Merge pull request #29338 from geneontology/issue-histone-reader

created new terms, fixes #29337, fixes #24912, Change modification-de…

src/ontology/go-edit.obo

@@ -163668,7 +163668,7 @@ relationship: part_of GO:0044304 ! main axon
 id: GO:0030674
 name: protein-macromolecule adaptor activity
 namespace: molecular_function
-def: "The binding activity of a protein that brings together two or more macromolecules in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid." [GOC:bf, GOC:mah, GOC:vw]
+def: "An adaptor activity that brings together two or more macromolecules in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid." [GOC:bf, GOC:mah, GOC:vw]
 subset: goslim_chembl
 subset: goslim_yeast
 synonym: "protein binding, bridging" EXACT []
@@ -359678,11 +359678,14 @@ creation_date: 2014-05-14T14:32:02Z
 
 [Term]
 id: GO:0061628
-name: H3K27me3 modified histone binding
+name: H3K27me3 histone reader activity
 namespace: molecular_function
-def: "Binding to a histone H3 in which the lysine residue at position 27 has been modified by trimethylation." [GOC:dph, PMID:23948251]
-synonym: "H3-K27me3 modified histone binding" EXACT [GOC:dph]
-is_a: GO:0035064 ! methylated histone binding
+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
+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: dph
 creation_date: 2014-05-14T15:36:53Z
 
@@ -359892,7 +359895,7 @@ creation_date: 2014-10-02T15:26:53Z
 id: GO:0061649
 name: ubiquitin-modified histone reader activity
 namespace: molecular_function
-def: "A molecular adaptor that recognizes and binds a histone protein containing a ubiquitination modification and that brings the target protein into contact with another protein to allow those proteins to function in a coordinated way." [GOC:dph, PMID:24526689]
+def: "A histone reader that recognizes a histone that bears a ubiquinated lysine residue." [GOC:dph, PMID:24526689]
 synonym: "ubiquitin modification-dependent histone binding" EXACT []
 synonym: "ubiquitinated histone binding" RELATED []
 is_a: GO:0140036 ! ubiquitin-modified protein reader activity
@@ -364105,10 +364108,13 @@ creation_date: 2018-09-04T13:40:52Z
 
 [Term]
 id: GO:0062072
-name: H3K9me3 modified histone binding
+name: H3K9me3 histone reader activity
 namespace: molecular_function
-def: "Binding to a histone H3 in which the lysine residue at position 9 has been modified by trimethylation." [PMID:30110338]
-is_a: GO:0035064 ! methylated histone binding
+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
+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: dph
 creation_date: 2018-09-05T12:58:43Z
 
@@ -450096,6 +450102,57 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i
 created_by: pg
 creation_date: 2024-11-12T09:29:56Z
 
+[Term]
+id: GO:0140002
+name: H3K4me3 histone reader activity
+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
+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
+creation_date: 2024-11-29T14:13:16Z
+
+[Term]
+id: GO:0140003
+name: H3K36me3 histone reader activity
+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
+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
+creation_date: 2024-11-29T14:20:22Z
+
+[Term]
+id: GO:0140004
+name: H3Q5ser histone reader activity
+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
+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
+creation_date: 2024-11-29T14:37:52Z
+
+[Term]
+id: GO:0140005
+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
+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:0140007
 name: KICSTOR complex
@@ -453960,7 +454017,7 @@ creation_date: 2020-05-06T07:47:09Z
 id: GO:0140463
 name: chromatin-protein adaptor activity
 namespace: molecular_function
-def: "The binding activity of a molecule that brings together a protein or a protein complex with a nucleosome, to establish or maintain the chromatin localization of the protein, or protein complex." [PMID:32277274]
+def: "An adaptor activity that brings together a protein and a region of the chromatin, such as a nucleosome, to establish or maintain the chromatin localization of the protein, or the complex to which it belongs." [PMID:32277274]
 synonym: "chromatin adaptor" EXACT []
 synonym: "chromatin adaptor activity" EXACT []
 synonym: "chromatin receptor" EXACT []
@@ -454940,7 +454997,7 @@ creation_date: 2020-11-25T16:07:58Z
 id: GO:0140566
 name: histone reader activity
 namespace: molecular_function
-def: "A chromatin adaptor that recognizes specific forms of histones, 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:32260176, PMID:34726351]
 synonym: "epigenetic reader" BROAD []
 synonym: "histone reader" EXACT []
 is_a: GO:0140463 ! chromatin-protein adaptor activity
@@ -584071,10 +584128,13 @@ creation_date: 2015-10-28T22:31:13Z
 
 [Term]
 id: GO:1990889
-name: H4K20me3 modified histone binding
+name: H4K20me3 histone reader activity
 namespace: molecular_function
-def: "Binding to a histone H4 in which the lysine residue at position 20 has been modified by trimethylation." [PMID:22150589]
-is_a: GO:0035064 ! methylated histone binding
+def: "A histone reader that recognizes a histone H4 trimethylated at lysine 20." [PMID:22150589]
+synonym: "H4K20me3 modified histone binding" NARROW []
+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: al
 creation_date: 2015-10-30T15:43:09Z