Merge pull request #27887 from geneontology/issue-27071

Obsoleted class III/IV DNA-(apurinic or apyrimidinic site) endonuclea…

src/ontology/go-edit.obo

@@ -323209,8 +323209,8 @@ synonym: "collagenase A activity" EXACT []
 synonym: "collagenase I activity" RELATED []
 synonym: "collagenase MMP-1" RELATED []
 synonym: "kollaza" RELATED []
-synonym: "matrix metalloproteinase-18" RELATED []
 synonym: "matrix metalloproteinase-1" RELATED []
+synonym: "matrix metalloproteinase-18" RELATED []
 synonym: "matrix metalloproteinase-8" RELATED []
 synonym: "metallocollagenase activity" RELATED []
 synonym: "metalloproteinase-1" RELATED []
@@ -330736,8 +330736,8 @@ synonym: "modulation by symbiont of defense-related host MAP kinase-mediated sig
 synonym: "modulation by symbiont of host innate immune response MAPK kinase signaling" NARROW []
 synonym: "modulation of defense-related host MAPK-mediated signal transduction pathway by organism" NARROW []
 synonym: "modulation of defense-related host mitogen activated protein kinase-mediated signal transduction pathway by organism" NARROW []
-synonym: "perturbation of host innate immune response MAPK kinase signaling" NARROW []
 synonym: "perturbation by symbiont of host MAP kinase signal transduction pathway" EXACT []
+synonym: "perturbation of host innate immune response MAPK kinase signaling" NARROW []
 synonym: "perturbation of host MAP signal transduction pathway" EXACT []
 synonym: "perturbation of host MAPK kinase signaling pathway" EXACT []
 synonym: "perturbation of host MAPK signal transduction pathway" EXACT []
@@ -336739,26 +336739,29 @@ creation_date: 2011-08-12T11:53:26Z
 
 [Term]
 id: GO:0052719
-name: apurinic/apyrimidinic endoribonuclease activity
+name: RNA-(apurinic or apyrimidinic site) endonuclease activity
 namespace: molecular_function
 def: "Catalysis of the hydrolysis of ester linkages immediately 5' to an apurinic/apyrimidinic (AP; also called abasic) site within a ribonucleic acid molecule by creating internal breaks, generating a single-strand break with 5'-ribose phosphate and 3'-hydroxyl ends." [PMID:19401441]
 synonym: "abasic endoribonuclease activity" EXACT []
 synonym: "AP endoribonuclease activity" EXACT []
 synonym: "apurinic endoribonuclease activity" NARROW []
 synonym: "apyrimidinic endoribonuclease activity" NARROW []
 is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27071" xsd:anyURI
 
 [Term]
 id: GO:0052720
 name: class II DNA-(apurinic or apyrimidinic site) endonuclease activity
 namespace: molecular_function
 alt_id: GO:0140079
-def: "Catalysis of the hydrolysis of ester linkages immediately 5' to an apurinic/apyrimidinic (AP; also called abasic) site within a deoxyribonucleic acid molecule by creating internal breaks, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends." [PMID:19401441]
+def: "Catalysis of the hydrolysis of ester linkages immediately 5' to an apurinic/apyrimidinic (AP; also called abasic) site within a deoxyribonucleic acid molecule by creating internal breaks, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends." [PMID:1698278]
 comment: Class II AP endonuclease is a nuclease, but not Class I, III and IV.
+synonym: "class II AP endonuclease activity" RELATED []
 synonym: "class II DNA-(apurinic or apyrimidinic site) lyase activity" EXACT []
 is_a: GO:0003906 ! DNA-(apurinic or apyrimidinic site) endonuclease activity
 is_a: GO:0016888 ! endodeoxyribonuclease activity, producing 5'-phosphomonoesters
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13409" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27071" xsd:anyURI
 created_by: pg
 creation_date: 2017-07-24T11:46:03Z
 
@@ -400184,7 +400187,6 @@ synonym: "modulation by symbiont of host NF-kappaB-mediated signal transduction
 synonym: "perturbation of host canonical NF-kappaB cascade" RELATED []
 synonym: "perturbation of host I-kappaB kinase/NF-kappaB cascade" EXACT []
 synonym: "symbiont-mediated perturbation of host canonical NF-kappaB cascade" RELATED []
-synonym: "symbiont-mediated perturbation of host canonical NF-kappaB cascade" RELATED []
 is_a: GO:0052027 ! symbiont-mediated perturbation of host signal transduction pathway
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25571" xsd:anyURI
 created_by: jl
@@ -447759,7 +447761,9 @@ namespace: molecular_function
 def: "Catalysis of the cleavage of an AP site 3' of the baseless site by a beta-lyase mechanism, leaving an unsaturated aldehyde, termed a 3'-(4-hydroxy-5-phospho-2-pentenal) residue, and a 5'-phosphate." [PMID:1698278, RHEA:66592]
 comment: Note that this term is does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. Class II AP endonuclease is a nuclease, but not Class I, III and IV.
 synonym: "AP endonuclease class I activity" RELATED []
+synonym: "AP lyase activity" RELATED []
 synonym: "AP site-DNA 5'-phosphomonoester-lyase activity" EXACT []
+synonym: "class I AP endonuclease activity" RELATED []
 synonym: "class I DNA-(apurinic or apyrimidinic site) lyase activity" EXACT []
 synonym: "DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase activity" EXACT []
 synonym: "DNA-(apurinic or apyrimidinic site) lyase activity" EXACT []
@@ -447770,20 +447774,22 @@ xref: Wikipedia:AP_endonuclease
 is_a: GO:0003906 ! DNA-(apurinic or apyrimidinic site) endonuclease activity
 is_a: GO:0016835 ! carbon-oxygen lyase activity
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22262" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27071" xsd:anyURI
 created_by: pg
 creation_date: 2017-07-24T11:33:34Z
 
 [Term]
 id: GO:0140080
-name: class III/IV DNA-(apurinic or apyrimidinic site) endonuclease activity
+name: obsolete class III/IV DNA-(apurinic or apyrimidinic site) endonuclease activity
 namespace: molecular_function
-def: "Catalysis of the cleavage of an AP site 3' and 5' of the baseless site, generating a 3'-phosphate and a 5'-OH." [PMID:2519777]
-comment: Note that this term is does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. Class II AP endonuclease is a nuclease, but not Class I, III and IV.
+def: "OBSOLETE. Catalysis of the cleavage of an AP site 3' and 5' of the baseless site, generating a 3'-phosphate and a 5'-OH." [PMID:2519777]
+comment: Note that this term is does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. Class II AP endonuclease is a nuclease, but not Class I, III and IV.\nThe reason for obsoletion is that there is no longer credible evidence that this function exists.
 synonym: "endonuclease III" RELATED []
 synonym: "endonuclease IV" RELATED []
 xref: Wikipedia:AP_endonuclease
-is_a: GO:0003906 ! DNA-(apurinic or apyrimidinic site) endonuclease activity
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22262" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27071" xsd:anyURI
+is_obsolete: true
 created_by: pg
 creation_date: 2017-07-24T11:48:18Z