Ready for re-review: add new epilepsy terms/variable age and neonatal/infantile epilepsy syndrome terms #8555

nicolevasilevsky · 2025-01-10T16:43:42Z

… syndrome’

…y syndrome'

and add syn

sabrinatoro

@nicolevasilevsky Please see my comments in line.
There are a few parentage that I disagree with or that I don't understand.

sabrinatoro · 2025-01-14T13:40:39Z

src/ontology/mondo-edit.obo

+[Term]
+id: MONDO:0800487
+name: variable-age onset idiopathic generalized epilepsy syndrome
+def: "Any idiopathic generalized epilepsy syndrome that has a variable-age onset." [https://orcid.org/0000-0001-5208-3432]


Based on this definition, this term should be a child of "idiopathic generalized epilepsy", which it currently doesn't have.

I added this parent.

I have some questions about this relationship, but I'll bring it up at the workshop on Friday

sabrinatoro · 2025-01-14T13:48:58Z

src/ontology/mondo-edit.obo

+name: variable-age onset focal epilepsy syndrome
+def: "An epilepsy syndrome characterized by focal seizures where age at seizure onset varies." [https://www.epilepsydiagnosis.org/syndrome/epilepsy-syndrome-groupoverview.html]
+synonym: "VAOFAS" EXACT [https://www.epilepsydiagnosis.org/syndrome/epilepsy-syndrome-groupoverview.html]
+is_a: MONDO:0100036 {source="https://www.epilepsydiagnosis.org/syndrome/epilepsy-syndrome-groupoverview.html"} ! variable-age onset epilepsy syndrome


BAsed on the definition, shouldn't this term also be a "focal epilepsy"?

I added this parent but I would like to discuss this further at the workshop.

But thinking about this- it makes sense because we have:
epilepsy
-epilepsy syndrome

so it makes sense to have:
-more specific epilepsy
--more specific epilepsy syndrome

eg

-focal epilepsy
--variable-age focal epilepsy syndrome

I created a slide about this to the workshop so we can discuss further and reassure ourselves

sabrinatoro · 2025-01-14T13:50:27Z

src/ontology/mondo-edit.obo

+[Term]
+id: MONDO:0800493
+name: familial mesial temporal lobe epilepsy
+def: "A focal epilepsy syndrome where the age at onset is typically in adolescence or adulthood. Affected individuals have focal aware seizures with mesial temporal lobe features, especially prominent déjà vu. Most patients have a normal MRI, and seizures respond to treatment. A subgroup is recognised that have antecedent febrile seizures, hippocampal atrophy, and drug resistant seizures. Direct questioning of relatives may be required to identify this familial epilepsy syndrome, as many individuals consider their déjà vu experiences as mild and they may not have been diagnosed as seizures." [https://www.epilepsydiagnosis.org/syndrome/other-familial-temporal-lobe-overview.html]


if the definition is "a focal epilepsy syndrome where (...)", then "focal epilepsy syndrome" must be a parent.

we don't have a term called 'focal epilepsy syndrome' but I added 'focal epilepsy' as a parent

sabrinatoro · 2025-01-14T13:51:34Z

src/ontology/mondo-edit.obo

+id: MONDO:0800494
+name: variable-age onset combined generalized and focal epilepsy syndrome
+def: "An epilepsy syndrome characterized by a combined generalized and focal epilepsy syndromes where age at seizure onset varies." [https://www.epilepsydiagnosis.org/syndrome/epilepsy-syndrome-groupoverview.html]
+is_a: MONDO:0100036 {source="https://www.epilepsydiagnosis.org/syndrome/epilepsy-syndrome-groupoverview.html"} ! variable-age onset epilepsy syndrome


based on the definition, should this also be a "combined generalized and focal epilepsy"?

