Keratan sulfate degradation (R-HSA-2022857)

geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)

8 stars 0 forks source link

Keratan sulfate degradation (R-HSA-2022857) #171

Open ukemi opened 2 years ago

ukemi commented 2 years ago

[x] Create a mouse model
[x] Open an ontology ticket to examine the children of galactosidase activity. https://github.com/geneontology/go-ontology/issues/23375
[x] Add GO BP term GO:0006897 "endocytosis" to reaction R-HSA-2046239 "Extracellular KSPG translocates to the lysosome for degradation", to distinguish it from all others in this pathway, which are parts of GO:0042340 "keratan sulfate catabolism"
[ ] Make the mouse model production

ukemi commented 2 years ago

Trying to evidence the mouse model for this pathway is extremely difficult. It may be because mice don't degrade KS in the same way humans do or because the distribution of KS is different in rats and mice than it is in humans, and the appropriate measurements have not been done (PMID:33266180, PMID:30528226, PMID:3160342, PMID:29396849).

deustp01 commented 2 years ago

Aside from the BP tweak to reaction R-HSA-2046239, I don't see anything to fix now in the human pathway. Two items for the future:

with expert help, sort out the chemistry better, getting intermediates right and possibly allowing for glycolipid sources of keratan sulfate as well as the glycoprotein sources annotated now.
posibly coupled to the first future item, annotate tissue specificity.

deustp01 commented 2 years ago

On the 95% - 5% rule, I'd be inclined to set this one aside for now and knock off some of the others that look more straightforward. Pushing edge cases that show real differences between species is important, but this looks like one in which the data are limited enough so that it will be hard to sort out what's different from what just hasn't been studied very well.