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Mondo Disease Ontology
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[NTR]GATA1-Related X-Linked Cytopenia #1018

Closed miajsullivan closed 4 years ago

miajsullivan commented 4 years ago

Preferred term label: GATA1-Related X-Linked Cytopenia

Synonyms: GATA1-Related Cytopenia

Definition: X-Linked cytopenia characterized by anemia and/or thrombocytopenia. Additional features including platelet dysfunction, dyserythropoesis, mild beta-thalassemia, neutropenia, or congenital erythropoetic porphyria may be present. These GATA1 variants are germline as opposed to GATA1 variants seen in leukemia.

PMID: 20301538 PMID: 28895773 PMID: 18930124

currently there are several MONDO ID's that are not fully encompassing:

beta-thalassemia x-linked thrombocytopenia syndrome MONDO ID 0010745 Thrombocytopenia x - linked with or without dyserythropoetic anemia MONDO ID 0010308 x-linked dyserythropoetic anemia with abnormal platelets and neutropenia MONDO ID 0010444 thrombocytopenia with congenital dyserythropoetic anemia MONDO ID 0019031

Parent term: hematologic disease?

Your nano-attribution (ORCID): I am unsure what this is

This suggestion comes from the ClinGen Hemostasis/Thrombosis gene curation expert panel.

nicolevasilevsky commented 4 years ago

@miajsullivan is there a URL for the ClinGen Hemostasis/Thrombosis gene curation expert panel?

This is ORCID: https://orcid.org/

miajsullivan commented 4 years ago

ORCID: 0000-0001-6964-7302

URL for the ClinGen Hemostasis/Thrombosis gene Curation expert panel: https://clinicalgenome.org/affiliation/40028/

nicolevasilevsky commented 4 years ago

note to self - add subclass Of assertion: 'disease has basis in dysfunction of' some GATA1

miajsullivan commented 4 years ago

When is the January release? I assume the MONDO ID is not active until the release, correct?

nicolevasilevsky commented 4 years ago

@cmungall will you be doing a Mondo release soon?

miajsullivan commented 4 years ago

Sorry to be bothersome, I am waiting for this MONDO ID to be published in order to curate the gene for a ClinGen panel. Is there any estimate on when the January release will happen? Thank you in advance.

nicolevasilevsky commented 4 years ago

Sorry for the delay @miajsullivan, I believe the next release will be at the end of the month.

nicolevasilevsky commented 4 years ago

@miajsullivan a question came up about this term - what is the relationship of this term to these four diseases in OMIM:

Do you think this new term is a superclass of these?

miajsullivan commented 4 years ago

This new term would be the superclass of the following three diseases:

Thank you, Mia

From: Nicole Vasilevsky notifications@github.com Sent: Tuesday, January 28, 2020 3:12 PM To: monarch-initiative/mondo mondo@noreply.github.com Cc: Mia Sullivan MSullivan@Versiti.org; Mention mention@noreply.github.com Subject: Re: [monarch-initiative/mondo] [NTR]GATA1-Related X-Linked Cytopenia (#1018)

Caution: This Email originated from outside of Versiti.

@miajsullivanhttps://github.com/miajsullivan a question came up about this term - what is the relationship of this term to these four diseases in OMIM:

Do you think this new term is a superclass of these?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/monarch-initiative/mondo/issues/1018?email_source=notifications&email_token=AN6GAJGU4WZKHDXG5INE6ETRACNQPA5CNFSM4JU5VC4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKE5F7Q#issuecomment-579457790, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AN6GAJAB2BDTWNFVBXEUHB3RACNQPANCNFSM4JU5VC4A.

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nicolevasilevsky commented 4 years ago

Thanks for your quick response! I'll implement this change

courtneythaxton commented 4 years ago

@nicolevasilevsky Do you have an estimate of the release for this information?

nicolevasilevsky commented 4 years ago

This should be available in the February release

courtneythaxton commented 4 years ago

@nicolevasilevsky Thanks! will that be at the end of the month, or in the middle? I have noticed you sometimes have fortnight (every two week) releases.

nicolevasilevsky commented 4 years ago

@cmungall usually releases at the beginning of each month

courtneythaxton commented 4 years ago

@nicolevasilevsky Again, thank you for this information and for your help!

nicolevasilevsky commented 4 years ago

I just released it IS february. So this will probably be available in the March release (I was thinking it was still January!)

miajsullivan commented 4 years ago

this is not active as a MONDO ID yet. W?ill this not go live until April's release?