I added this parent

sabrinatoro · 2025-01-14T13:52:57Z

src/ontology/mondo-edit.obo

+[Term]
+id: MONDO:0800495
+name: variable-age epilepsy syndrome with developmental and/or epileptic encephalopathy or progressive neurological deterioration
+def: "An epilepsy syndrome characterized by seizures along with developmental and/or epileptic encephalopathy or progressive neurological deterioration where age at seizure onset varies." [https://www.epilepsydiagnosis.org/syndrome/epilepsy-syndrome-groupoverview.html]


I don't like the "and/or", but I guess this is what people call it. So that's ok

sabrinatoro · 2025-01-14T14:03:13Z

src/ontology/mondo-edit.obo

 relationship: disease_has_feature HP:0002121 ! Generalized non-motor (absence) seizure
 relationship: disease_has_feature HP:0011147 ! Typical absence seizure
+relationship: excluded_subClassOf MONDO:0850093 {source="DOID:0050708", source="https://orcid.org/0000-0001-5208-3432"} ! absence epilepsy


based on the name and the definition, it seems weird to exclude this parent.
What is the reasoning behind this?

we are going to obsolete this term (see #8468)

sabrinatoro · 2025-01-14T14:07:21Z

src/ontology/mondo-edit.obo

 def: "An epilepsy syndrome that has an onset during variable ages and stages of life." [https://www.epilepsydiagnosis.org/syndrome/ffevf-overview.html#]
-synonym: "variable age at onset electroclinical syndrome" BROAD []
+synonym: "variable age at onset electroclinical syndrome" BROAD [DOID:0050706]


I am questioning the synonym scope. Why is it "broad"?
(note, I don't know anything about epilepsy :-) )

it was broad before, I just added the xref (from what it looks like). But this term is equiv to DOID:0050706, so I think the synonym should be exact - I updated that.

But in the workshop, we decided to obsolete the term 'electroclinical syndrome' (see #8450 and see #8561).

What I think should be done here is to create a new term called 'variable age onset epilepsy syndrome' that is distinct from this class. And we should obsolete this this class, per the decision to obsolete the electroclinical syndrome terms.

sabrinatoro · 2025-01-14T14:09:22Z

src/ontology/mondo-edit.obo

@@ -538135,7 +538156,7 @@ def: "An epilepsy syndrome associated with infantile period seizures, complete o
 subset: gard_rare {source="MONDO:GARD"}
 subset: rare
 synonym: "SeLFNIE" EXACT ABBREVIATION [https://www.epilepsydiagnosis.org/syndrome/nei-overview.html]
-is_a: MONDO:0100022 {source="https://clinicalgenome.org/affiliation/40005/"} ! neonatal/infantile epilepsy syndrome


I think we should keep this parent. It is more high-level, but it was requested by a ClinGen expert panel, so it is good to keep even if it is redundant.

sabrinatoro · 2025-01-14T14:10:56Z

src/ontology/mondo-edit.obo

-is_a: MONDO:0100030 {source="https://orcid.org/0000-0001-8486-0558"} ! adolescent/adult-onset epilepsy syndrome
-is_a: MONDO:0850093 {source="https://orcid.org/0000-0001-5208-3432"} ! absence epilepsy
+is_a: MONDO:0800487 {source="https://www.epilepsydiagnosis.org/syndrome/jae-overview.html"} ! variable-age onset idiopathic generalized epilepsy syndrome
+relationship: excluded_subClassOf MONDO:0100030 {source="https://orcid.org/0000-0001-8486-0558"} ! adolescent/adult-onset epilepsy syndrome


make sure to add your orcid to indicate that you have reviewed and ok-ed this excluded SC. (I know, it is a bit weird)

sabrinatoro · 2025-01-14T14:13:34Z

src/ontology/mondo-edit.obo

-is_a: MONDO:0850093 {source="https://orcid.org/0000-0001-5208-3432"} ! absence epilepsy
+is_a: MONDO:0800487 {source="https://www.epilepsydiagnosis.org/syndrome/jae-overview.html"} ! variable-age onset idiopathic generalized epilepsy syndrome
+relationship: excluded_subClassOf MONDO:0100030 {source="https://orcid.org/0000-0001-8486-0558"} ! adolescent/adult-onset epilepsy syndrome
+relationship: excluded_subClassOf MONDO:0850093 {source="https://orcid.org/0000-0001-5208-3432"} ! absence epilepsy


The term is 'juvenile absence epilepsy'. It seems weird to exclude the "absence epilepsy" parent. Also, the definition includes "absence seizure". What is the rational?

we will obsolete 'absence epilepsy'

sabrinatoro · 2025-01-14T14:37:18Z

@nicolevasilevsky I just saw (and approved and merged) the PR about obsoleting "absence epilepsy".
Some of my comments/requests are therefore mute. Please ignore them.

