add new terms #8792

nicolevasilevsky · 2025-02-26T23:12:11Z

@katiermullen

I created logical axioms for the terms and the superclasses are inferred (rather than asserting the superclasses)
I added the parent 'skeletal dysplasia' to osteochondrodysplasia because a synonym of osteochondrodysplasia is congenital skeletal dysplasia (this ensured the subclasses are inferred in [NTR/gene] SLC26A2-related skeletal dysplasia #8753)
add equiv axiom to 'osteogenesis imperfecta, COL1A2-related, dog' (see [NTR/gene] COL1A2-related osteogenesis imperfecta #8757)
exclude superclass from 'Kniest dysplasia' (as this is a feature) and update definition) (address [NTR/gene] COL2A1-related spondyloepiphyseal dysplasia #8763)

FYI, this is my robot template

close #8785
close #8753
close #8754
close #8757
close #8758
close #8759
close #8763
close #8778
close #8784

and superclass

a synonym of osteochondrodysplasia is congenital skeletal dysplasia

update def

update dbxrefs and source for 'TOR1AIP1-related nuclear envelopathy' and children

nicolevasilevsky · 2025-02-28T05:08:23Z

@sabrinatoro and/or @cmungall - do either of you want to review this PR? ClinGen requested a lot of new grouping classes based on gene names. I checked where synonyms should be added to existing terms instead and did that in a couple cases. Otherwise, I thought their grouping classes made sense.

katiermullen

@nicolevasilevsky please see in-line comments

katiermullen · 2025-03-03T16:05:25Z

src/ontology/mondo-edit.obo

+[Term]
+id: MONDO:0100591
+name: TOR1AIP1-related multisystem disorder
+def: "TOR1AIP1-related multisystem disorder is a rare, early-onset disorder affecting multiple organ systems that is caused by variation in the TOR1AIP1 gene. Clinical features reported in affected individuals are variable but may include hypotonia, dystonia, cerebellar atrophy, contractures, cardiomyopathy, microcephaly, cataract, deafness, skeletal anomalies, progeroid appearance and other facial dysmorphism, and nephrolithiasis. TOR1AIP1-related multisystem disorder, like TOR1AIP1-related myopathy, is considered a subtype of the broader phenotypic spectrum of TOR1AIP1-related nuclear envelopathy caused by loss of function of the TOR1AIP1 gene." [https://clinicalgenome.org/affiliation/40060/, https://clinicalgenome.org/affiliation/40151/, PMID:25425325, PMID:30723199, PMID:32055997]


Consider putting some of the details in a comment.

katiermullen · 2025-03-03T16:07:10Z

src/ontology/mondo-edit.obo

+
+[Term]
+id: MONDO:0100604
+name: TOR1AIP1-related nuclear envelopathy


Can you confirm that the child of this term, 'TOR1AIP1-related myopathy' is distinct from the grandchild term 'autosomal recessive limb-girdle muscular dystrophy type 2Y'?

I think myopathies and muscular dystrophies are distinct:
https://pubmed.ncbi.nlm.nih.gov/11562568/

katiermullen · 2025-03-03T16:13:37Z

src/ontology/mondo-edit.obo

@@ -107017,7 +107017,7 @@ synonym: "congenital anomaly of cartilage" NARROW []
 synonym: "congenital skeletal dysplasia" EXACT [NCIT:C84978]
 synonym: "osteochondrodysplasia" EXACT [DOID:2256, NCIT:C84978]
 synonym: "osteochondrodysplasia syndrome" EXACT [DOID:2256]
-synonym: "skeletal dysplasia" RELATED []
+synonym: "skeletal dysplasia" BROAD []


Do you have a reference for this syn?

katiermullen · 2025-03-03T16:15:46Z

src/ontology/mondo-edit.obo

@@ -164388,7 +164389,7 @@ property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/3571/metatro
 [Term]
 id: MONDO:0007987
 name: Kniest dysplasia
-def: "Kniest dysplasia is a severe type II collagenopathy characterized by a short trunk and limbs, prominent joints and midface hypoplasia (round face with a flat nasal root)." [Orphanet:485]
+def: "A rare type 2 collagen-related bone disorder characterized by moderately severe chondrodysplasia with disproportionate short stature of prenatal onset, prominent joints with restricted mobility, large epiphyses and dumbbell deformity of the long bones. It was first described in 1952 by Dr Wilhelm Kniest, a German pediatrician." [Orphanet:485]


I think the last sentence of the definition could be placed in a comment or excluded?

