pnrobinson
commented
1 year ago So this is what I mean about the critical importance of writing things down in English.
does chondrocalcinosis arise from a disruption of metabolism?
I would argue that this is irrelevant. Metabolism is not a concept with well defined boundaries and is some cases has an extremely broad definition, e.g., https://medlineplus.gov/ency/article/002257.htm. Given this definition, perhaps half of Mondo would be a metabolic disease.
I think that Mondo should classify diseases in a way that reflects the medical disciplines that treat diseases, not by (all) phenotypic features and not by etiology (unless the clinical classification uses etiology). If we do this, then we have the Inborn errors or metabolism, and there is essentially no debate about which diseases are part of this set, and we get a clear and well structured ontology and can use computation to infer whether any given disease has metabolic aspects.
Having just computational documents is like not being able to see the forest for the trees. We really need to write down our philosophy in a human language.
From an email with @pnrobinson
Note that currently this is-a is only supported by NCIT, which we know has some dubious classifications. Previously we have jointly filed issues with NCIT to sync changes, but it's not clear if that is worth the effort.
also in the same thread:
@nicolevasilevsky or @sabrinatoro can you show Peter our design pattern documentation?
In this particular case, there should be no philosophy. We look at the text definition and where present the logical definition:
A congenital disorder (due to inherited enzyme abnormality) or acquired (due to failure of a metabolically important organ) disorder resulting from an abnormal metabolic process
The logical definition is in terms of GO:0008152 ! metabolic process
In this case, our SOP (not philosophy) would be to say
It seems some forms of chondrocalcinosis may arise as a result of metabolic disorders (e.g. by elevating the concentration of either calcium or pyrophosphate ions, or affecting pyrophosphate transport), it is not a metabolic disorder by the current definitions in mondo, so we should remove the edge.
In mondo's defence, there are a number of sources that do conflate the classification, e.g.
https://rarediseases.org/rare-diseases/chondrocalcinosis-familial-articular/#:~:text=Chondrocalcinosis%202%20(CCAL2)%20is%20a,eventual%20damage%20to%20affected%20joints.
Chondrocalcinosis 2 (CCAL2) is a genetic type of calcium pyrophosphate deposition disease (CPDD), a metabolic disorder characterized by deposits of calcium pyrophosphate dihydrate crystals (CPPD) in joint cartilage and eventual damage to affected joints.
https://emedicine.medscape.com/article/330936-overview
Calcium pyrophosphate deposition (CPPD) disease is a metabolic arthropathy caused by the deposition