From bf546cd60a63f6d887855134250eb586795c11c7 Mon Sep 17 00:00:00 2001 From: Yousif <153126037+yshwetar@users.noreply.github.com> Date: Mon, 8 Jul 2024 19:05:50 -0400 Subject: [PATCH 1/6] Update DEE31A and 31B Addresses #7641 - Updated names and synonyms to represent new medical understanding of DEE31 as DEE31A - Updated definitions for 31A and 31B from OMIM. Included my ORCID and OMIM as annotations - Included broad and exact synonyms, along with ORCID and OMIM annotations for these --- src/ontology/mondo-edit.obo | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index a9ae6a22b9..1eb709be8b 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -334863,15 +334863,17 @@ relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/ [Term] id: MONDO:0014598 -name: developmental and epileptic encephalopathy, 31 -def: "Any early infantile epileptic encephalopathy in which the cause of the disease is a mutation in the DNM1 gene." [MONDO:patterns/disease_series_by_gene] +name: developmental and epileptic encephalopathy, 31A +def: "Autosomal dominant neurologic disorder presenting with global developmental delay apparent in early infancy." [https://orcid.org/0000-0002-0587-4693, MONDO:patterns/disease_series_by_gene, OMIM:616346] subset: gard_rare {source="GARD:16094", source="MONDO:GARD"} subset: nord_rare {source="MONDO:NORD"} subset: rare synonym: "DEE31" BROAD ABBREVIATION [OMIM:616346] +synonym: "DEE31A" EXACT [OMIM:616346] synonym: "developmental and epileptic encephalopathy 31" BROAD [OMIM:616346, OMIM:genemap2] +synonym: "Developmental and epileptic encephalopathy 31A, autosomal dominant" EXACT [https://orcid.org/0000-0001-9310-0163] synonym: "DNM1 early infantile epileptic encephalopathy" EXACT [MONDO:design_pattern, MONDO:patterns/disease_series_by_gene] -synonym: "DNM1-Encephalopathy and Neurodevelopmental Disorder" BROAD [] +synonym: "DNM1-Encephalopathy and Neurodevelopmental Disorder" BROAD [https://orcid.org/0000-0001-9310-0163] synonym: "early infantile epileptic encephalopathy caused by mutation in DNM1" EXACT [MONDO:design_pattern] synonym: "EIEE31" EXACT ABBREVIATION [MONDO:Lexical, OMIM:616346] synonym: "epileptic encephalopathy, early infantile, 31" EXACT [MONDO:Lexical, OMIM:616346] @@ -553738,10 +553740,12 @@ is_a: MONDO:0019952 {source="OMIM:620351"} ! congenital myopathy [Term] id: MONDO:0957248 name: developmental and epileptic encephalopathy 31B +def: "Autosomal recessive neurologic disorder characterized by early-onset epilepsy, generalized muscular hypotonia, visual impairment, and severe neurodevelopmental delay." [https://orcid.org/0000-0002-0587-4693, OMIM:620352] subset: gard_rare {source="MONDO:GARD"} subset: nord_rare {source="MONDO:NORD"} subset: rare -synonym: "DNM1-Encephalopathy and Neurodevelopmental Disorder" BROAD [] +synonym: "Developmental and epileptic encephalopathy 31B, autosomal recessive" EXACT [https://orcid.org/0000-0001-9310-0163, OMIM:620352] +synonym: "DNM1-Encephalopathy and Neurodevelopmental Disorder" BROAD [https://orcid.org/0000-0001-9310-0163] xref: DOID:0070376 {source="MONDO:equivalentTo"} xref: MEDGEN:1841095 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:620352 {source="MONDO:equivalentTo"} From 5f1c7403a93a701c240a1c2b8886c269ac2fb7f8 Mon Sep 17 00:00:00 2001 From: Yousif <153126037+yshwetar@users.noreply.github.com> Date: Tue, 9 Jul 2024 04:53:31 -0400 Subject: [PATCH 2/6] Update definitons for 31A and 31B Replaced broad defintion for 31A. Changed definition for 31B to be of similar structure to 31A --- src/ontology/mondo-edit.obo | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 1eb709be8b..53e8c717ad 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -334864,7 +334864,7 @@ relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/ [Term] id: MONDO:0014598 name: developmental and epileptic encephalopathy, 31A -def: "Autosomal dominant neurologic disorder presenting with global developmental delay apparent in early infancy." [https://orcid.org/0000-0002-0587-4693, MONDO:patterns/disease_series_by_gene, OMIM:616346] +def: "Any early infantile epileptic encephalopathy in which the cause of the disease is a heterozygous mutation in the DNM1 gene." [https://orcid.org/0000-0002-0587-4693, MONDO:patterns/disease_series_by_gene, OMIM:616346] subset: gard_rare {source="GARD:16094", source="MONDO:GARD"} subset: nord_rare {source="MONDO:NORD"} subset: rare @@ -553740,7 +553740,7 @@ is_a: MONDO:0019952 {source="OMIM:620351"} ! congenital myopathy [Term] id: MONDO:0957248 name: developmental and epileptic encephalopathy 31B -def: "Autosomal recessive neurologic disorder characterized by early-onset epilepsy, generalized muscular hypotonia, visual impairment, and severe neurodevelopmental delay." [https://orcid.org/0000-0002-0587-4693, OMIM:620352] +def: "Any early infantile epileptic encephalopathy in which the cause of the disease is a homozygous mutation in the DNM1 gene." [https://orcid.org/0000-0002-0587-4693, OMIM:620352] subset: gard_rare {source="MONDO:GARD"} subset: nord_rare {source="MONDO:NORD"} subset: rare From 53e2171e9c7a82e211107ed95d62323d2eb4785a Mon Sep 17 00:00:00 2001 From: Yousif <153126037+yshwetar@users.noreply.github.com> Date: Wed, 10 Jul 2024 10:48:14 -0400 Subject: [PATCH 3/6] Updated DEE31A and 31B definitions Changed definition to be for developmental and epileptic encephalopathies, and not early developmental and epileptic encephalopathies. Also added a comma to 31B naming --- src/ontology/mondo-edit.obo | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 53e8c717ad..191e6bf2f8 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -334864,7 +334864,7 @@ relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/ [Term] id: MONDO:0014598 name: developmental and epileptic encephalopathy, 31A -def: "Any early infantile epileptic encephalopathy in which the cause of the disease is a heterozygous mutation in the DNM1 gene." [https://orcid.org/0000-0002-0587-4693, MONDO:patterns/disease_series_by_gene, OMIM:616346] +def: "Any developmental and epileptic encephalopathy in which the cause of the disease is a heterozygous mutation in the DNM1 gene." [https://orcid.org/0000-0002-0587-4693, MONDO:patterns/disease_series_by_gene, OMIM:616346] subset: gard_rare {source="GARD:16094", source="MONDO:GARD"} subset: nord_rare {source="MONDO:NORD"} subset: rare @@ -553739,8 +553739,8 @@ is_a: MONDO:0019952 {source="OMIM:620351"} ! congenital myopathy [Term] id: MONDO:0957248 -name: developmental and epileptic encephalopathy 31B -def: "Any early infantile epileptic encephalopathy in which the cause of the disease is a homozygous mutation in the DNM1 gene." [https://orcid.org/0000-0002-0587-4693, OMIM:620352] +name: developmental and epileptic encephalopathy, 31B +def: "Any developmental and epileptic encephalopathy in which the cause of the disease is a homozygous mutation in the DNM1 gene." [https://orcid.org/0000-0002-0587-4693, OMIM:620352] subset: gard_rare {source="MONDO:GARD"} subset: nord_rare {source="MONDO:NORD"} subset: rare From 46b26a15513f9e5e0d712b0eca53a178994e0359 Mon Sep 17 00:00:00 2001 From: Yousif <153126037+yshwetar@users.noreply.github.com> Date: Thu, 11 Jul 2024 19:03:12 -0400 Subject: [PATCH 4/6] Removing letter capitalization Synonyms have letters capitalized - this was removed. --- src/ontology/mondo-edit.obo | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 191e6bf2f8..78c3249c41 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -334871,9 +334871,9 @@ subset: