"hearing loss, autosomal recessive 57"	"deafness, autosomal recessive 57"	oio:hasNarrowSynonym
MONDO:0016297	"prelingual non-syndromic genetic hearing loss"	"prelingual non-syndromic genetic deafness"	oio:hasNarrowSynonym
MONDO:0012460	"autosomal recessive nonsyndromic hearing loss 67"	"autosomal recessive nonsyndromic deafness 67"	oio:hasNarrowSynonym
MONDO:0013269	"autosomal recessive nonsyndromic hearing loss 91"	"autosomal recessive nonsyndromic deafness 91"	oio:hasNarrowSynonym
MONDO:0014853	"autosomal dominant nonsyndromic hearing loss 70"	"autosomal dominant nonsyndromic deafness 70"	oio:hasNarrowSynonym
MONDO:0010967	"autosomal recessive nonsyndromic hearing loss 7"	"autosomal recessive nonsyndromic deafness 7"	oio:hasNarrowSynonym
MONDO:0010576	"X-linked mixed hearing loss with perilymphatic gusher"	"X-linked mixed deafness with perilymphatic gusher"	oio:hasNarrowSynonym
MONDO:0100368	"RPE65-related recessive retinopathy"	"retinitis pigmentosa 20"	oio:hasNarrowSynonym
MONDO:0019497	"nonsyndromic genetic hearing loss"	"nonsyndromic genetic deafness"	oio:hasNarrowSynonym
MONDO:0011364	"autosomal recessive nonsyndromic hearing loss 16"	"autosomal recessive nonsyndromic deafness 16"	oio:hasNarrowSynonym
MONDO:0011031	"autosomal dominant nonsyndromic hearing loss 10"	"autosomal dominant nonsyndromic deafness 10"	oio:hasNarrowSynonym
MONDO:0019587	"autosomal dominant nonsyndromic hearing loss"	"autosomal dominant nonsyndromic deafness"	oio:hasNarrowSynonym
MONDO:0019588	"hearing loss, autosomal recessive"	"deafness, autosomal recessive"	oio:hasNarrowSynonym
MONDO:0012003	"autosomal recessive nonsyndromic hearing loss 39"	"autosomal recessive nonsyndromic deafness 39"	oio:hasNarrowSynonym
MONDO:0012445	"autosomal recessive nonsyndromic hearing loss 59"	"autosomal recessive nonsyndromic deafness 59"	oio:hasNarrowSynonym
MONDO:0013537	"autosomal recessive nonsyndromic hearing loss 29"	"autosomal recessive nonsyndromic deafness 29"	oio:hasNarrowSynonym
MONDO:0011351	"autosomal recessive nonsyndromic hearing loss 21"	"autosomal recessive nonsyndromic deafness 21"	oio:hasNarrowSynonym
MONDO:0012670	"autosomal recessive nonsyndromic hearing loss 63"	"autosomal recessive nonsyndromic deafness 63"	oio:hasNarrowSynonym
MONDO:0011774	"autosomal recessive nonsyndromic hearing loss 30"	"autosomal recessive nonsyndromic deafness 30"	oio:hasNarrowSynonym
MONDO:0010986	"autosomal recessive nonsyndromic hearing loss 9"	"autosomal recessive nonsyndromic deafness 9"	oio:hasNarrowSynonym
MONDO:0014603	"autosomal dominant nonsyndromic hearing loss 40"	"autosomal dominant nonsyndromic deafness 40"	oio:hasNarrowSynonym
MONDO:0100445	"LCA5-related retinopathy"	"Leber congenital amaurosis 5"	oio:hasNarrowSynonym
MONDO:0011912	"autosomal recessive nonsyndromic hearing loss 37"	"autosomal recessive nonsyndromic deafness 37"	oio:hasNarrowSynonym
MONDO:0012170	"autosomal recessive nonsyndromic hearing loss 36"	"autosomal recessive nonsyndromic deafness 36"	oio:hasNarrowSynonym
MONDO:0012326	"autosomal recessive nonsyndromic hearing loss 42"	"autosomal recessive nonsyndromic deafness 42"	oio:hasNarrowSynonym
MONDO:0010987	"autosomal recessive nonsyndromic hearing loss 8"	"autosomal recessive nonsyndromic deafness 8"	oio:hasNarrowSynonym
MONDO:0013984	"autosomal recessive nonsyndromic hearing loss 84B"	"autosomal recessive nonsyndromic deafness 84B"	oio:hasNarrowSynonym
MONDO:0009076	"autosomal recessive nonsyndromic hearing loss 1A"	"autosomal recessive nonsyndromic deafness 1A"	oio:hasNarrowSynonym
MONDO:0019589	"obsolete syndromic genetic hearing loss"	"syndromic genetic deafness"	oio:hasNarrowSynonym
MONDO:0100447	"ATF6-related retinopathy"	"achromatopsia 7"	oio:hasNarrowSynonym
MONDO:0010484	"hearing loss, X-linked 6"	"deafness, X-linked 6"	oio:hasNarrowSynonym
MONDO:0011067	"autosomal recessive nonsyndromic hearing loss 12"	"autosomal recessive nonsyndromic deafness 12"	oio:hasNarrowSynonym
MONDO:0013929	"autosomal recessive nonsyndromic hearing loss 98"	"autosomal recessive nonsyndromic deafness 98"	oio:hasNarrowSynonym
MONDO:0014428	"autosomal recessive nonsyndromic hearing loss 102"	"autosomal recessive nonsyndromic deafness 102"	oio:hasNarrowSynonym
MONDO:0014237	"autosomal recessive nonsyndromic hearing loss 76"	"autosomal recessive nonsyndromic deafness 76"	oio:hasNarrowSynonym
MONDO:0012355	"autosomal recessive nonsyndromic hearing loss 28"	"autosomal recessive nonsyndromic deafness 28"	oio:hasNarrowSynonym
MONDO:0010378	"X-linked hereditary sensory and autonomic neuropathy with hearing loss"	"X-linked hereditary sensory and autonomic neuropathy with deafness"	oio:hasNarrowSynonym
MONDO:0013963	"autosomal recessive nonsyndromic hearing loss 93"	"autosomal recessive nonsyndromic deafness 93"	oio:hasNarrowSynonym