…drome'

…epsy syndrome'

sabrinatoro

I think it is ok.
I am approving and merging. There are still some changes that might be done after more experts feedback, but it is ok for not.

WIP: add new epilepsy terms

ca491ac

close #8455

nicolevasilevsky requested review from sabrinatoro and twhetzel as code owners January 10, 2025 16:43

nicolevasilevsky marked this pull request as draft January 10, 2025 16:44

nicolevasilevsky added 21 commits January 10, 2025 08:59

‘variable age onset epilepsy’ should be reclassified under ‘epilepsy…

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… syndrome’

fix trailing whitespace

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reclassify 'epilepsy of infancy with migrating focal seizures'

c793a70

reclassify West syndrome

c512704

reclassify Dravet syndrome

11ef014

reclsasify terms under 'neonatal/infantile-onset self-limited epileps…

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…y syndrome'

add abbreviation synonym type

86da645

revise syn scope

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relabel term

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add dbxref to def

2ff67f0

reclassify 'juvenile myoclonic epilepsy'

d9f39ac

fix qc

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reclassify terms

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exclude from QC

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reclassify terms

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add term tracker item

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reclassify term

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add ORCID

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exclude superclass from reflex epilepsy

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revise labels

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reclassify 'epilepsy with generalized tonic-clonic seizures'

37bcda1

and add syn

nicolevasilevsky marked this pull request as ready for review January 10, 2025 23:18

nicolevasilevsky changed the title ~~WIP: add new epilepsy terms~~ Ready for review: add new epilepsy terms Jan 10, 2025

nicolevasilevsky assigned sabrinatoro Jan 10, 2025

nicolevasilevsky changed the title ~~Ready for review: add new epilepsy terms~~ Ready for review: add new epilepsy terms/variable age and neonatal/infantile epilepsy syndrome terms Jan 13, 2025

sabrinatoro requested changes Jan 14, 2025

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sabrinatoro assigned nicolevasilevsky and unassigned sabrinatoro Jan 14, 2025

revise excluded sublassOf

5c76dfe

nicolevasilevsky added 7 commits January 14, 2025 06:38

update syn and superclass

0b40273

add orcid

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add parent to 'variable-age onset idiopathic generalized epilepsy syn…

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…drome'

add parent to 'variable-age onset focal epilepsy syndrome'

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Merge branch 'master' into issue-8455

12f31d4

add parent to familial mesial temporal lobe epilepsy

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add parent to 'variable-age onset combined generalized and focal epil…

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…epsy syndrome'

nicolevasilevsky changed the title ~~Ready for review: add new epilepsy terms/variable age and neonatal/infantile epilepsy syndrome terms~~ Ready for re-review: add new epilepsy terms/variable age and neonatal/infantile epilepsy syndrome terms Jan 14, 2025

nicolevasilevsky assigned sabrinatoro and unassigned nicolevasilevsky Jan 14, 2025

nicolevasilevsky added 2 commits January 14, 2025 08:16

exclude QC

bfca641

revise superclasses for 'juvenile absence epilepsy'

036358b

sabrinatoro approved these changes Jan 14, 2025

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sabrinatoro merged commit 1b77858 into master Jan 14, 2025
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sabrinatoro deleted the issue-8455 branch January 14, 2025 19:32

nicolevasilevsky restored the issue-8455 branch January 14, 2025 20:02

nicolevasilevsky mentioned this pull request Jan 14, 2025

Request for new term: variable-age onset epilepsy syndrome #8574

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nicolevasilevsky added the epilepsy label Jan 17, 2025

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Ready for re-review: add new epilepsy terms/variable age and neonatal/infantile epilepsy syndrome terms #8555

Ready for re-review: add new epilepsy terms/variable age and neonatal/infantile epilepsy syndrome terms #8555

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Ready for re-review: add new epilepsy terms/variable age and neonatal/infantile epilepsy syndrome terms #8555

Ready for re-review: add new epilepsy terms/variable age and neonatal/infantile epilepsy syndrome terms #8555

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