From bb7bd7fb5de9c51f996a5d11e9a268da3a7702a6 Mon Sep 17 00:00:00 2001 From: Raymond Lee Date: Fri, 8 Nov 2024 16:23:18 -0800 Subject: [PATCH 1/6] Reinstated 2 terms; #29149 --- src/ontology/go-edit.obo | 25 +- src/ontology/imports/go_taxon_constraints.owl | 305 ++++++++++-------- src/taxon_constraints/only_in_taxon.ofn | 6 + src/taxon_constraints/only_in_taxon.tsv | 3 +- 4 files changed, 182 insertions(+), 157 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index 242e56f0ce..1c84cfbba8 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -119663,15 +119663,14 @@ is_obsolete: true [Term] id: GO:0016172 -name: obsolete antifreeze activity +name: antifreeze activity namespace: molecular_function -def: "OBSOLETE. Inhibits the formation of ice crystals in organismal fluid (e.g. blood) at below freezing exogenous temperatures." [GOC:jl] -comment: This term was made obsolete because it refers to a biological process. +def: "Inhibits the growth and recrystallization of ice crystals, thereby lowering the freezing point of water and preventing cellular damage at subzero temperatures. This activity is observed in various cold-adapted organisms, including certain fish, insects, and plants, and contributes to survival in extreme cold environments by stabilizing supercooled liquid states." [GOC:cjm] +comment: Note that this term was reinstated from obsolete. synonym: "antifreeze activity" EXACT [] -is_obsolete: true -consider: GO:0042309 -consider: GO:0050825 -consider: GO:0050826 +xref: InterPro:IPR000104 +is_a: GO:0050825 ! ice binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29149" xsd:anyURI [Term] id: GO:0016173 @@ -147848,14 +147847,14 @@ replaced_by: GO:0046689 [Term] id: GO:0019833 -name: obsolete ice nucleation activity +name: ice nucleation activity namespace: molecular_function -def: "OBSOLETE. Catalysis of the formation of ice crystals in extracellular fluid at relatively high temperatures (up to -2 degrees C) to protect the organism from damage by intracellular ice formation. Ice nucleation proteins function by binding an ice crystal and then encouraging it to form larger crystals. Ice nucleation is a chemical process but these proteins can positively regulate it. There are two different uses of ice nucleation proteins: bacteria secrete them extracellularly to cause a host organism's cells to freeze and die, and fish use them to protect themselves from intracellular ice formation." [GOC:ai, GOC:jl] -comment: This term was made obsolete because it represents a biological process. +def: "Catalysis of the formation of ice crystals in extracellular fluid at relatively high temperatures (up to -2 degrees Celsius) to protect the organism from damage by intracellular ice formation. This process is commonly found in certain bacteria, such as Pseudomonas syringae, and plays roles in environmental adaptation and plant pathogenesis." [PMID:35551271] {comment="GOC:cjm", comment="UniProt:KW-0387"} +comment: Note that this term was reinstated from obsolete. synonym: "ice nucleation activity" EXACT [] -is_obsolete: true -consider: GO:0042309 -consider: GO:0050825 +xref: TC:9.B.133.1.1 +is_a: GO:0050825 ! ice binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29149" xsd:anyURI [Term] id: GO:0019834 diff --git a/src/ontology/imports/go_taxon_constraints.owl b/src/ontology/imports/go_taxon_constraints.owl index 301630e722..e6fb0e2ad1 100644 --- a/src/ontology/imports/go_taxon_constraints.owl +++ b/src/ontology/imports/go_taxon_constraints.owl @@ -12997,6 +12997,25 @@ + + + + + + + + + + + + + + + + + + + @@ -13221,27 +13240,27 @@ - + - + - + - + PMID:12722949 - + PMID:12722949 @@ -15079,27 +15098,27 @@ - + - + - + - + PMID:11082195 - + PMID:11082195 @@ -18164,12 +18183,12 @@ - - - + + + - + @@ -18177,7 +18196,7 @@ - + @@ -18185,26 +18204,26 @@ - + - + PMID:37550452 - + PMID:37550452 - + PMID:37550452 @@ -19681,7 +19700,7 @@ - + @@ -19698,7 +19717,7 @@ - + @@ -19711,11 +19730,11 @@ - + - + @@ -19723,7 +19742,7 @@ - + @@ -19731,26 +19750,26 @@ - + - + GOC:kmv - + GOC:kmv - + GOC:kmv @@ -19951,27 +19970,27 @@ - + - + - + - + PMID:15803654 - + PMID:15803654 @@ -23271,27 +23290,27 @@ - + - + - + - + PMID:28326 - + PMID:28326 @@ -24581,27 +24600,27 @@ - + - + - + - + PMID:16535664 - + PMID:16535664 @@ -24610,27 +24629,27 @@ - + - + - + - + PMID:15073291 - + PMID:15073291 @@ -24692,27 +24711,27 @@ - + - + - + - + PMID:17400742 - + PMID:17400742 @@ -24972,21 +24991,21 @@ - - - + + - - - + + + + - + @@ -24994,7 +25013,7 @@ - + @@ -25002,11 +25021,11 @@ - + - + @@ -25014,7 +25033,7 @@ - + @@ -25022,64 +25041,64 @@ - + - + - + - + PMID:34140356 - + PMID:34140356 - + https://en.wikipedia.org/wiki/Animal_echolocation - + PMID:34140356 - + PMID:34140356 - + https://en.wikipedia.org/wiki/Animal_echolocation - + PMID:34140356 - + PMID:34140356 @@ -25380,24 +25399,24 @@ - - - - - - - - - + + + + + + + + + - + @@ -25405,7 +25424,7 @@ - + @@ -25413,7 +25432,7 @@ - + @@ -25421,7 +25440,7 @@ - + @@ -25429,7 +25448,7 @@ - + @@ -25437,7 +25456,7 @@ - + @@ -25445,7 +25464,7 @@ - + @@ -25453,7 +25472,7 @@ - + @@ -25461,92 +25480,92 @@ - + - + - + - + - + PMID:21311032 - + PMID:21311032 - + PMID:21311032 - + PMID:21311032 - + PMID:21311032 - + PMID:21311032 - + PMID:21311032 - + PMID:21311032 - + PMID:21311032 - + PMID:21311032 - + PMID:21311032 - + PMID:21311032 @@ -27260,27 +27279,27 @@ - + - + - + - + PMID:23212898 - + PMID:23212898 @@ -30722,27 +30741,27 @@ - + - + - + - + PMID:33031395 - + PMID:33031395 @@ -34194,12 +34213,12 @@ - - - + + + - + @@ -34207,7 +34226,7 @@ - + @@ -34215,26 +34234,26 @@ - + - + PMID:18068186 - + PMID:18068186 - + PMID:18068186 @@ -35481,27 +35500,27 @@ - + - + - + - + PMID:24739148 - + PMID:24739148 @@ -35529,27 +35548,27 @@ - + - + - + - + PMID:15557260 - + PMID:15557260 @@ -35558,27 +35577,27 @@ - + - + - + - + PMID:31546611 - + PMID:31546611 @@ -38744,5 +38763,5 @@ - + diff --git a/src/taxon_constraints/only_in_taxon.ofn b/src/taxon_constraints/only_in_taxon.ofn index 0b64dec41e..da7fd926b7 100644 --- a/src/taxon_constraints/only_in_taxon.ofn +++ b/src/taxon_constraints/only_in_taxon.ofn @@ -309,6 +309,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2494,6 +2495,11 @@ SubClassOf(Annotation( "PMI SubClassOf(Annotation( "PMID:10629216"^^xsd:string) Annotation( "PMID:14504266"^^xsd:string) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:10629216"^^xsd:string) Annotation( "PMID:14504266"^^xsd:string) ObjectAllValuesFrom( )) +# Class: () + +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + # Class: () SubClassOf( ObjectSomeValuesFrom( )) diff --git a/src/taxon_constraints/only_in_taxon.tsv b/src/taxon_constraints/only_in_taxon.tsv index 4cdef17e23..f539f23d0c 100644 --- a/src/taxon_constraints/only_in_taxon.tsv +++ b/src/taxon_constraints/only_in_taxon.tsv @@ -924,4 +924,5 @@ GO:0030428 cell septum NCBITaxon:Union_0000020 Fungi or Bacteria GO:0018679 dibenzothiophene-5,5-dioxide monooxygenase activity NCBITaxon:Union_0000004 Prokaryota GO:0031639 plasminogen activation NCBITaxon:7742 Vertebrata GO:0009331 glycerol-3-phosphate dehydrogenase complex NCBITaxon:Union_0000004 Prokaryota -GO:0160208 fibrous body-membranous organelle NCBITaxon:6231 Nematoda +GO:0160208 fibrous body-membranous organelle NCBITaxon:6231 Nematoda +GO:0019833 ice nucleation activity NCBITaxon:2 Bacteria From 9fba8bb33d249201e913514644d256f66f87f7f8 Mon Sep 17 00:00:00 2001 From: Raymond Lee Date: Fri, 8 Nov 2024 16:28:42 -0800 Subject: [PATCH 2/6] Added a column; #29149 --- src/taxon_constraints/only_in_taxon.