Closed sjm41 closed 8 months ago
deustp01
commented
8 months ago @ukemi Is the occasion to review pathway boundaries for Reactome Glycogen metabolism (R-HSA-8982491) and possibly define a canonical pathway with variants as in the cross-referencing scheme here, in our spare time?
ukemi
commented
8 months ago Good idea. I already did a bit of this to make the glycogen metabolism mouse models. http://noctua.geneontology.org/editor/graph/gomodel:623d156d00000029 http://noctua.geneontology.org/editor/graph/gomodel:623d156d00000699 http://noctua.geneontology.org/editor/graph/gomodel:623d156d00000752 http://noctua.geneontology.org/editor/graph/gomodel:623d156d00000939
All of these were based on the Reactome import.
sjm41
commented
8 months ago FYI, the two glycogen-related terms now look like this (after adding the missing MetaCyc xrefs):
id: GO:0005978 name: glycogen biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues." [ISBN:0198506732] synonym: "glycogen anabolism" EXACT [] synonym: "glycogen biosynthesis" EXACT [] synonym: "glycogen formation" EXACT [] synonym: "glycogen synthesis" EXACT [] xref: MetaCyc:GLYCOGENSYNTH-PWY xref: MetaCyc:PWY-5067 xref: MetaCyc:PWY-7900 is_a: GO:0005977 ! glycogen metabolic process is_a: GO:0009250 ! glucan biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:28087 ! glycogen property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27107" xsd:anyURI
id: GO:0005980 name: glycogen catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues." [ISBN:0198506732] synonym: "glycogen breakdown" EXACT [] synonym: "glycogen catabolism" EXACT [] synonym: "glycogen degradation" EXACT [] synonym: "glycogenolysis" EXACT [GOC:sl] xref: MetaCyc:GLYCOCAT-PWY xref: MetaCyc:PWY-5941 xref: MetaCyc:PWY-7662 intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:28087 ! glycogen property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27107" xsd:anyURI
glycogen biosynthetic process (GO:0005978) ADD: glycogen biosynthesis II (from UDP-D-Glucose) (MetaCyc:PWY-5067) glycogen biosynthesis III (from α-maltose 1-phosphate) (MetaCyc:PWY-7900)
glycogen catabolic process (GO:0005980) ADD: glycogen degradation II (MetaCyc:PWY-5941) glycogen degradation III (via anhydrofructose) (MetaCyc:PWY-7662)
pentose-phosphate shunt, non-oxidative branch (GO:0009052) REMOVE: pentose phosphate pathway (partial) (MetaCyc:P21-PWY) ADD: pentose phosphate pathway (non-oxidative branch) II (MetaCyc:PWY-8178)
pentose-phosphate shunt, oxidative branch (GO:0009052) ADD: pentose phosphate pathway (oxidative branch) II (PWY-7796)
hyaluronan catabolic process (GO:0030214) ADD: hyaluronan degradation (MetaCyc:PWY-7645)
heparan sulfate proteoglycan biosynthetic process (GO:0015012)* ADD: heparan sulfate biosynthesis (MetaCyc:PWY-6558)
chondroitin sulfate biosynthetic process (GO:0030206) ADD: chondroitin sulfate biosynthesis (MetaCyc:PWY-6567)
dermatan sulfate biosynthetic process (GO:0030208) ADD: dermatan sulfate biosynthesis (MetaCyc:PWY-6568)
chondroitin sulfate catabolic process (GO:0030207) ADD: chondroitin sulfate degradation (metazoa) (MetaCyc:PWY-6573) chondroitin sulfate degradation I (bacterial) (MetaCyc:PWY-6572)
dermatan sulfate catabolic process (GO:0030209) ADD: dermatan sulfate degradation (metazoa) (MetaCyc:PWY-6576) dermatan sulfate degradation I (bacterial) (MetaCyc:PWY-7646)
D-glucuronate catabolic process (GO:0042840) ADD: β-D-glucuronide and D-glucuronate degradation (PWY-7247) D-glucuronate degradation I (PWY-5525) D-glucuronate degradation II (PWY-6501) D-glucuronate degradation III (PWY-8390)
chitin biosynthetic process (GO:0006031) ADD: chitin biosynthesis (MetaCyc:PWY-6981)
chitin catabolic process (GO:0006032) ADD: chitin deacetylation (MetaCyc:PWY-7118) chitin degradation I (archaea) (MetaCyc:PWY-6855) chitin degradation II (Vibrio) (MetaCyc:PWY-6902) chitin degradation III (Serratia) (MetaCyc:PWY-7822)
mannose catabolic process (GO:0019309) ADD: D-mannose degradation II (MetaCyc:PWY3O-1743)
N-acetylglucosamine catabolic process (GO:0006046) ADD: N-acetylglucosamine degradation I (MetaCyc:GLUAMCAT-PWY) N-acetylglucosamine degradation II (MetaCyc:PWY-6517)
O-glycan processing (GO:0016266) ADD: mucin core 1 and core 2 O-glycosylation (MetaCyc:PWY-7433)
protein O-linked mannosylation (GO:0035269) ADD: protein O-mannosylation I (yeast) (MetaCyc:PWY-7921) protein O-mannosylation II (mammals, core M1 and core M2) (MetaCyc:PWY-7922) protein O-mannosylation III (mammals, core M3) (MetaCyc:PWY-7979)
GDP-mannose biosynthetic process (GO:0009298) ADD: GDP-mannose biosynthesis (MetaCyc:PWY-5659)
UDP-N-acetylgalactosamine biosynthetic process (GO:0019277) REMOVE: UDP-N-acetyl-D-glucosamine biosynthesis II (MetaCyc:UDPNACETYLGALSYN-PWY) ADD: UDP-N-acetyl-D-galactosamine biosynthesis I (MetaCyc:PWY-5512) UDP-N-acetyl-D-galactosamine biosynthesis II (MetaCyc:PWY-5514) UDP-N-acetyl-D-galactosamine biosynthesis III (MetaCyc:PWY-8013)
UDP-N-acetylglucosamine biosynthetic process (GO:0006048) ADD: UDP-N-acetyl-D-glucosamine biosynthesis II (MetaCyc:UDPNACETYLGALSYN-PWY)
UDP-galactose biosynthetic process (GO:0052574) ADD: UDP-α-D-galactose biosynthesis (MetaCyc:PWY-7344)
UDP-glucuronate biosynthetic process (GO:0006065) ADD: UDP-α-D-glucuronate biosynthesis (from UDP-glucose) (MetaCyc:PWY-7346)