SCID CTPS1 to CID CTPS1 #8882

yshwetar · 2025-03-20T13:07:47Z

Changed label to not include 'severe'
Updated definition to not include 'severe'
Added previous label as a related synoynm
Included ORCID and PMID as necessary

Closes #8178 - Renamed term to combined immunodeficiency due to CTPS1 deficiency, instead of a 'severe' combined immunodeficiency due to CTPS1 deficency - Added ORCID and PMID - Added previous label as a related synonym - Subclass of combined immunodeficiency and immunodeficiency. No long a subclass of severe combined immunodeficiency

sabrinatoro

@yshwetar, please see questions and requested changes in lines.

In addition, if might be good to add the following:

a logical definition (as long as it makes sense)
a comment to say that this disease is not always severe (since other resources say it is). That would help users understand the differences.

sabrinatoro · 2025-03-20T23:49:47Z

src/ontology/mondo-edit.obo

@@ -309897,7 +309897,7 @@ subset: ordo_malformation_syndrome {source="Orphanet:280576"}
 subset: orphanet_rare {source="Orphanet:280576"}
 subset: otar {source="MONDO:OTAR"}
 subset: rare
-synonym: "BANF1-related neurodevelopmental syndrome" EXACT CLINGEN_LABEL [https://search.clinicalgenome.org/CCID:008387]
+synonym: "BANF1-related neurodevelopmental syndrome" EXACT CLINGEN_LABEL [https://search.clinicalgenome.org/CCID\:008387]


@yshwetar did you make this change?
Please make sure the url is correct (ie without the " \ ")

I did not - it has been showing up in my GH diff everytime I do a new PR

I will update this when I resolve the conflict.

sabrinatoro · 2025-03-20T23:51:06Z

src/ontology/mondo-edit.obo

-name: severe combined immunodeficiency due to CTPS1 deficiency
-def: "Severe combined immunodeficiency (SCID) due to CTPS1 deficiency is a rare primary immunodeficiency disorder due to impaired capacity of activated T- and B-cells to proliferate in response to antigen receptor-mediated activation characterized by early-onset, severe, persistent and/or recurrent viral infections due to Epstein-Barr virus (EBV) and Varicella Zoster virus (VZV), (including generalized varicella), as well as recurrent sino-pulmonary bacterial infections due to encapsulated pathogens." [Orphanet:420573]
+name: combined immunodeficiency due to CTPS1 deficiency
+def: "Combined immunodeficiency due to CTPS1 deficiency is a rare primary immunodeficiency disorder due to impaired capacity of activated T- and B-cells to proliferate in response to antigen receptor-mediated activation characterized by early-onset, severe, persistent and/or recurrent viral infections due to Epstein-Barr virus (EBV) and Varicella Zoster virus (VZV), (including generalized varicella), as well as recurrent sino-pulmonary bacterial infections due to encapsulated pathogens." [https://orcid.org/0000-0002-0587-4693, Orphanet:420573, PMID:24870241]


You don't need to include "Combined immunodeficiency due to CTPS1 deficiency is" at the beginning of the definition (ie you don't need to repeat the term label)

Please review the definition. Should it still include "severe"?

Sorry, the previous definition had it that way except saying 'severe combined....'. But that makes sense! Thanks

sabrinatoro · 2025-03-20T23:53:15Z

src/ontology/mondo-edit.obo

 synonym: "IMD24" RELATED ABBREVIATION [MONDO:Lexical, OMIM:615897]
 synonym: "immunodeficiency 24" RELATED [MONDO:Lexical, OMIM:615897]
 synonym: "immunodeficiency type 24" EXACT [MONDORULE:2, OMIM:615897]
-synonym: "SCID due to CTPS1 deficiency" EXACT [Orphanet:420573]
+synonym: "SCID due to CTPS1 deficiency" RELATED [Orphanet:420573]
+synonym: "severe combined immunodeficiency due to CTPS1 deficiency" RELATED [] {source="https://orcid.org/0000-0002-0587-4693"}


synonyms require an x-ref, and not a source.

Question for you: is this disease "never" severe, or is it "sometimes" severe?
Depending on the answer to this question, you might need to update the scope of the synonym.

From what I understand no. Hence why I put it as a related synonym. If it did sometimes present as severe, I would have done a narrow synonym.

Also I changed it to a x-ref!

@yshwetar these are still showing as narrow synonyms, and "source" instead of x-ref.

