beta thalassemia - Githubissues

Mondo term (ID and Label) beta thalassemia http://purl.obolibrary.org/obo/MONDO_0019402

Suggested revision and reasons MONDO_0019402 has an exact synonym of thalassemia Major but there is also beta-thalassemia major MONDO:0016486 MONDO:0013517: has no definition, a comment that maybe it should be merged

is it desirable to have a term for beta thal caused by a mutaton in the locus control region?
I defer to thalassemia experts about if/how to capture beta+ and beta

@JadeHotchkiss @Khuthalamnika @scdodev @gmazandu

Could any of you weigh in on the question above? Thank you!

What is the question Nicole?

Sent from my iPhone

On 15 Jul 2020, at 00:15, Nicole Vasilevsky notifications@github.com wrote:

@JadeHotchkiss @Khuthalamnika @scdodev @gmazandu

Could any of you weigh in on the question above? Thank you!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

I think beta-thalassemia is categorized according to the severity there is major and intermediate. The Major is more severe than intermediate.

This can have a subgroup under beta-thalassemia or merged (they are more of the severity of the disease)

              beta-thalassemia major

              beta-thalassemia intermediate

There is also compound inheritance which is Sickle beta plus (Sβ+) thalassemia

Below is the definition for Sickle beta plus (Sβ+) thalassemia got from the expert (Prof Kwaku Ohene-Frempong)

A gene that limits beta-globin A production from the other parent (S/beta-plus thalassemia [SCD-Sbeta+] with reduced production of beta-A globin)

Sb+ thalassemia is an inherited condition. Hemoglobin S comes from one parent and Beta plus thalassemia comes from the other parent. Instead of appearing round (like donuts), red blood cells are somewhat small, pale, and misshapen.

Hope this helps

On Wed, Jul 15, 2020 at 4:01 AM khuthala mnika mnikakhuthala@gmail.com wrote:

What is the question Nicole?

Sent from my iPhone

On 15 Jul 2020, at 00:15, Nicole Vasilevsky notifications@github.com wrote:

@JadeHotchkiss https://github.com/JadeHotchkiss @Khuthalamnika https://github.com/Khuthalamnika @scdodev https://github.com/scdodev @gmazandu https://github.com/gmazandu

Could any of you weigh in on the question above? Thank you!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/monarch-initiative/mondo/issues/1756#issuecomment-658440468, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJQZFKHLS75MR6AG33GVO53R3TKJRANCNFSM4OVVNARQ .

-- Khuthala Mnika SADaCC Research Fellow

Division of Human Genetics, Department of Pathology

3.14 Wernher & Beit North Building

Faculty of Health Sciences , University of Cape Town

Telephone: 021 406 6501 <%2B27%20%280%2921%20406%206501>

Hi Nicole

I am not an expert in this, but liaised with the SCD experts to come up with this hierarchy for the Beta Thalassemia class in the SCDO: [image: image.png]

Beta Thalassemia Major (with exact synonym "Thalassemia Major") is a clinical phenotype of Beta Thalassemia.

Please bear in mind, the SCD community made changes to the terminology regarding beta plus and beta minus ( https://academic.oup.com/database/article/doi/10.1093/database/baz118/5626537 ). Here is the relevant excerpt from the paper: [image: image.png] I would suggest:

Remove "thalassemia Major" as an exact synonym from MONDO_0019402.
What you have for "beta-thalassemia HBB/LCRB" MONDO:0013517 is not defined. It is replaced in the SCDO by "Clinical Phenotype of Beta Thalassemia". Perhaps rather use our term?
What you have as "Thalassemia Minor" MONDO:0044210 seems to be equivalent to our "Beta Thalassemia Trait" (we have Beta Thalassemia Minor as an exact synonym). Probably best to make it a sibling of "beta-thalassemia major" MONDO:0016486.
Not sure where your "thalassemia, beta+, silent allele" fits in...perhaps it should be merged with " Thalassemia Minor"?

Best to get an expert to weigh in on this discussion!

Kind regards, Jade Hotchkiss

On Wed, Jul 15, 2020 at 4:32 AM Khuthalamnika notifications@github.com wrote:

I think beta-thalassemia is categorized according to the severity there is major and intermediate. The Major is more severe than intermediate.

This can have a subgroup under beta-thalassemia or merged (they are more of the severity of the disease)

beta-thalassemia major

beta-thalassemia intermediate

There is also compound inheritance which is Sickle beta plus (Sβ+) thalassemia

Below is the definition for Sickle beta plus (Sβ+) thalassemia got from the expert (Prof Kwaku Ohene-Frempong)

A gene that limits beta-globin A production from the other parent (S/beta-plus thalassemia [SCD-Sbeta+] with reduced production of beta-A globin)

Sb+ thalassemia is an inherited condition. Hemoglobin S comes from one parent and Beta plus thalassemia comes from the other parent. Instead of appearing round (like donuts), red blood cells are somewhat small, pale, and misshapen.