rare synonym: "DEE31" BROAD ABBREVIATION [OMIM:616346] synonym: "DEE31A" EXACT [OMIM:616346] synonym: "developmental and epileptic encephalopathy 31" BROAD [OMIM:616346, OMIM:genemap2] -synonym: "Developmental and epileptic encephalopathy 31A, autosomal dominant" EXACT [https://orcid.org/0000-0001-9310-0163] +synonym: "developmental and epileptic encephalopathy 31A, autosomal dominant" EXACT [https://orcid.org/0000-0001-9310-0163] synonym: "DNM1 early infantile epileptic encephalopathy" EXACT [MONDO:design_pattern, MONDO:patterns/disease_series_by_gene] -synonym: "DNM1-Encephalopathy and Neurodevelopmental Disorder" BROAD [https://orcid.org/0000-0001-9310-0163] +synonym: "DNM1-encephalopathy and neurodevelopmental disorder" BROAD [https://orcid.org/0000-0001-9310-0163] synonym: "early infantile epileptic encephalopathy caused by mutation in DNM1" EXACT [MONDO:design_pattern] synonym: "EIEE31" EXACT ABBREVIATION [MONDO:Lexical, OMIM:616346] synonym: "epileptic encephalopathy, early infantile, 31" EXACT [MONDO:Lexical, OMIM:616346] @@ -553744,8 +553744,8 @@ def: "Any developmental and epileptic encephalopathy in which the cause of the d subset: gard_rare {source="MONDO:GARD"} subset: nord_rare {source="MONDO:NORD"} subset: rare -synonym: "Developmental and epileptic encephalopathy 31B, autosomal recessive" EXACT [https://orcid.org/0000-0001-9310-0163, OMIM:620352] -synonym: "DNM1-Encephalopathy and Neurodevelopmental Disorder" BROAD [https://orcid.org/0000-0001-9310-0163] +synonym: "developmental and epileptic encephalopathy 31B, autosomal recessive" EXACT [https://orcid.org/0000-0001-9310-0163, OMIM:620352] +synonym: "DNM1-encephalopathy and neurodevelopmental Disorder" BROAD [https://orcid.org/0000-0001-9310-0163] xref: DOID:0070376 {source="MONDO:equivalentTo"} xref: MEDGEN:1841095 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:620352 {source="MONDO:equivalentTo"} From 3993699d558628e2f4692e82e4ac7bc09aabe240 Mon Sep 17 00:00:00 2001 From: Yousif <153126037+yshwetar@users.noreply.github.com> Date: Fri, 12 Jul 2024 08:23:37 -0400 Subject: [PATCH 5/6] DEE31B lower case synonym Changed 'Disorder' to 'disorder' in synonym for 31B --- src/ontology/mondo-edit.obo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 78c3249c41..c7f53d667d 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -553745,7 +553745,7 @@ subset: gard_rare {source="MONDO:GARD"} subset: nord_rare {source="MONDO:NORD"} subset: rare synonym: "developmental and epileptic encephalopathy 31B, autosomal recessive" EXACT [https://orcid.org/0000-0001-9310-0163, OMIM:620352] -synonym: "DNM1-encephalopathy and neurodevelopmental Disorder" BROAD [https://orcid.org/0000-0001-9310-0163] +synonym: "DNM1-encephalopathy and neurodevelopmental disorder" BROAD [https://orcid.org/0000-0001-9310-0163] xref: DOID:0070376 {source="MONDO:equivalentTo"} xref: MEDGEN:1841095 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:620352 {source="MONDO:equivalentTo"} From c7c1449fdd27e2917144d70f0b768a8430fe3270 Mon Sep 17 00:00:00 2001 From: Nicole Vasilevsky Date: Fri, 12 Jul 2024 15:15:29 -0700 Subject: [PATCH 6/6] add term tracker item --- src/ontology/mondo-edit.obo | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index c7f53d667d..49cbffa232 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -334889,6 +334889,7 @@ is_a: MONDO:0018614 {source="Orphanet:442835/btnt"} ! undetermined early-onset e is_a: MONDO:0100062 {source="DC-OMIM:616346", source="MONDO:Redundant", source="OMIM:616346"} ! developmental and epileptic encephalopathy relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/2972 {source="MONDO:mim2gene_medgen"} ! DNM1 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7641" xsd:anyURI [Term] id: MONDO:0014599