Inherited metabolic disease classification

[pnrobinson]

Let's build out the respective parts of Mondo according to An international classification of inherited metabolic disorders (ICIMD) https://onlinelibrary.wiley.com/doi/abs/10.1002/jimd.12348 There is a supplemental file we can work with.

[nicolevasilevsky]

@matentzn I added this to our one-on-one agenda, we are wondering if we can script in some of these classifications as outlined in the table in this paper.

[nicolevasilevsky]

Note to self, this is the spreadsheet from skeletal dysplasia

[nicolevasilevsky]

website: http://www.icimd.org/

[nicolevasilevsky]

@pnrobinson @cmungall @matentzn @sabrinatoro Could any of you help me with the classifications under section 1: Disorders of amino acid metabolism' (MONDO:0004736 'inherited disorder of amino acid metabolism') in the spreadsheet.

The authors say that 1.2 Organic acidurias is a type of 'Disorders of amino acid metabolism'. When I classify MONDO:0000688 'inherited organic acidemia' as a subtype of MONDO:0004736 'inherited disorder of amino acid metabolism' in Mondo, the classes are inferred to be equivalent.

MONDO:0004736 'inherited disorder of amino acid metabolism' has the logical def:

'inborn errors of metabolism'
 and ('disease caused by disruption of' some 'cellular amino acid metabolic process')

MONDO:0000688 'inherited organic acidemia' has the logical def:

'inborn errors of metabolism' and ('disease caused by disruption of' some 'organic acid metabolic process')

organic acid metabolic process is a superclass of cellular amino acid metabolic process in GO.

First question: is the author's classification incorrect?

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Second question, is the logical axiom on inborn disorder of amino acid and other organic acid metabolism correct?

'inborn errors of metabolism'
 and ('disease disrupts' some 'organic acid metabolic process')

This axiom suggests the label should be 'inborn disorder of organic acid metabolism', not 'inborn disorder of amino acid and other organic acid metabolism', right?

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Third question what is the difference between these two patterns?

• https://raw.githubusercontent.com/monarch-initiative/mondo/master/src/patterns/dosdp-patterns/inborn_metabolic.yaml
• https://raw.githubusercontent.com/monarch-initiative/mondo/master/src/patterns/dosdp-patterns/inborn_metabolic_disrupts.yaml

[pnrobinson]

'inborn errors of metabolism'
 and ('disease disrupts' some 'organic acid metabolic process')

is wrong because it is restricted to organic acid . Also, it is quite an underspecification of this disease group. I am not sure, though, that we gain a lot by not just relying on an asserted class hierarchy here.

[pnrobinson]

'inborn errors of metabolism'
 and ('disease caused by disruption of' some 'cellular amino acid metabolic process')

This is also wrong because it is limited to amino acids. And as above, it is quite an underspecification. I think it might be fine not to logically define these classes, as I doubt it is possible to do so in an accurate way. Instead, classes like this should be simply undefined classes that we use to help define the subclasses

[nicolevasilevsky]

I talked to Peter - I'll add these classes exactly as they are described and classified in the paper/table.

[nicolevasilevsky]

@sabrinatoro I am reassigning this to you. It's a really big project and will take a lot of time to complete.

[pnrobinson]

happy to chip in

[cmungall]

The branch currently contains fake metabolic diseases like:

id: MONDO:0017739
name: disorder of lysosomal-related organelles
subset: disease_grouping
subset: ordo_group_of_disorders {source="Orphanet:309340"}
xref: Orphanet:309340 {source="MONDO:equivalentTo"}
xref: UMLS:CN227186 {source="MONDO:equivalentTo"}
is_a: MONDO:0019052 {source="Orphanet:309340"} ! inborn errors of metabolism

he two diseases under it are not metabolic, they are both caused by mutations in the lysosomal protease cathepsin C gene, which is a protease, not metabolic. this was marked as rescue in the mordor spreadsheet but it should clearly be obsoleted