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Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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Review: nephropathic cystinosis and AKL #960

Closed cmungall closed 4 years ago

cmungall commented 4 years ago

id: MONDO:0021725 name: Abderhalden-Kaufmann-Lignac syndrome def: "A rare autosomal-recessive, lysomal storage childhood disorder involving deposits of cystine crystals in various parts of the body, including the bone marrow, conjunctiva and cornea." [http://www.checkorphan.org/diseases/abderhalden-kaufmann-lignac-syndrome, https://orcid.org/0000-0001-5208-3432, https://www.medigoo.com/articles/abderhalden-kaufmann-lignac-syndrome/, PMID:3606421]

All of the definition citations for AKL are dubious.

this is blank https://rarediseases.info.nih.gov/diseases/10074/abderhalden-kaufmann-lignac-syndrome

there is one pmid, in russian https://www.ncbi.nlm.nih.gov/pubmed/3606421 "A case of nephropathic cystinosis (Abderhalden-Lignac-Kaufmann disease) in a 8-month girl is reported"

Is the MONDO ID describing the case, or ALK? The abstract seems to state that ALK is just a synonym for nephropathic cystinosis, and these should be merged. I am not seeing any evidence for a distinct disease here

Is this disease any different from AR

cmungall commented 4 years ago

Also:

id: MONDO:0009065 name: cystinosis, nephropathic def: "Cystinosis is an inherited condition in which the body accumulates the amino acid cystine (a building block of proteins) within the cells. Excess cystine forms crystals that can build up and damage cells. These crystals can negatively affect many systems in the body, especially the kidneys and eyes. There are three distinct types of cystinosis: nephropathic cystinosis, intermediate cystinosis, and non-nephropathic or ocular cystinosis. All three types of cystinosis are caused by mutations in the CTNS gene andinherited in an autosomal recessive pattern." [https://rarediseases.info.nih.gov/diseases/9755/nephropathic-cystinosis]

The definition is for a more generic class, cystinosis

cmungall commented 4 years ago

this structure is dubious:

image

MONDO:0009065 cystinosis, nephropathic: is equiv to https://omim.org/entry/219800 which looks like generic entry but may be for infantile form? MONDO:0009066 juvenile nephropathic cystinosis: is equiv to https://omim.org/entry/219900 late onset juvenile form

cmungall commented 4 years ago

@nicolevasilevsky I merged MONDO:0009065 into MONDO:0009066 can you deal with AKL?

nicolevasilevsky commented 4 years ago

Sure thing, Chris!

@GARDinfocenter FYI- I am going to merge this term (https://rarediseases.info.nih.gov/diseases/10074/abderhalden-kaufmann-lignac-syndrome) with 'cystinosis, nephropathic'. Maybe you want to merge this page with https://rarediseases.info.nih.gov/diseases/9755/nephropathic-cystinosis?

GARDInfoCenter commented 4 years ago

Thanks for letting us know. I have forwarded this to our team.

Best, Maria

From: Nicole Vasilevsky notifications@github.com Sent: Thursday, November 14, 2019 4:46 PM To: monarch-initiative/mondo mondo@noreply.github.com Cc: Della Rocca, Maria Maria.DellaRocca@icf.com; Mention mention@noreply.github.com Subject: Re: [monarch-initiative/mondo] Review: nephropathic cystinosis and AKL (#960)

Sure thing, Chris!

@GARDInfoCenterhttps://github.com/GARDInfoCenter FYI- I am going to merge this term (https://rarediseases.info.nih.gov/diseases/10074/abderhalden-kaufmann-lignac-syndrome) with 'cystinosis, nephropathic'. Maybe you want to delete the GARD page?

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nicolevasilevsky commented 4 years ago

Hi @GARDInfoCenter, no rush, but just checking if you had any updates on this. Thanks!

GARDInfoCenter commented 4 years ago

We have retired AKL but for now will continue to list nephropathic cystinosis.

maglott commented 4 years ago

I think there is still a problem with capturing the concept of nephroplastic cystinosis

I think there should be nodes for

nicolevasilevsky commented 4 years ago