From dc45eef6340bbe41020e3e3cc364e784febbbe79 Mon Sep 17 00:00:00 2001 From: Pascale Gaudet Date: Fri, 6 Dec 2024 18:03:08 +0100 Subject: [PATCH 1/2] created new terms fixes #29384 --- src/ontology/go-edit.obo | 132 ++++++++++++++++++++++++++++++++++++--- 1 file changed, 125 insertions(+), 7 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index d8ffe99509..e76783ee1c 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -359721,7 +359721,7 @@ namespace: molecular_function def: "A histone reader that recognizes a histone H3 trimethylated at lysine 27." [GOC:dph, PMID:23948251] synonym: "H3-K27me3 modified histone binding" NARROW [] synonym: "H3K27me3 modified histone binding" NARROW [] -is_a: GO:0140566 ! histone reader activity +is_a: GO:0140006 ! H3 histone reader activity relationship: has_part GO:0035064 ! methylated histone binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27427" xsd:anyURI @@ -364151,7 +364151,7 @@ name: H3K9me3 histone reader activity namespace: molecular_function def: "A histone reader that recognizes a histone H3 trimethylated at lysine 9." [PMID:30110338] synonym: "H3K9me3 modified histone binding" NARROW [] -is_a: GO:0140566 ! histone reader activity +is_a: GO:0140006 ! H3 histone reader activity relationship: has_part GO:0035064 ! methylated histone binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27427" xsd:anyURI @@ -450168,9 +450168,9 @@ namespace: molecular_function def: "A histone reader that recognizes a histone H3 trimethylated at lysine 4." [PMID:15647753, PMID:23318260] synonym: "H3-K4me3 modified histone binding" NARROW [] synonym: "H3K4me3 modified histone binding" NARROW [] -is_a: GO:0140566 ! histone reader activity +is_a: GO:0140006 ! H3 histone reader activity relationship: has_part GO:0035064 ! methylated histone binding -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29337" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29384" xsd:anyURI created_by: pg creation_date: 2024-11-29T14:13:16Z @@ -450181,7 +450181,7 @@ namespace: molecular_function def: "A histone reader that recognizes a histone H3 trimethylated at lysine 36." [PMID:15489290, PMID:16364921] synonym: "H3-K36me3 modified histone binding" NARROW [] synonym: "H3K36me3 modified histone binding" NARROW [] -is_a: GO:0140566 ! histone reader activity +is_a: GO:0140006 ! H3 histone reader activity relationship: has_part GO:0035064 ! methylated histone binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29337" xsd:anyURI created_by: pg @@ -450194,7 +450194,7 @@ namespace: molecular_function def: "A histone reader that recognizes a histone H3 serotonylated at glutamine 5." [PMID:34144982] synonym: "H3Q5-serotonin histone reader activity" EXACT [] synonym: "H3Q5-serotonin modified histone binding" NARROW [] -is_a: GO:0140566 ! histone reader activity +is_a: GO:0140006 ! H3 histone reader activity relationship: has_part GO:0035064 ! methylated histone binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29337" xsd:anyURI created_by: pg @@ -450206,12 +450206,23 @@ name: H4K20me2 histone reader activity namespace: molecular_function def: "A histone reader that recognizes a histone H4 dimethylated at lysine 20." [PMID:22150589] synonym: "H4K20me2 modified histone binding" NARROW [] -is_a: GO:0140566 ! histone reader activity +is_a: GO:0140008 ! H4 histone reader activity relationship: has_part GO:0035064 ! methylated histone binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24912" xsd:anyURI created_by: pg creation_date: 2024-11-29T15:16:39Z +[Term] +id: GO:0140006 +name: H3 histone reader activity +namespace: molecular_function +def: "A histone reader that specifically binds either to an unmodified histone H3 or a form modified by a post-translational modification on a specific residue. The most common PTMs on histones are methylation, acetylation and phosphorylation." [PMID:24984779, PMID:34726351] +is_a: GO:0140566 ! histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27427" xsd:anyURI +created_by: pg +creation_date: 2024-12-06T13:03:19Z + [Term] id: GO:0140007 name: KICSTOR complex @@ -450222,6 +450233,17 @@ relationship: capable_of_part_of GO:1903432 ! regulation of TORC1 signaling created_by: pg creation_date: 2017-03-10T12:47:30Z +[Term] +id: