CS/DS degradation (R-HSA-2024101)

[ukemi]

• Make mouse models: http://noctua.geneontology.org/editor/graph/gomodel:627d95ee00000955 and DS
• can R-HSA-2065233 be mapped to 'hydrolase activity, hydrolyzing O-glycosyl compounds' GO:0004553?
  It's already mapped to the is_a child GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds. Is that too fine-grained?
• Should we relax the BP mapping since this pathway covers both CS GO:0030207 and DS GO:0030209 catabolism? GO:0006027 glycosaminoglycan catabolic process? Yes - done
• R-HSA-1793207 only accounts for the C4S chain, should we introduce N-acetylgalactosamine-6-sulfatase activity enabled by GALNS to account for C6S?
• R-HSA-1793209 is mapped to hyalurononglucosaminidase activity (GO:0004415), but the definition "Catalysis of the random hydrolysis of (1->4) linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate." seems too specific in that it doesn't say chondroitin or hyaluronan. However, the synonyms include 'chondroitinase activity'. Should we relax the definition or create a new term for hyaluronan and chondroitin? "Catalysis of the random hydrolysis of (1->4) linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in glycosaminoglycans ."
• PMID:19889881 Should Hyal4 be added to the chondroitin-specific pathway?
• Note that ChEBI has heparan but not chondroitin. Neither of the chains in the Reactome heparan pathway seem to be related to the heparan entry in ChEBI.
• I see this over and over. An author isolates an enzyme, assyas for it at t low pH, finds that it is optimum there and says that this is evidence that it is active in the lysosome, it makes sense if the enzyme is intracellular, but is it IDA? That's what I have been saying.
• I extended the mouse CS catabolism to go all the way through the Hexb activity. Alternatively, we could create a separate pathway for the catabolism of the common linker. See Reactome pathway diagram for how we might do this.
• I left Hyal3 as a candidate with no evidence, do we think this is a good idea?

[ukemi]

http://noctua.geneontology.org/editor/graph/gomodel:627d95ee00000955