Mia Sullivan

From: Nicole Vasilevsky notifications@github.com Sent: Friday, April 3, 2020 12:19 PM To: monarch-initiative/mondo Cc: Mia Sullivan; Mention Subject: Re: [monarch-initiative/mondo] [NTR]GATA1-Related X-Linked Cytopenia (#1018)

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Closed #1018https://github.com/monarch-initiative/mondo/issues/1018 via #1037https://github.com/monarch-initiative/mondo/pull/1037.

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nicolevasilevsky commented 4 years ago

Hi @miajsullivan this was added to Mondo and the release was done today, you should now see it in the latest release file.

MONDO:0100089 'GATA1-Related X-Linked Cytopenia'

Sorry for the delay! Let me know if you need anything else.

miajsullivan commented 4 years ago

Nicole,

Sorry if you are the wrong person to pursue this with. I am trying to start a curation for my ClinGen group - upon opening a new Gene-Disease caution in prompts you to add the Gene name and MONDO ID. You can either look it up or add the MONDO ID (if you know it). I have tried both ways and it is not accepting the MONDO ID if I put the number in and if I look up by gene-disease, it is not listed. I've attached a screen shot for you.

Mia ?

From: Nicole Vasilevsky notifications@github.com Sent: Monday, April 6, 2020 5:00 PM To: monarch-initiative/mondo Cc: Mia Sullivan; Mention Subject: Re: [monarch-initiative/mondo] [NTR]GATA1-Related X-Linked Cytopenia (#1018)

Caution: This Email originated from outside of Versiti.

Hi @miajsullivanhttps://github.com/miajsullivan this was added to Mondo and the release was done today, you should now see it in the latest release file.

MONDO:0100089 'GATA1-Related X-Linked Cytopenia'

Sorry for the delay! Let me know if you need anything else.

- You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/monarch-initiative/mondo/issues/1018#issuecomment-610059689, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AN6GAJGQGX3P5ITZYNDJXZDRLJGH7ANCNFSM4JU5VC4A.

**** CONFIDENTIALITY NOTICE **** This transmission may contain confidential or protected information. If you have received this transmission in error, or are not the intended recipient, you are hereby notified that any review, dissemination, distribution, or duplication of this communication is strictly prohibited. Please do not forward or reply to this message. Immediately delete this message and all attachments and send a separate notice to Privacy@Versiti.org.

courtneythaxton commented 4 years ago

Hi Mia,

I can help with this issue. Likely this is because the ontology lookup system (OLShttps://www.ebi.ac.uk/ols/ontologies/mondo) hosted by EMBL-EBI has not updated the MonDO ID yet. It can take a few days after a release for them to update the records and changes.

If by the end of this week you do not see the update in OLS, then I would contact them at ols-support@ebi.ac.uk to indicate the need to update based on the new release.

I have had to do this a couple of times. It happens very infrequently, but is a possibility.

I hope this helps!

Courtney

Courtney Thaxton, Ph.D. Director of the ClinGen- Affiliated UNC Biocuration and Coordination Core Assistant Professor- Research Dept. of Genetics 120 Mason Farm Road 5100 B, Genetic Medicine Building CB#7264 University of North Carolina, Chapel Hill, NC 27599 919-966-9562

From: miajsullivan notifications@github.com<mailto:notifications@github.com> Reply-To: monarch-initiative/mondo reply@reply.github.com<mailto:reply@reply.github.com> Date: Tuesday, April 7, 2020 at 9:46 AM To: monarch-initiative/mondo mondo@noreply.github.com<mailto:mondo@noreply.github.com> Cc: Courtney Thaxton courtney_thaxton@med.unc.edu<mailto:courtney_thaxton@med.unc.edu>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [monarch-initiative/mondo] [NTR]GATA1-Related X-Linked Cytopenia (#1018)

Nicole,

Sorry if you are the wrong person to pursue this with. I am trying to start a curation for my ClinGen group - upon opening a new Gene-Disease caution in prompts you to add the Gene name and MONDO ID. You can either look it up or add the MONDO ID (if you know it). I have tried both ways and it is not accepting the MONDO ID if I put the number in and if I look up by gene-disease, it is not listed. I've attached a screen shot for you.

Mia ?

From: Nicole Vasilevsky notifications@github.com<mailto:notifications@github.com> Sent: Monday, April 6, 2020 5:00 PM To: monarch-initiative/mondo Cc: Mia Sullivan; Mention Subject: Re: [monarch-initiative/mondo] [NTR]GATA1-Related X-Linked Cytopenia (#1018)

Caution: This Email originated from outside of Versiti.