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/taxon_constraints/only_in_taxon.tsv b/src/taxon_constraints/only_in_taxon.tsv index f539f23d0c..22ff567400 100644 --- a/src/taxon_constraints/only_in_taxon.tsv +++ b/src/taxon_constraints/only_in_taxon.tsv @@ -924,5 +924,5 @@ GO:0030428 cell septum NCBITaxon:Union_0000020 Fungi or Bacteria GO:0018679 dibenzothiophene-5,5-dioxide monooxygenase activity NCBITaxon:Union_0000004 Prokaryota GO:0031639 plasminogen activation NCBITaxon:7742 Vertebrata GO:0009331 glycerol-3-phosphate dehydrogenase complex NCBITaxon:Union_0000004 Prokaryota -GO:0160208 fibrous body-membranous organelle NCBITaxon:6231 Nematoda -GO:0019833 ice nucleation activity NCBITaxon:2 Bacteria +GO:0160208 fibrous body-membranous organelle NCBITaxon:6231 Nematoda +GO:0019833 ice nucleation activity NCBITaxon:2 Bacteria \ No newline at end of file From c01bdacb82267159898bcd2b5ff366c5a9ce9148 Mon Sep 17 00:00:00 2001 From: Raymond Lee Date: Fri, 8 Nov 2024 16:42:53 -0800 Subject: [PATCH 3/6] Added a column; #29149 --- src/ontology/go-edit.obo | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index 1c84cfbba8..68345e4dea 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -119667,7 +119667,6 @@ name: antifreeze activity namespace: molecular_function def: "Inhibits the growth and recrystallization of ice crystals, thereby lowering the freezing point of water and preventing cellular damage at subzero temperatures. This activity is observed in various cold-adapted organisms, including certain fish, insects, and plants, and contributes to survival in extreme cold environments by stabilizing supercooled liquid states." [GOC:cjm] comment: Note that this term was reinstated from obsolete. -synonym: "antifreeze activity" EXACT [] xref: InterPro:IPR000104 is_a: GO:0050825 ! ice binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29149" xsd:anyURI @@ -147851,7 +147850,6 @@ name: ice nucleation activity namespace: molecular_function def: "Catalysis of the formation of ice crystals in extracellular fluid at relatively high temperatures (up to -2 degrees Celsius) to protect the organism from damage by intracellular ice formation. This process is commonly found in certain bacteria, such as Pseudomonas syringae, and plays roles in environmental adaptation and plant pathogenesis." [PMID:35551271] {comment="GOC:cjm", comment="UniProt:KW-0387"} comment: Note that this term was reinstated from obsolete. -synonym: "ice nucleation activity" EXACT [] xref: TC:9.B.133.1.1 is_a: GO:0050825 ! ice binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29149" xsd:anyURI @@ -317651,9 +317649,7 @@ id: GO:0050825 name: ice binding namespace: molecular_function def: "Binding to ice, water reduced to the solid state by cold temperature. It is a white or transparent colorless substance, crystalline, brittle, and viscoidal." [GOC:curators] -synonym: "antifreeze activity" RELATED [] synonym: "ice crystal binding" EXACT [] -synonym: "ice nucleation activity" RELATED [] synonym: "ice nucleation inhibitor activity" RELATED [] is_a: GO:0005488 ! binding intersection_of: GO:0036094 ! small molecule binding From c65848d82ce2a45aebc0df1fdd1fc6f3317c0ad7 Mon Sep 17 00:00:00 2001 From: Raymond Lee Date: Fri, 8 Nov 2024 16:54:49 -0800 Subject: [PATCH 4/6] Fixed def XREF. --- src/ontology/go-edit.obo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index 68345e4dea..8113dbb879 