GO:0140008 +name: H4 histone reader activity +namespace: molecular_function +def: "A histone reader that specifically binds either to an unmodified histone H4 or a form modified by a post-translational modification on a specific residue. The most common PTMs on histones are methylation, acetylation and phosphorylation." [PMID:24984779, PMID:27890782] +is_a: GO:0140566 ! histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29384" xsd:anyURI +created_by: pg +creation_date: 2024-12-06T13:09:47Z + [Term] id: GO:0140009 name: L-aspartate import across plasma membrane @@ -450246,6 +450268,30 @@ relationship: part_of GO:0070777 ! D-aspartate transmembrane transport created_by: pg creation_date: 2017-03-13T11:15:15Z +[Term] +id: GO:0140011 +name: H4K12ac histone reader activity +namespace: molecular_function +def: "A histone reader that recognizes a histone H4 acetylated at lysine 12." [PMID:14731392] +synonym: "H4K12ac modified histone binding" NARROW [] +is_a: GO:0140008 ! H4 histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29384" xsd:anyURI +created_by: pg +creation_date: 2024-12-06T15:08:12Z + +[Term] +id: GO:0140012 +name: H4K5ac histone reader activity +namespace: molecular_function +def: "A histone reader that recognizes a histone H4 acetylated at lysine 5." [PMID:18406326, PMID:20709061] +synonym: "H4K5ac modified histone binding" NARROW [] +is_a: GO:0140008 ! H4 histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29384" xsd:anyURI +created_by: pg +creation_date: 2024-12-06T15:38:06Z + [Term] id: GO:0140013 name: meiotic nuclear division @@ -450273,6 +450319,30 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pg creation_date: 2017-03-23T14:44:23Z +[Term] +id: GO:0140015 +name: H3K14ac histone reader activity +namespace: molecular_function +def: "A histone reader that recognizes a histone H3 acetylated at lysine 14." [PMID:30110338] +synonym: "H3K14ac modified histone binding" NARROW [] +is_a: GO:0140006 ! H3 histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29384" xsd:anyURI +created_by: pg +creation_date: 2024-12-06T15:39:27Z + +[Term] +id: GO:0140017 +name: H3K18cr histone reader activity +namespace: molecular_function +def: "A histone reader that recognizes a histone H3 crotonylated at lysine 18." [PMID:27105114] +synonym: "H3K18cr modified histone binding" NARROW [] +is_a: GO:0140006 ! H3 histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29384" xsd:anyURI +created_by: pg +creation_date: 2024-12-06T15:41:32Z + [Term] id: GO:0140018 name: regulation of cytoplasmic translational fidelity @@ -450283,6 +450353,18 @@ is_a: GO:1900247 ! regulation of cytoplasmic translational elongation created_by: pg creation_date: 2017-04-06T12:27:10Z +[Term] +id: GO:0140019 +name: H3K9cr histone reader activity +namespace: molecular_function +def: "A histone reader that recognizes a histone H3 crotonylated at lysine 9." [PMID:27105114] +synonym: "H3K18cr modified histone binding" NARROW [] +is_a: GO:0140006 ! H3 histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29384" xsd:anyURI +created_by: pg +creation_date: 2024-12-06T15:43:48Z + [Term] id: GO:0140020 name: DNA methyltransferase complex @@ -450482,6 +450564,18 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pg creation_date: 2017-05-18T06:29:27Z +[Term] +id: GO:0140038 +name: H3K27cr histone reader activity +namespace: molecular_function +def: "A histone reader that recognizes a histone H3 crotonylated at lysine 27." [PMID:27105114] +synonym: "H3K27cr modified histone binding" NARROW [] +is_a: GO:0140006 ! H3 histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29384" xsd:anyURI +created_by: pg +creation_date: 2024-12-06T15:44:30Z + [Term] id: GO:0140039 name: cell-cell adhesion in response to extracellular stimulus @@ -450549,6 +450643,30 @@ intersection_of: has_target_end_location GO:0070056 ! prospore membrane leading created_by: pg creation_date: 2017-06-19T09:20:13Z +[Term] +id: GO:0140044 +name: H3K18ac histone reader activity +namespace: molecular_function +def: "A histone reader that recognizes a histone H3 acetylated at lysine 18." [PMID:30110338] +synonym: "H3K18ac modified histone binding" NARROW [] +is_a: GO:0140006 ! H3 histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29384" xsd:anyURI +created_by: pg +creation_date: 2024-12-06T15:47:07Z + +[Term] +id: GO:0140046 +name: H4K16ac histone reader activity +namespace: molecular_function +def: "A histone reader that recognizes a histone H4 acetylated at lysine 16." [PMID:16085498] +synonym: "H4K16ac modified histone binding" NARROW [] +is_a: GO:0140008 ! H4 histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29384" xsd:anyURI +created_by: pg +creation_date: 2024-12-06T15:53:35Z + [Term] id: GO:0140048 name: manganese ion export across plasma membrane From 210d902c20faad1926640ecd5c80120c701257a6 Mon Sep 17 00:00:00 2001 From: Pascale Gaudet Date: Fri, 6 Dec 2024 18:22:22 +0100 Subject: [PATCH 2/2] created new terms fixes #29384 --- src/ontology/go-edit.obo | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index e76783ee1c..0c22d425e9 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -450216,7 +450216,7 @@ creation_date: 2024-11-29T15:16:39Z id: GO:0140006 name: H3 histone reader activity namespace: molecular_function -def: "A histone reader that specifically binds either to an unmodified histone H3 or a form modified by a post-translational modification on a specific residue. The most common PTMs on histones are methylation, acetylation and phosphorylation." [PMID:24984779, PMID:34726351] +def: "A histone reader that specifically binds either to an unmodified histone H3 or a form modified by a post-translational modification on a specific residue. The most common PTMs on histones are methylation, acetylation and phosphorylation." [PMID:11498575, PMID:25688442, PMID:31082667, PMID:34726351] is_a: GO:0140566 ! histone reader activity relationship: has_part GO:0035064 ! methylated histone binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27427" xsd:anyURI @@ -450237,7 +450237,7 @@ creation_date: 2017-03-10T12:47:30Z id: GO:0140008 name: H4 histone reader activity namespace: molecular_function -def: "A histone reader that specifically binds either to an unmodified histone H4 or a form modified by a post-translational modification on a specific residue. The most common PTMs on histones are methylation, acetylation and phosphorylation." [PMID:24984779, PMID:27890782] +def: "A histone reader that specifically binds either to an unmodified histone H4 or a form modified by a post-translational modification on a specific residue. The most common PTMs on histones are methylation, acetylation and phosphorylation." [PMID:11498575, PMID:25688442, PMID:31082667, PMID:34726351] is_a: GO:0140566 ! histone reader activity relationship: has_part GO:0035064 ! methylated histone binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29384" xsd:anyURI @@ -450358,7 +450358,7 @@ id: GO:0140019 name: H3K9cr histone reader activity namespace: molecular_function def: "A histone reader that recognizes a histone H3 crotonylated at lysine 9." [PMID:27105114] -synonym: "H3K18cr modified histone binding" NARROW [] +synonym: "H3K9cr modified histone binding" NARROW [] is_a: GO:0140006 ! H3 histone reader activity relationship: has_part GO:0035064 ! methylated histone binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29384" xsd:anyURI @@ -455185,7 +455185,7 @@ creation_date: 2020-11-25T16:07:58Z id: GO:0140566 name: histone reader activity namespace: molecular_function -def: "A chromatin adaptor activity that brings together a protein and a specific form of histone, either modified by a post-translational modification, or the unmodified form. Histone readers have roles in many processes, including in centromere function or in modulating the accessibility of cis-regulatory regions to the transcription machinery." [PMID:11498575, PMID:25688442, PMID:31082667, PMID:32260176, PMID:34726351] +def: "A chromatin adaptor activity that brings together a protein and a specific form of histone, either modified by a post-translational modification, or the unmodified form. Histone readers have roles in many processes, including in centromere function or in modulating the accessibility of cis-regulatory regions to the transcription machinery." [PMID:11498575, PMID:25688442, PMID:31082667, PMID:34726351] synonym: "epigenetic reader" BROAD [] synonym: "histone reader" EXACT [] is_a: GO:0140463 ! chromatin-protein adaptor activity