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monarch-initiative / mondo

Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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Bulk request for MONDO IDs #6882

Closed acoffey26 closed 8 months ago

acoffey26 commented 10 months ago

Hi, I have 9 diseases/disorders I would like to request a MONDO ID for based on gene curations performed using the ClinGen framework Mondo_bulk_submission_ILMN_17_Nov_2023.xlsx . I have filled in the template for bulk submissions as directed - see attached. Thank you in advance for your help! Best wishes, Alison

nicolevasilevsky commented 10 months ago

thank you @acoffey26. We'll review these soon and let you know if we have any questions.

nicolevasilevsky commented 9 months ago

@acoffey26 to confirm, you want to replace the definition for MONDO:0100061 'PRPS1 deficiency disorder'?

acoffey26 commented 9 months ago

Sorry should have deleted that row!

Please start from row 5.

Thank you,

Alison

@.***

Alison Coffey, PhD Senior Manager, Clinical Genomics, Illumina Services Laboratory, San Diego Medical Genomics Research 858.202.4500 @.**@.> www.illumina.comhttp://www.illumina.com/

@.***

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From: Nicole Vasilevsky @.> Sent: Tuesday, December 12, 2023 5:23 PM To: monarch-initiative/mondo @.> Cc: Coffey, Alison @.>; Mention @.> Subject: Re: [monarch-initiative/mondo] Bulk request for MONDO IDs (Issue #6882)

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nicolevasilevsky commented 9 months ago

sounds good, thanks!

nicolevasilevsky commented 9 months ago

@acoffey26 Is there a clingen working group URL that I can associate with these requests?

acoffey26 commented 9 months ago

We are requesting these for internal gene curations performed using the ClinGen framework but they will be presented to the Syndromic Disorders GCEP over time. Does that help? https://clinicalgenome.org/affiliation/40060/

We come under the “Other” group https://clinicalgenome.org/working-groups/clinical-domain/other/ @.***

Alison Coffey, PhD Senior Manager, Clinical Genomics, Illumina Services Laboratory, San Diego Medical Genomics Research 858.202.4500 @.**@.> www.illumina.comhttp://www.illumina.com/

@.***

@.https://www.facebook.com/illuminainc/ @. https://www.linkedin.com/company/illumina @.*** https://twitter.com/illumina

From: Nicole Vasilevsky @.> Sent: Tuesday, December 12, 2023 6:33 PM To: monarch-initiative/mondo @.> Cc: Coffey, Alison @.>; Mention @.> Subject: Re: [monarch-initiative/mondo] Bulk request for MONDO IDs (Issue #6882)

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@acoffey26https://urldefense.com/v3/__https:/github.com/acoffey26__;!!HrbR-XT-OQ!Q7M8aBpnB3edRSnFDbgVYiu0A-rIf2tSw3-gy2iDM0_3u-QcA1fUkjlmuF_3zzhhLRiKt26pA--luQt3qsoMeEmA2A$ Is there a clingen working group URL that I can associate with these requests?

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nicolevasilevsky commented 9 months ago

perfect, thanks!

nicolevasilevsky commented 9 months ago

@acoffey26 Another question: The spreadshseet specifies that MONDO:0010011 schizencephaly should be a child of COL4A1-related disorders but I don't see evidence of COL4A1 being involved in this term on the OMIM page: https://omim.org/entry/269160

Is this a mistake or if not, could you please provide evidence of that?

Thank you!

nicolevasilevsky commented 9 months ago

@acoffey26 There is a request for MONDO:0009974 'familial hemophagocytic lymphohistiocytosis type 1' to be a child of FHL1-related myopathy, but this does not seem correct to me. Could you confirm and provide evidence? Thanks!

and MONDO:0010680 'X-linked Emery-Dreifuss muscular dystrophy' is also requested to be a child of FHL1-related myopathy, but in Mondo, the gene involved is EMD, not FHL1.

nicolevasilevsky commented 9 months ago

@acoffey26 for KIF7-related ciliopathies, this ID was added to be a child, but this is not a valid ID: MONDO:00111778

acoffey26 commented 8 months ago

Hi,

Thank you for your email re a problem with ID MONDO:00111778.

Please accept my apologies, this was a typo on our part and the ID should be MONDO:0011778.

Please let me know if you have any further questions re this ID,

Thank you for your help,

Best wishes,

Alison

@.***

Alison Coffey, PhD Senior Manager, Clinical Genomics, Illumina Services Laboratory, San Diego Medical Genomics Research 858.202.4500 @.**@.> www.illumina.comhttp://www.illumina.com/

@.***

@.https://www.facebook.com/illuminainc/ @. https://www.linkedin.com/company/illumina @.*** https://twitter.com/illumina

From: Nicole Vasilevsky @.> Sent: Thursday, December 14, 2023 7:05 PM To: monarch-initiative/mondo @.> Cc: Coffey, Alison @.>; Mention @.> Subject: Re: [monarch-initiative/mondo] Bulk request for MONDO IDs (Issue #6882)

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acoffey26 commented 8 months ago

Hi,

Thank you for your enquiry re the inclusion of MONDO:0009974 'familial hemophagocytic lymphohistiocytosis type 1' to be a child of FHL1-related myopathy.