Hope this helps

On Wed, Jul 15, 2020 at 4:01 AM khuthala mnika mnikakhuthala@gmail.com wrote:

What is the question Nicole?

Sent from my iPhone

On 15 Jul 2020, at 00:15, Nicole Vasilevsky notifications@github.com wrote:

@JadeHotchkiss https://github.com/JadeHotchkiss @Khuthalamnika https://github.com/Khuthalamnika @scdodev https://github.com/scdodev @gmazandu https://github.com/gmazandu

Could any of you weigh in on the question above? Thank you!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/monarch-initiative/mondo/issues/1756#issuecomment-658440468 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AJQZFKHLS75MR6AG33GVO53R3TKJRANCNFSM4OVVNARQ

.

-- Khuthala Mnika SADaCC Research Fellow

Division of Human Genetics, Department of Pathology

3.14 Wernher & Beit North Building

Faculty of Health Sciences , University of Cape Town

Telephone: 021 406 6501 <%2B27%20%280%2921%20406%206501>

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/monarch-initiative/mondo/issues/1756#issuecomment-658509378, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGFSYXSQCWXTB5FEIUE75LDR3UIMFANCNFSM4OVVNARQ .

The current release of the SCDO can be viewed through WebProtege here: https://webprotege.stanford.edu/#projects/101e67d7-1e48-481a-9498-e585fadd4cbb/edit/Classes

On Wed, Jul 15, 2020 at 2:58 PM Jade Hotchkiss giant.plankton@gmail.com wrote:

Hi Nicole

I am not an expert in this, but liaised with the SCD experts to come up with this hierarchy for the Beta Thalassemia class in the SCDO: [image: image.png]

Beta Thalassemia Major (with exact synonym "Thalassemia Major") is a clinical phenotype of Beta Thalassemia.

Please bear in mind, the SCD community made changes to the terminology regarding beta plus and beta minus ( https://academic.oup.com/database/article/doi/10.1093/database/baz118/5626537 ). Here is the relevant excerpt from the paper: [image: image.png] I would suggest:

Remove "thalassemia Major" as an exact synonym from MONDO_0019402.

What you have for "beta-thalassemia HBB/LCRB" MONDO:0013517 is not defined. It is replaced in the SCDO by "Clinical Phenotype of Beta Thalassemia". Perhaps rather use our term?

What you have as "Thalassemia Minor" MONDO:0044210 seems to be equivalent to our "Beta Thalassemia Trait" (we have Beta Thalassemia Minor as an exact synonym). Probably best to make it a sibling of "beta-thalassemia major" MONDO:0016486.

Not sure where your "thalassemia, beta+, silent allele" fits in...perhaps it should be merged with " Thalassemia Minor"?

Best to get an expert to weigh in on this discussion!

Kind regards, Jade Hotchkiss

On Wed, Jul 15, 2020 at 4:32 AM Khuthalamnika notifications@github.com wrote:

I think beta-thalassemia is categorized according to the severity there is major and intermediate. The Major is more severe than intermediate.

This can have a subgroup under beta-thalassemia or merged (they are more of the severity of the disease)

beta-thalassemia major

beta-thalassemia intermediate

There is also compound inheritance which is Sickle beta plus (Sβ+) thalassemia

Below is the definition for Sickle beta plus (Sβ+) thalassemia got from the expert (Prof Kwaku Ohene-Frempong)

A gene that limits beta-globin A production from the other parent (S/beta-plus thalassemia [SCD-Sbeta+] with reduced production of beta-A globin)

Sb+ thalassemia is an inherited condition. Hemoglobin S comes from one parent and Beta plus thalassemia comes from the other parent. Instead of appearing round (like donuts), red blood cells are somewhat small, pale, and misshapen.

Hope this helps

On Wed, Jul 15, 2020 at 4:01 AM khuthala mnika mnikakhuthala@gmail.com wrote:

What is the question Nicole?

Sent from my iPhone

On 15 Jul 2020, at 00:15, Nicole Vasilevsky notifications@github.com wrote:

@JadeHotchkiss https://github.com/JadeHotchkiss @Khuthalamnika https://github.com/Khuthalamnika @scdodev https://github.com/scdodev @gmazandu https://github.com/gmazandu

Could any of you weigh in on the question above? Thank you!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/monarch-initiative/mondo/issues/1756#issuecomment-658440468 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AJQZFKHLS75MR6AG33GVO53R3TKJRANCNFSM4OVVNARQ

.

-- Khuthala Mnika SADaCC Research Fellow

Division of Human Genetics, Department of Pathology

3.14 Wernher & Beit North Building

Faculty of Health Sciences , University of Cape Town

Telephone: 021 406 6501 <%2B27%20%280%2921%20406%206501>

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/monarch-initiative/mondo/issues/1756#issuecomment-658509378, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGFSYXSQCWXTB5FEIUE75LDR3UIMFANCNFSM4OVVNARQ .

For your reference, "Clinical Phenotype of Beta Thalassemia" which I suggested you use from the SCDO has the ID SCDO:0000251.

