Merge pull request #28727 from geneontology/issue-28714

Obsoleted oligosaccharyltransferase complex subtypes; fixes #28714.

src/ontology/go-edit.obo

@@ -76864,13 +76864,17 @@ consider: GO:0008380
 id: GO:0008250
 name: oligosaccharyltransferase complex
 namespace: cellular_component
-def: "A protein complex that is found in the endoplasmic reticulum membrane of eukaryotes and transfers lipid-linked oligosaccharide precursor to asparagine residues on nascent proteins. In yeast, the complex includes at least nine different subunits, whereas in mammalian cells at least three different forms of the complex have been detected." [ISBN:0879695595, PMID:15835887]
+def: "A protein complex that is found in the endoplasmic reticulum membrane of eukaryotes and transfers lipid-linked oligosaccharide precursor to asparagine residues on nascent proteins. The complex includes at least eight non-identical subunits. Different forms of the complex containing distinct subunits have been detected in mammals." [PMID:15835887, PMID:31810196, PMID:32316603]
 synonym: "oligosaccharyl transferase complex" EXACT []
 synonym: "OST complex" EXACT []
+synonym: "OSTCI" NARROW []
+synonym: "OSTCII" NARROW []
+synonym: "OSTCIII" NARROW []
 intersection_of: GO:0140534 ! endoplasmic reticulum protein-containing complex
 intersection_of: capable_of GO:0004576 ! oligosaccharyl transferase activity
 relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
 relationship: part_of GO:0016020 ! membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28714" xsd:anyURI
 
 [Term]
 id: GO:0008251
@@ -209587,27 +209591,36 @@ relationship: part_of GO:0005886 ! plasma membrane
 
 [Term]
 id: GO:0034998
-name: oligosaccharyltransferase I complex
+name: obsolete oligosaccharyltransferase I complex
 namespace: cellular_component
-def: "An oligosaccharyltransferase (OST) complex that contains at least seven polypeptides and is the major OST complex in mammalian cells. Of the three forms of mammalian OST complex identified, the OSTI complex has the weakest affinity for ribosomes." [PMID:15835887]
+def: "OBSOLETE. An oligosaccharyltransferase (OST) complex that contains at least seven polypeptides and is the major OST complex in mammalian cells. Of the three forms of mammalian OST complex identified, the OSTI complex has the weakest affinity for ribosomes." [PMID:15835887]
+comment: The reason for obsoletion is that the meaning of the term is ambiguous and the data from the paper for which the term was requested can be accurately described using GO:0008250 oligosaccharyltransferase complex.
 synonym: "OSTCI" EXACT []
-is_a: GO:0008250 ! oligosaccharyltransferase complex
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28714" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0008250
 
 [Term]
 id: GO:0034999
-name: oligosaccharyltransferase II complex
+name: obsolete oligosaccharyltransferase II complex
 namespace: cellular_component
-def: "An oligosaccharyltransferase (OST) complex that contains the seven polypeptides found in OST complex I, plus heterotrimeric Sec61alpha-beta-gamma. Of the three forms of mammalian OST complexes identified, the OSTII complex has intermediate affinity for ribosomes." [GOC:BHF, PMID:15835887]
+def: "OBSOLETE. An oligosaccharyltransferase (OST) complex that contains the seven polypeptides found in OST complex I, plus heterotrimeric Sec61alpha-beta-gamma. Of the three forms of mammalian OST complexes identified, the OSTII complex has intermediate affinity for ribosomes." [GOC:BHF, PMID:15835887]
+comment: The reason for obsoletion is that the meaning of the term is ambiguous and the data from the paper for which the term was requested can be accurately described using GO:0008250 oligosaccharyltransferase complex.
 synonym: "OSTCII" EXACT []
-is_a: GO:0008250 ! oligosaccharyltransferase complex
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28714" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0008250
 
 [Term]
 id: GO:0035000
-name: oligosaccharyltransferase III complex
+name: obsolete oligosaccharyltransferase III complex
 namespace: cellular_component
-def: "An oligosaccharyltransferase (OST) complex that contains the seven polypeptides found in OST complex I, plus heterotrimeric Sec61alpha-beta-gamma and the tetrameric TRAP complex. Of the three forms of mammalian OST complexes identified, the OSTIII complex has the strongest affinity for ribosomes." [PMID:15835887]
+def: "OBSOLETE. An oligosaccharyltransferase (OST) complex that contains the seven polypeptides found in OST complex I, plus heterotrimeric Sec61alpha-beta-gamma and the tetrameric TRAP complex. Of the three forms of mammalian OST complexes identified, the OSTIII complex has the strongest affinity for ribosomes." [PMID:15835887]
+comment: The reason for obsoletion is that the meaning of the term is ambiguous and the data from the paper for which the term was requested can be accurately described using GO:0008250 oligosaccharyltransferase complex.
 synonym: "OSTCIII" EXACT []
-is_a: GO:0008250 ! oligosaccharyltransferase complex
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28714" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0008250
 
 [Term]
 id: GO:0035001