[sabrinatoro]

@nicolevasilevsky maybe you have institutional knowledge of these terms. From what I can tell, these have "narrow synonyms" that should be "exact synonyms". I cannot find evidence why they are "narrow". Do you remember anything about these? Would you agree that these (and all the versions of these synonyms) should be "exact synonyms"? Thank you!

[sabrinatoro]

@nicolevasilevsky They were added as "narrow synonym" in this issue based on genemap. But I am still confused.

[nicolevasilevsky]

We intentionally changed deafness to hearing loss per this request: https://github.com/monarch-initiative/mondo/issues/551

and Chris suggested that deafness be a narrow synonym of hearing loss.

[sabrinatoro]

Thank you @nicolevasilevsky. In practice though, there are exact synonym though? I think having them as narrow synonyms is causing some issues (e.g. groups are using narrow synonyms as preferred labels). I'll bring this up on the call.

[nicolevasilevsky]

I don't think it's technically correct to make them exact synonyms because you can have mild hearing loss that is not deafness, see Heidi's comment: https://github.com/monarch-initiative/mondo/issues/551#issue-385440764

I think it would be better to ask ClinGen if we can move the preferred label to match the primary label. Heidi is from ClinGen.

[nicolevasilevsky]

@sabrinatoro I will link the this issue and issue #551 to the terms above, so we remember this conversation!

[sabrinatoro]

@courtneythaxton , could you please share some input on this issue? I sent you an email with a more detailed background and context. Thank you!

[courtneythaxton]

I think it might be good to go back to the Hearing Loss EPs/CDWG and ask them about the narrow to exact match. From the ticket #551 there does appear to be a difference in deafness (profound hearing loss) and "hearing loss", so there may be a need to create new nodes instead of synonyms.

I emailed Sabrina and offered our DNAC February call, as Heidi and the other ClinGen Disease Naming Advisory Committee (DNAC) members would be able to weigh in. This also is a call Ada attends :).

[sabrinatoro]

I had an email conversation with Heidi Rehm and Marina DiStefano. They confirmed that the term to use should be the "hearing loss" one (and not the "deafness" one).

In summary, the labels in the list above, and not the narrow synonyms, should be the "ClinGen_label" (FKA ClinGen_preferred).

@matentzn : Please let me know how I can help

[twhetzel]

Is this related to https://github.com/monarch-initiative/mondo/pull/7112

[twhetzel]

Should this be closed with https://github.com/monarch-initiative/mondo/pull/7227 now merged?

[nicolevasilevsky]

oh yes, can be closed!