And it is correct that they should be narrow synonym.

sabrinatoro · 2025-03-20T23:55:10Z

src/ontology/mondo-edit.obo

@@ -331805,8 +331807,10 @@ xref: OMIM:615897 {source="Orphanet:420573", source="MONDO:equivalentTo", source
 xref: Orphanet:420573 {source="OMIM:615897", source="MONDO:equivalentTo"}
 xref: SCTID:763623001 {source="MONDO:equivalentTo"}
 xref: UMLS:C4014617 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:863054"}
-is_a: MONDO:0044201 {source="Orphanet:420573"} ! T+ B+ severe combined immunodeficiency


in addition to removing the SubClassOf annotation, you need to add an "excluded Subclass Of" annotation. See documentation here

- Updated definition, removing the word severe, and the repeat of the label - Related synonym annotation changed from dbxref to a source - excluded subclass annotation added - Logical definition added

sabrinatoro

@yshwetar I think some of your changes are not showing.

sabrinatoro · 2025-03-21T21:21:04Z

src/ontology/mondo-edit.obo

@@ -309897,7 +309897,7 @@ subset: ordo_malformation_syndrome {source="Orphanet:280576"}
 subset: orphanet_rare {source="Orphanet:280576"}
 subset: otar {source="MONDO:OTAR"}
 subset: rare
-synonym: "BANF1-related neurodevelopmental syndrome" EXACT CLINGEN_LABEL [https://search.clinicalgenome.org/CCID:008387]
+synonym: "BANF1-related neurodevelopmental syndrome" EXACT CLINGEN_LABEL [https://search.clinicalgenome.org/CCID\:008387]


I will update this when I resolve the conflict.

sabrinatoro · 2025-03-21T21:23:02Z

src/ontology/mondo-edit.obo

 synonym: "IMD24" RELATED ABBREVIATION [MONDO:Lexical, OMIM:615897]
 synonym: "immunodeficiency 24" RELATED [MONDO:Lexical, OMIM:615897]
 synonym: "immunodeficiency type 24" EXACT [MONDORULE:2, OMIM:615897]
-synonym: "SCID due to CTPS1 deficiency" EXACT [Orphanet:420573]
+synonym: "SCID due to CTPS1 deficiency" RELATED [Orphanet:420573]
+synonym: "severe combined immunodeficiency due to CTPS1 deficiency" RELATED [] {source="https://orcid.org/0000-0002-0587-4693"}


@yshwetar these are still showing as narrow synonyms, and "source" instead of x-ref.

And it is correct that they should be narrow synonym.

sabrinatoro · 2025-03-21T21:24:35Z

src/ontology/mondo-edit.obo

 relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/2519 {source="MONDO:mim2gene_medgen"} ! CTPS1
+property_value: excluded_subClassOf "'T+ B+ severe combined immunodeficiency'" xsd:string {source="https://orcid.org/0000-0002-0587-4693"}


you need to also have the original source (here: Orphanet:420573)

sabrinatoro · 2025-03-21T21:33:10Z

src/ontology/mondo-edit.obo

 synonym: "SCID due to CTPS1 deficiency" EXACT [DOID:0111938, Orphanet:420573]
+synonym: "SCID due to CTPS1 deficiency" RELATED [] {source="Orphanet:420573"}
+synonym: "severe combined immunodeficiency due to CTPS1 deficiency" RELATED [] {source="https://orcid.org/0000-0002-0587-4693"}


@yshwetar please review these synonym scope and x-ref instead of "source" annotation

yshwetar added 2 commits November 14, 2024 09:49

Exact synonym CTPS1 related combined ID

d9a1f58

Closes #8178

sabrinatoro requested changes Mar 20, 2025

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sabrinatoro assigned yshwetar Mar 21, 2025

Update CID CTPS1

9747689

- Updated definition, removing the word severe, and the repeat of the label - Related synonym annotation changed from dbxref to a source - excluded subclass annotation added - Logical definition added

yshwetar assigned sabrinatoro and unassigned yshwetar Mar 21, 2025

sabrinatoro requested changes Mar 21, 2025

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sabrinatoro added 3 commits March 21, 2025 14:27

Merge branch 'master' into issue-8178

2dfd595

normalization

723e12e

Update mondo-edit.obo

224d3ad

sabrinatoro requested changes Mar 21, 2025

View reviewed changes

sabrinatoro assigned yshwetar and unassigned sabrinatoro Mar 21, 2025

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SCID CTPS1 to CID CTPS1 #8882

SCID CTPS1 to CID CTPS1 #8882

yshwetar commented Mar 20, 2025

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		relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/2519 {source="MONDO:mim2gene_medgen"} ! CTPS1
		property_value: excluded_subClassOf "'T+ B+ severe combined immunodeficiency'" xsd:string {source="https://orcid.org/0000-0002-0587-4693"}

SCID CTPS1 to CID CTPS1 #8882

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SCID CTPS1 to CID CTPS1 #8882

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