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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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'glycogen biosynthetic process' parents #28968

Closed sjm41 closed 2 months ago

sjm41 commented 2 months ago

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 {source="skos:narrowMatch"} xref: MetaCyc:PWY-5067 {source="skos:narrowMatch"} xref: MetaCyc:PWY-7900 {source="skos:narrowMatch"} 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 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI

@pgaudet the two asserted is_a parents here could/should be removed, right? They are covered by the LD.

pgaudet commented 2 months ago

That seems correct. To test this, you can just remove the asserted classes, synchronize the reasoner, and check if they come back as inferred superclasses.

In any case, we should not make these assertions for chemicals. If the proper groupings are missing, we need to check with ChEBI.

OK?

Thanks, Pascale

sjm41 commented 2 months ago

Yep, I did the test you suggested and it looks good. So I'll go ahead and action this.

sjm41 commented 2 months ago

Looks like the same goes for the asserted is_a on this term, so I'll remove that too:

id: GO:0061621 name: canonical glycolysis namespace: biological_process def: "The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP." [GOC:dph, ISBN:0201090910, ISBN:0879010479] xref: MetaCyc:ANAGLYCOLYSIS-PWY xref: Wikipedia:Glycolysis is_a: GO:0061620 ! glycolytic process through glucose-6-phosphate intersection_of: GO:0061620 ! glycolytic process through glucose-6-phosphate intersection_of: has_part GO:0004365 ! glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity intersection_of: has_primary_input CHEBI:4167 ! D-glucopyranose intersection_of: has_primary_input CHEBI:57540 ! NAD(1-) intersection_of: has_primary_output CHEBI:57945 ! NADH(2-) intersection_of: starts_with GO:0004340 ! glucokinase activity created_by: dph creation_date: 2014-04-14T09:21:54Z