We reviewed our request and agree that this is not a suitable child term for FHL1-related myopathy so would ike to revise our request and remove this term. The edited child terms for FHL1-related myopathy are now suggested as:

MONDO:0010401|MONDO:0010415|MONDO:0010414|MONDO:0010292|MONDO:0010400|MONDO:0010680

Many thanks for your help,

Best wishes,

Alison

acoffey26 commented 8 months ago

Dear Nicole,

Thank you for your email and enquiry re MONDO:0010011 schizencephaly being a child of COL4A1-related disorders.

We listed schizencephaly as a child term based on a reference to schizencephaly in OMIM and a publication listed in GeneReviews.

If you open up the clinical synopsis page in OMIM for the disorders associated with COL4A1 ( https://www.omim.org/clinicalSynopsis/table?mimNumber=180000,614519,611773,175780,618564), schizencephaly is listed under BRAIN SMALL VESSEL DISEASE 1 WITH OR WITHOUT OCULAR ANOMALIES; BSVD1 in the section on Central Nervous System.

It is also discussed in PMID: 23225343 (see attached) which describes the finding of variants in COL4A1 in individuals with schizencephaly and suggests the expansion of phenotypic spectrum of COL4A1-related disorders to include schizencephaly.

I hope this provides enough evidence for the inclusion of schizencephaly as a child term, please let me know if you have any further questions and we will be happy to help.

Thank you for your help and careful review,

Best wishes,

Alison

@.***

Alison Coffey, PhD Senior Manager, Clinical Genomics, Illumina Services Laboratory, San Diego Medical Genomics Research 858.202.4500 @.**@.> www.illumina.comhttp://www.illumina.com/

@.***

@.https://www.facebook.com/illuminainc/ @. https://www.linkedin.com/company/illumina @.*** https://twitter.com/illumina

From: Nicole Vasilevsky @.> Sent: Thursday, December 14, 2023 6:55 PM To: monarch-initiative/mondo @.> Cc: Coffey, Alison @.>; Mention @.> Subject: Re: [monarch-initiative/mondo] Bulk request for MONDO IDs (Issue #6882)

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@acoffey26https://urldefense.com/v3/__https:/github.com/acoffey26__;!!HrbR-XT-OQ!XumveqRmJfrjwprMxk0kG4-Jv_EppH8lAmnqhVtsc20r9p_H2FvbU5Pe0-xPpsgBwn4HI428HQ2E86-byVKdnk6YoQ$ Another question: The spreadshseet specifies that MONDO:0010011 schizencephaly should be a child of COL4A1-related disorders but I don't see evidence of COL4A1 being involved in this term on the OMIM page: https://omim.org/entry/269160https://urldefense.com/v3/__https:/omim.org/entry/269160__;!!HrbR-XT-OQ!XumveqRmJfrjwprMxk0kG4-Jv_EppH8lAmnqhVtsc20r9p_H2FvbU5Pe0-xPpsgBwn4HI428HQ2E86-byVILLMK4OQ$

Is this a mistake or if not, could you please provide evidence of that?

Thank you!

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nicolevasilevsky commented 8 months ago

Hi, Thank you for your enquiry re the inclusion of MONDO:0009974 'familial hemophagocytic lymphohistiocytosis type 1' to be a child of FHL1-related myopathy. We reviewed our request and agree that this is not a suitable child term for FHL1-related myopathy so would ike to revise our request and remove this term. The edited child terms for FHL1-related myopathy are now suggested as: - X-linked myopathy with postural muscle atrophy - myopathy, reducing body, X-linked, childhood-onset - myopathy, reducing body, X-linked, early-onset, severe - Uruguay Faciocardiomusculoskeletal syndrome - X-linked scapuloperoneal muscular dystrophy - X-linked Emery-Dreifuss muscular dystrophy MONDO:0010401|MONDO:0010415|MONDO:0010414|MONDO:0010292|MONDO:0010400|MONDO:0010680 Many thanks for your help, Best wishes, Alison

Hi @acoffey26 According to OMIM, the gene EMD is implicated in 'X-linked Emery-Dreifuss muscular dystrophy'. Only this class ('X-linked myopathy with postural muscle atrophy') is stated to have an FHL1 variation.

nicolevasilevsky commented 8 months ago

I added MONDO:0018829 'familial schizencephaly' as a child of 'COL4A1-related disorder'

nicolevasilevsky commented 8 months ago

I revised 'COL4A1-related disorder' to be a child of 'hereditary disease' and removed the parent 'vascular disorder' because the vascular phenotypes seem to be only a component of this disease and not every child term is a vascular disorder. This was causing 'familial schizencephaly' to be incorrectly inferred as a child of 'neurovascular disorder'.

Please let me know if I am incorrect, thanks!

nicolevasilevsky commented 8 months ago

If this is closed and there are still changes needed, please feel free to reopen this ticket, thanks!