On Wed, Jul 15, 2020 at 3:01 PM Jade Hotchkiss giant.plankton@gmail.com wrote:

The current release of the SCDO can be viewed through WebProtege here:

https://webprotege.stanford.edu/#projects/101e67d7-1e48-481a-9498-e585fadd4cbb/edit/Classes

On Wed, Jul 15, 2020 at 2:58 PM Jade Hotchkiss giant.plankton@gmail.com wrote:

Hi Nicole

I am not an expert in this, but liaised with the SCD experts to come up with this hierarchy for the Beta Thalassemia class in the SCDO: [image: image.png]

Beta Thalassemia Major (with exact synonym "Thalassemia Major") is a clinical phenotype of Beta Thalassemia.

Please bear in mind, the SCD community made changes to the terminology regarding beta plus and beta minus ( https://academic.oup.com/database/article/doi/10.1093/database/baz118/5626537 ). Here is the relevant excerpt from the paper: [image: image.png] I would suggest:

Remove "thalassemia Major" as an exact synonym from MONDO_0019402.

What you have for "beta-thalassemia HBB/LCRB" MONDO:0013517 is not defined. It is replaced in the SCDO by "Clinical Phenotype of Beta Thalassemia". Perhaps rather use our term?

What you have as "Thalassemia Minor" MONDO:0044210 seems to be equivalent to our "Beta Thalassemia Trait" (we have Beta Thalassemia Minor as an exact synonym). Probably best to make it a sibling of "beta-thalassemia major" MONDO:0016486.

Not sure where your "thalassemia, beta+, silent allele" fits in...perhaps it should be merged with " Thalassemia Minor"?

Best to get an expert to weigh in on this discussion!

Kind regards, Jade Hotchkiss

On Wed, Jul 15, 2020 at 4:32 AM Khuthalamnika notifications@github.com wrote:

I think beta-thalassemia is categorized according to the severity there is major and intermediate. The Major is more severe than intermediate.

This can have a subgroup under beta-thalassemia or merged (they are more of the severity of the disease)

beta-thalassemia major

beta-thalassemia intermediate

There is also compound inheritance which is Sickle beta plus (Sβ+) thalassemia

Below is the definition for Sickle beta plus (Sβ+) thalassemia got from the expert (Prof Kwaku Ohene-Frempong)

A gene that limits beta-globin A production from the other parent (S/beta-plus thalassemia [SCD-Sbeta+] with reduced production of beta-A globin)

Sb+ thalassemia is an inherited condition. Hemoglobin S comes from one parent and Beta plus thalassemia comes from the other parent. Instead of appearing round (like donuts), red blood cells are somewhat small, pale, and misshapen.

Hope this helps

On Wed, Jul 15, 2020 at 4:01 AM khuthala mnika mnikakhuthala@gmail.com wrote:

What is the question Nicole?

Sent from my iPhone

On 15 Jul 2020, at 00:15, Nicole Vasilevsky notifications@github.com wrote:

@JadeHotchkiss https://github.com/JadeHotchkiss @Khuthalamnika https://github.com/Khuthalamnika @scdodev https://github.com/scdodev @gmazandu https://github.com/gmazandu

Could any of you weigh in on the question above? Thank you!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/monarch-initiative/mondo/issues/1756#issuecomment-658440468 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AJQZFKHLS75MR6AG33GVO53R3TKJRANCNFSM4OVVNARQ

.

-- Khuthala Mnika SADaCC Research Fellow

Division of Human Genetics, Department of Pathology

3.14 Wernher & Beit North Building

Faculty of Health Sciences , University of Cape Town

Telephone: 021 406 6501 <%2B27%20%280%2921%20406%206501>

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/monarch-initiative/mondo/issues/1756#issuecomment-658509378, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGFSYXSQCWXTB5FEIUE75LDR3UIMFANCNFSM4OVVNARQ .

Thank you so much @JadeHotchkiss and @Khuthalamnika!

Action items: Note - Jade asked Ambroise Wonkam to review her suggestions below and he agreed with this course of action (via email).

[x] Remove "thalassemia Major" as an exact synonym from MONDO_0019402. -> I changed this to a related synonym
[x] What you have for "beta-thalassemia HBB/LCRB" MONDO:0013517 is not defined. It is replaced in the SCDO by "Clinical Phenotype of Beta Thalassemia". Perhaps rather use our term?
[x] xref SCDO:0000251 -> I added the text def from SCDO and xref'd SCDO and annotated it as an equivalent class

What you have as "Thalassemia Minor" MONDO:0044210 seems to be equivalent to our "Beta Thalassemia Trait" (we have Beta Thalassemia Minor as an exact synonym).

[x] Probably best to make it a sibling of "beta-thalassemia major" MONDO:0016486.
[ ] Not sure where your "thalassemia, beta+, silent allele" fits in...perhaps it should be merged with " Thalassemia Minor"?

monarch-initiative / mondo

beta thalassemia #1756