Merge pull request #25749 from geneontology/vw-14-07-23-part1

closes #25734; closes #25727; closes #25726; closes #25722; closes #2…

src/ontology/go-edit.obo

@@ -15991,7 +15991,7 @@ id: GO:0002144
 name: cytosolic tRNA wobble base thiouridylase complex
 namespace: cellular_component
 def: "A complex of two proteins involved in the thiolation of uridine 34 (U34) of tRNAs decoding two-family box triplets." [PMID:17062623, PMID:18391219]
-synonym: "Cut1-Cut2 complex" NARROW []
+synonym: "Ctu1-Ctu2 complex" NARROW []
 synonym: "tRNA thiouridylase" BROAD []
 is_a: GO:0140535 ! intracellular protein-containing complex
 is_a: GO:1902494 ! catalytic complex
@@ -171612,6 +171612,7 @@ namespace: molecular_function
 def: "Catalysis of the reaction: peptidyl L-proline + 2-oxoglutarate + O2 = peptidyl trans-4-hydroxy-L-proline + succinate + CO2." [GOC:mah]
 synonym: "HIF-type prolyl 4-hydroxylase" NARROW []
 synonym: "prolyl 4-hydroxylase" BROAD []
+xref: RHEA:63484
 is_a: GO:0031543 ! peptidyl-proline dioxygenase activity
 
 [Term]
@@ -280362,11 +280363,9 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i
 id: GO:0046933
 name: proton-transporting ATP synthase activity, rotational mechanism
 namespace: molecular_function
-def: "Enables the synthesis of ATP from ADP and phosphate by the transfer of protons from one side of a membrane to the other by a rotational mechanism driven by a gradient according to the reaction: ADP + H2O + phosphate + H+(in) -> ATP + H+(out)." [RHEA:57720]
+def: "Enables the synthesis of ATP from ADP and phosphate by the transfer of protons from one side of a membrane to the other by a rotational mechanism driven by a gradient according to the reaction: ADP + H2O + phosphate + H+(in) -> ATP + H+(out)." [RHEA:57722]
 synonym: "H+-transporting ATP synthase activity" RELATED [EC:7.1.2.2]
-synonym: "hydrogen ion translocating F-type ATPase activity" EXACT []
 synonym: "hydrogen ion transporting ATP synthase activity, rotational mechanism" EXACT []
-synonym: "hydrogen ion transporting two-sector ATPase activity" EXACT []
 xref: EC:7.1.2.2
 xref: MetaCyc:ATPSYN-RXN
 xref: RHEA:57720
@@ -280375,6 +280374,7 @@ is_a: GO:0015252 ! proton channel activity
 is_a: GO:0016874 ! ligase activity
 relationship: part_of GO:0015986 ! proton motive force-driven ATP synthesis
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19380" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25727" xsd:anyURI
 
 [Term]
 id: GO:0046934
@@ -280647,7 +280647,7 @@ is_a: GO:0046958 ! nonassociative learning
 id: GO:0046961
 name: proton-transporting ATPase activity, rotational mechanism
 namespace: molecular_function
-def: "Enables the transfer of protons from one side of a membrane to the other according to the reaction: ATP + H2O + H+(in) = ADP + phosphate + H+(out), by a rotational mechanism." [RHEA:57721]
+def: "Enables the transfer of protons from one side of a membrane to the other according to the reaction: ATP + H2O + H+(in) -> ADP + phosphate + H+(out), by a rotational mechanism." [RHEA:57721]
 synonym: "ATP phosphohydrolase (H+-transporting) activity" NARROW []
 synonym: "ATP synthase activity" NARROW [EC:7.1.2.2]
 synonym: "chloroplast ATPase activity" NARROW [EC:7.1.2.2]
@@ -335220,14 +335220,16 @@ creation_date: 2011-08-16T04:28:23Z
 id: GO:0052735
 name: tRNA (cytosine-3-)-methyltransferase activity
 namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 3-methylcytosine." [PMID:21518804, PMID:21518805]
+def: "Catalysis of the reaction: a cytidine in tRNA + S-adenosyl-L-methionine = an N3-methylcytidine in tRNA + H+ + S-adenosyl-L-homocysteine." [RHEA:60908]
 synonym: "S-adenosyl-L-methionine:tRNA (cytosine-3-)-methyltransferase activity" EXACT []
 synonym: "S-adenosyl-L-methionine:tRNA cytosine-3-methyltransferase activity" EXACT []
 synonym: "transfer ribonucleate cytosine 3-methyltransferase activity" EXACT []
 synonym: "tRNA (cytosine 3)-methyltransferase activity" EXACT []
 synonym: "tRNA cytosine 3-methyltransferase activity" EXACT []
 synonym: "tRNA cytosine-3-methyltransferase activity" EXACT []
+xref: RHEA:60908
 is_a: GO:0016427 ! tRNA (cytosine) methyltransferase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25722" xsd:anyURI
 
 [Term]
 id: GO:0052736
@@ -369990,10 +369992,12 @@ creation_date: 2009-06-19T11:44:37Z
 id: GO:0070735
 name: protein-glycine ligase activity
 namespace: molecular_function
-def: "Catalysis of the posttranslational transfer of one or more glycine residues to a specific glutamate residue on a target protein." [GOC:mah, PMID:19524510]
+def: "ATP + glycine + L-glutamyl-[protein] = ADP + glycyl-L-glutamyl-[protein] + H+ + phosphate." [RHEA:67180]
 synonym: "protein glycylase activity" EXACT [GOC:mah]
+xref: RHEA:67180
 is_a: GO:0016881 ! acid-amino acid ligase activity
 is_a: GO:0140096 ! catalytic activity, acting on a protein
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25720" xsd:anyURI
 created_by: mah
 creation_date: 2009-06-19T01:51:21Z