Hi @miajsullivanhttps://github.com/miajsullivan this was added to Mondo and the release was done today, you should now see it in the latest release file.

MONDO:0100089 'GATA1-Related X-Linked Cytopenia'

Sorry for the delay! Let me know if you need anything else.

- You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/monarch-initiative/mondo/issues/1018#issuecomment-610059689, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AN6GAJGQGX3P5ITZYNDJXZDRLJGH7ANCNFSM4JU5VC4A.

**** CONFIDENTIALITY NOTICE **** This transmission may contain confidential or protected information. If you have received this transmission in error, or are not the intended recipient, you are hereby notified that any review, dissemination, distribution, or duplication of this communication is strictly prohibited. Please do not forward or reply to this message. Immediately delete this message and all attachments and send a separate notice to Privacy@Versiti.orgmailto:Privacy@Versiti.org.

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miajsullivan commented 4 years ago

​great! thank you much.

Mia

From: courtneythaxton notifications@github.com Sent: Tuesday, April 7, 2020 8:51 AM To: monarch-initiative/mondo Cc: Mia Sullivan; Mention Subject: Re: [monarch-initiative/mondo] [NTR]GATA1-Related X-Linked Cytopenia (#1018)

Hi Mia,

I can help with this issue. Likely this is because the ontology lookup system (OLShttps://www.ebi.ac.uk/ols/ontologies/mondo) hosted by EMBL-EBI has not updated the MonDO ID yet. It can take a few days after a release for them to update the records and changes.

If by the end of this week you do not see the update in OLS, then I would contact them at ols-support@ebi.ac.uk to indicate the need to update based on the new release.

I have had to do this a couple of times. It happens very infrequently, but is a possibility.

I hope this helps!

Courtney

Courtney Thaxton, Ph.D. Director of the ClinGen- Affiliated UNC Biocuration and Coordination Core Assistant Professor- Research Dept. of Genetics 120 Mason Farm Road 5100 B, Genetic Medicine Building CB#7264 University of North Carolina, Chapel Hill, NC 27599 919-966-9562

From: miajsullivan notifications@github.com<mailto:notifications@github.com> Reply-To: monarch-initiative/mondo reply@reply.github.com<mailto:reply@reply.github.com> Date: Tuesday, April 7, 2020 at 9:46 AM To: monarch-initiative/mondo mondo@noreply.github.com<mailto:mondo@noreply.github.com> Cc: Courtney Thaxton courtney_thaxton@med.unc.edu<mailto:courtney_thaxton@med.unc.edu>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [monarch-initiative/mondo] [NTR]GATA1-Related X-Linked Cytopenia (#1018)

Nicole,

Sorry if you are the wrong person to pursue this with. I am trying to start a curation for my ClinGen group - upon opening a new Gene-Disease caution in prompts you to add the Gene name and MONDO ID. You can either look it up or add the MONDO ID (if you know it). I have tried both ways and it is not accepting the MONDO ID if I put the number in and if I look up by gene-disease, it is not listed. I've attached a screen shot for you.

Mia ?

From: Nicole Vasilevsky notifications@github.com<mailto:notifications@github.com> Sent: Monday, April 6, 2020 5:00 PM To: monarch-initiative/mondo Cc: Mia Sullivan; Mention Subject: Re: [monarch-initiative/mondo] [NTR]GATA1-Related X-Linked Cytopenia (#1018)

Caution: This Email originated from outside of Versiti.

Hi @miajsullivanhttps://github.com/miajsullivan this was added to Mondo and the release was done today, you should now see it in the latest release file.

MONDO:0100089 'GATA1-Related X-Linked Cytopenia'

Sorry for the delay! Let me know if you need anything else.

- You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/monarch-initiative/mondo/issues/1018#issuecomment-610059689, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AN6GAJGQGX3P5ITZYNDJXZDRLJGH7ANCNFSM4JU5VC4A.

**** CONFIDENTIALITY NOTICE **** This transmission may contain confidential or protected information. If you have received this transmission in error, or are not the intended recipient, you are hereby notified that any review, dissemination, distribution, or duplication of this communication is strictly prohibited. Please do not forward or reply to this message. Immediately delete this message and all attachments and send a separate notice to Privacy@Versiti.orgmailto:Privacy@Versiti.org.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/monarch-initiative/mondo/issues/1018#issuecomment-610396524, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHYF4VJ3YRMSNGGNOV6XMKDRLMVFFANCNFSM4JU5VC4A.

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