Digenic diseases continued

[csbjohnson]

Reopen of accidentally closed PR #1229; addresses issue #1226.

[allenbaron]

I recommend you remove the created 'methylmalonic aciduria and homocystinuria' (DOID:0060915). I don't think the grouping for these subtypes is currently necessary. It can be added later if requested.

[allenbaron]

I think the added parent disease DOID:0060919 (currently named 'autoinflammatory disease') needs further review to determine whether it is needed and really should be added (check PubMed) and also to more clearly identify where in the tree these diseases should be added. If the parent term is going to be added it will need to have a different name.

[allenbaron]

A number of updates are needed to the definitions. They should all be shorter and generally fit the pattern: "A(n) {parent term} characterized by {symptoms, phenotypes, onset} that has_material_basis_in {genetic cause}." Also, source annotations need to be complete and formatted correctly has database_cross_reference's (hasDbXref) on the definition (let me know if you need assistance with this).

The appropriate parent(s) for the proteasome-associated autoinflammatory syndromes need(s) to be identified. I suggest reviewing the literature and proposing the top 3 current DO diseases that you'd consider to be the best fit, with emphasis on suggesting the most specific parent possible.

Let me know if you have any questions.

[allenbaron]

Is 'facioscapulohumeral muscular dystrophy 4' digenic? It appears to be missing the digenic inheritance axiom.

[csbjohnson]

Is 'facioscapulohumeral muscular dystrophy 4' digenic? It appears to be missing the digenic inheritance axiom.

Yes, I just added it and pushed it.

[lschriml]

I have added notes into the google doc.

…

On Thu, Oct 19, 2023 at 12:07 PM Claudia Sánchez-Beato Johnson < ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In src/ontology/doid-edit.owl <#1232 (comment)> : > +# Class: obo:DOID_0060919 (autoinflammatory disease) + +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060919 "disease_ontology") +AnnotationAssertion(oboInOwl:id obo:DOID_0060919 "DOID:0060919") +AnnotationAssertion(rdfs:label obo:DOID_0060919 "autoinflammatory ***@***.***) +SubClassOf(obo:DOID_0060919 obo:DOID_2914) Proposed possible parent terms <https://docs.google.com/spreadsheets/d/1yPTKZXNOTPDxKIjowzf082l2pM-6yt907cp66hwPGtw/edit#gid=1202994879> and supporting evidence. — Reply to this email directly, view it on GitHub <#1232 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABBB4DK2FD2BQJV6UPLYOKTYAFF5DAVCNFSM6AAAAAA3IXFWL6VHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMYTMOBYGE2DIOJVHE> . You are receiving this because you were mentioned.Message ID: ***@***.*** com>

-- Lynn M. Schriml, Ph.D. Associate Professor Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 ***@***.***

[csbjohnson]

Creation of "Proteasome-associated autoinflammatory syndrome" as a phenotypic series and parent term of Proteasome-associated autoinflammatory syndrome1 and Proteasome-associated autoinflammatory syndrome 3:

• Current child term definitions:

Proteosome-associated autoinflammatory syndrome Type 1
A proteasome-associated autoinflammatory syndrome characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 gene on chromosome 1q21.

Proteosome-associated autoinflammatory syndrome Type 3
A proteasome-associated autoinflammatory syndrome characterized by onset in early infancy, nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression pattern with onset in early infancy that has_material_basis_in a homozygous mutation in the PSMB4 gene on chromosome 1q21 or a heterozygous mutation in the PSMB4 gene and a heterozygous mutation in the PSMB9 gene on chromosome 6p21._

Proposed definition for Proteasome-associated autoinflammatory syndrome PS:

Autosomal recessive autoinflammatory syndrome characterized by early onset, dermatitis, lipodystrophy, dysregulation of the immune response, recurrent fever, joint contractures, Hepatosplenomegaly, anemia and calcifications.

Based on the following clinical feature similaries from PRAAS1 and PRAAS3

• Early on set:

Type 1: early childhood onset.
Type 3: onset in early infancy

• Dermatitis/skin:

Type 1: annular erythematous plaques on the face and extremities
Type 3: nodular dermatitis

• Lipodystrophy:

Type 1: partial lipodystrophy.
Type 3: panniculitis-induced lipodystrophy

• Immune dysregulation:

Type 1:laboratory evidence of immune dysregulation
Type 3: dysregulation of the immune response

• Recurrent fever:

Type 1 recurrent fever
Type 3 recurrent fever

• Joint contractures

Type 1 joint contractures
Type 3 joint contractures

• Hepatosplenomegaly

Type 1 Hepatosplenomegaly
Type 3 Hepatosplenomegaly

• Anemia

Type 1: microcytic anemia
Type 3: anemia

• Calcifications:

Type 1: basal ganglia calcifications,
Type 3: may have intracranial calcifications

[lschriml]

The definition of the parent term should start with " A syndrome
e.g.
A syndrome that is characterized by early onset, dermatitis, lipodystrophy, dysregulation of the immune response, recurrent fever, joint contractures, Hepatosplenomegaly, anemia and calcifications.