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -147848,7 +147848,7 @@ replaced_by: GO:0046689 id: GO:0019833 name: ice nucleation activity namespace: molecular_function -def: "Catalysis of the formation of ice crystals in extracellular fluid at relatively high temperatures (up to -2 degrees Celsius) to protect the organism from damage by intracellular ice formation. This process is commonly found in certain bacteria, such as Pseudomonas syringae, and plays roles in environmental adaptation and plant pathogenesis." [PMID:35551271] {comment="GOC:cjm", comment="UniProt:KW-0387"} +def: "Catalysis of the formation of ice crystals in extracellular fluid at relatively high temperatures (up to -2 degrees Celsius) to protect the organism from damage by intracellular ice formation. This process is commonly found in certain bacteria, such as Pseudomonas syringae, and plays roles in environmental adaptation and plant pathogenesis." [GOC:cjm, PMID:35551271, UniProt:KW-0387] comment: Note that this term was reinstated from obsolete. xref: TC:9.B.133.1.1 is_a: GO:0050825 ! ice binding From 8305ec7c0dda9a6b1001a5f1a691ec202daf2690 Mon Sep 17 00:00:00 2001 From: Raymond Lee Date: Mon, 11 Nov 2024 13:55:19 -0800 Subject: [PATCH 5/6] Moved Interpro to DEF XREF; #29149. --- src/ontology/go-edit.obo | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index dd2a23bd99..c3cd1265df 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -119669,9 +119669,8 @@ is_obsolete: true id: GO:0016172 name: antifreeze activity namespace: molecular_function -def: "Inhibits the growth and recrystallization of ice crystals, thereby lowering the freezing point of water and preventing cellular damage at subzero temperatures. This activity is observed in various cold-adapted organisms, including certain fish, insects, and plants, and contributes to survival in extreme cold environments by stabilizing supercooled liquid states." [GOC:cjm] +def: "Inhibits the growth and recrystallization of ice crystals, thereby lowering the freezing point of water and preventing cellular damage at subzero temperatures. This activity is observed in various cold-adapted organisms, including certain fish, insects, and plants, and contributes to survival in extreme cold environments by stabilizing supercooled liquid states." [GOC:cjm, InterPro:IPR000104] comment: Note that this term was reinstated from obsolete. -xref: InterPro:IPR000104 is_a: GO:0050825 ! ice binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29149" xsd:anyURI From d43681ab3cbb4a77348a79dea6981c9be26f01aa Mon Sep 17 00:00:00 2001 From: Raymond Lee Date: Mon, 11 Nov 2024 16:05:22 -0800 Subject: [PATCH 6/6] Added cortical endoplasmic reticulum membrane; fixes #29159. --- src/ontology/go-edit.obo | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index c3cd1265df..94f4390bd8 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -466435,6 +466435,19 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: rynl creation_date: 2024-09-27T05:19:27Z +[Term] +id: GO:0160219 +name: cortical endoplasmic reticulum membrane +namespace: cellular_component +def: "The lipid bilayer surrounding the cortical endoplasmic reticulum." [PMID:32735772] +is_a: GO:0005789 ! endoplasmic reticulum membrane +intersection_of: GO:0016020 ! membrane +intersection_of: bounding_layer_of GO:0032541 ! cortical endoplasmic reticulum +relationship: part_of GO:0032541 ! cortical endoplasmic reticulum +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29159" xsd:anyURI +created_by: rynl +creation_date: 2024-11-11T23:58:54Z + [Term] id: GO:0170001 name: ergothioneine transmembrane transporter activity