katiermullen · 2025-03-03T16:16:42Z

src/ontology/mondo-edit.obo

@@ -164412,14 +164413,14 @@ xref: Orphanet:485 {source="OMIM:156550", source="MONDO:equivalentTo"}
 xref: SCTID:53974002 {source="MONDO:equivalentTo"}
 xref: UMLS:C0265279 {source="MEDGEN:75559", source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
 is_a: MONDO:0005516 {source="DOID:0080045", source="MESH:C537207"} ! osteochondrodysplasia
-is_a: MONDO:0016761 {source="Orphanet:485"} ! spondyloepiphyseal dysplasia
 is_a: MONDO:0016763 {source="OMIM:156550"} ! spondylometaphyseal dysplasia
 is_a: MONDO:0022800 {source="Orphanet:485", source="PMID:31633310"} ! type 2 collagenopathy
 relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0007987 {source="MONDO:CLINGEN"}
 relationship: disease_has_feature HP:0000272 ! Malar flattening


There are no sources for these relationships. Is it possible to add them?

katiermullen · 2025-03-03T16:32:42Z

src/ontology/mondo-edit.obo

+[Term]
+id: MONDO:0100592
+name: SLC26A2-related skeletal dysplasia
+def: "Any skeletal disorder in which the cause of the disease is a variant in the SLC26A2 gene. This includes SLC26A2-related Achondrogenesis, SLC26A2-related atelosteogenesis, SLC26A2-related diastrophic dysplasia, and SLC26A2-related multiple epiphyseal dysplasia." [https://clinicalgenome.org/affiliation/40065/]


SLC26A2-related achondrogenesis (lower case)

revise def

fix typo

nicolevasilevsky · 2025-03-06T20:07:24Z

@katiermullen I addressed all of your comments
@sabrinatoro could you please take a look and make sure this aligns with the workflows you've been discussing with ClinGen for their new term requests?

nicolevasilevsky · 2025-03-07T07:07:58Z

open action items

note- per Chris' comment here (create new term COL1A2-related Ehlers-Danlos syndrome #8794 (comment)), I need to assert the superclasses too - I will do this

nicolevasilevsky and others added 10 commits February 26, 2025 15:10

add new terms

40fbfb7

Exclude QC

d64c8aa

add logical axiom

d8179f5

and superclass

Add parent 'skeletal dysplasia' to osteochondrodysplasia

ac5a1cf

a synonym of osteochondrodysplasia is congenital skeletal dysplasia

revise syn scope on osteochondrodysplasia

ab2df18

add synonym to MONDO:0008146 'osteogenesis imperfecta type 1'

ac7c6b5

add logical axiom and term tracker item

c546772

create equiv axiom for 'COL1A1-related Ehlers-Danlos syndrome'

a5f0f5f

exclude superclass from 'Kniest dysplasia'

5c1d750

update def

revise def - van Maldergem syndrome

6932b2a

update dbxrefs and source for 'TOR1AIP1-related nuclear envelopathy' and children

nicolevasilevsky requested a review from katiermullen February 27, 2025 00:24

nicolevasilevsky assigned katiermullen Feb 27, 2025

nicolevasilevsky marked this pull request as ready for review February 27, 2025 00:24

katiermullen reviewed Mar 3, 2025

View reviewed changes

katiermullen assigned nicolevasilevsky and unassigned katiermullen Mar 3, 2025

nicolevasilevsky added 2 commits March 6, 2025 12:01

add xref

4dd26ea

revise def

add sources

59a295b

fix typo

nicolevasilevsky assigned sabrinatoro and katiermullen and unassigned nicolevasilevsky Mar 6, 2025

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

add new terms #8792

add new terms #8792

nicolevasilevsky commented Feb 26, 2025 •

edited

Loading

nicolevasilevsky commented Feb 28, 2025

katiermullen left a comment

katiermullen Mar 3, 2025

nicolevasilevsky Mar 6, 2025

katiermullen Mar 3, 2025

nicolevasilevsky Mar 6, 2025

katiermullen Mar 3, 2025

nicolevasilevsky Mar 6, 2025

katiermullen Mar 3, 2025

nicolevasilevsky Mar 6, 2025

katiermullen Mar 3, 2025

nicolevasilevsky Mar 6, 2025

katiermullen Mar 3, 2025

nicolevasilevsky Mar 6, 2025

nicolevasilevsky commented Mar 6, 2025

nicolevasilevsky commented Mar 7, 2025

add new terms #8792

Are you sure you want to change the base?

add new terms #8792

Conversation

nicolevasilevsky commented Feb 26, 2025 • edited Loading

nicolevasilevsky commented Feb 28, 2025

katiermullen left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

nicolevasilevsky commented Mar 6, 2025

nicolevasilevsky commented Mar 7, 2025

open action items

nicolevasilevsky commented Feb 26, 2025 •

edited

Loading