search

monarch-initiative / mondo

Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
Creative Commons Attribution 4.0 International
233 stars 53 forks source link

pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1 (MONDO:0013878) #1548

Closed ValWood closed 4 years ago

ValWood commented 4 years ago

Term pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1 (MONDO:0013878)

def Any pulmonary fibrosis and/or bone marrow failure, Telomere-related in which the cause of the disease is a mutation in the TERT gene.

question Is this a disease? It looks like the symptoms of dyskeratosis congenita, autosomal dominant 1 (MONDO:0007485) A dyskeratosis congenita that has_material_basis_in an autosomal recessive mutation of TERT on chromosome 5p15.33.

A disease which is already a descendant of dyskeratosis congenita (MONDO:0015780) Dyskeratosis congenita (DC) is a rare ectodermal dysplasia that often presents with the classic triad of nail dysplasia, skin pigmentary changes, and oral leukoplakia associated with a high risk of bone marrow failure (BMF) and cancer.

nicolevasilevsky commented 4 years ago

Hi @ValWood My apologies, I don't understand the question. Would it be possible to reorganize the comments to add some headers to your comments, like I did above? (Term, def, question). That would be super helpful! :)

For MONDO:0013878, in the first part, I believe you are asking if this is a valid disease and if we should consider obsoleting it. I agree that this seems like a collection of phenotypes. Although sometimes diseases are named as such, we see this a lot in Mondo.

@cmungall could you advise? Note MONDO:0013878 comes from OMIM: OMIM:614742

ValWood commented 4 years ago

According to this PFBMFT1 https://www.ncbi.nlm.nih.gov/gtr/conditions/C3553617/ it isn't a TERT specific thing

nicolevasilevsky commented 4 years ago

The OMIM record says it is due to a mutation in the TERT gene: https://www.omim.org/entry/614742 I just skimmed it, but it looks like there are references supporting that.

nicolevasilevsky commented 4 years ago

The NCBI page says TERT is an associated gene: image

Is this the question? I am still a bit unclear - apologies!

ValWood commented 4 years ago

It seems that PFBMFT1 is a less severe later onset thing.

But the definition of pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1 (MONDO:0013878) isn't necessary and sufficient to differentiate it from

autosomal recessive dyskeratosis congenita 4 (MONDO:0027353) A dyskeratosis congenita that has_material_basis_in an autosomal recessive mutation of TERT on chromosome 5p15.33.

which is also TERT, and also has a symptom of "high risk of bone marrow failure (BMF) and cancer." see the parent term dyskeratosis congenita (MONDO:0015780), for the BMF part it is a feature of this class.

I don't think MONDO:0027353 is the same as PFBMFT1 but based on the current defs it is difficult to establish this.

ValWood commented 4 years ago

Oh I see what is happening now! When I cut and paste a query I usually start with the term, and the term definition. I cut and paste from the PomBAse page. Unfortunately when I do this only the definition gets transferred, not the term name. I need to copy-paste them individually. I keep seeing issues where I was sure I put the term name first!

If you see any like this just ping me and I will add the term I am querying. Sorry about that, it's super-confusing!

nicolevasilevsky commented 4 years ago

I don't think MONDO:0027353 is the same as PFBMFT1 but based on the current defs it is difficult to establish this.

I understand now! The definition of 'pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1' was created using a Mondo pattern. In OMIM, they say the mutation is on chromosome 5p15. Would this def be sufficient:

Any pulmonary fibrosis and/or bone marrow failure, Telomere-related disease in which the cause of the disease is a mutation in the TERT gene on chromosome 5p15.

ValWood commented 4 years ago

This def would still have the same problem

autosomal recessive dyskeratosis congenita 4 (MONDO:0027353) A dyskeratosis congenita that has_material_basis_in an autosomal recessive mutation of TERT on chromosome 5p15.33.

Is also a disease which has_material_basis_in in the same gene (TERT) and has BMF (according to its parent)

ValWood commented 4 years ago

Ah no this is OK. I am misreading. The pulmonary fibrosis has to be present in MONDO:0013878 and the BMF May be present.

can close....