Merge pull request #26356 from geneontology/02-11-23-vw-issues

closes #26342; closes #25267; closes #24424; closes #23886

src/ontology/go-edit.obo

@@ -301,12 +301,14 @@ id: GO:0000027
 name: ribosomal large subunit assembly
 namespace: biological_process
 def: "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit." [GOC:jl, PMID:30467428]
+subset: gocheck_do_not_annotate
 synonym: "50S ribosomal subunit assembly" NARROW [GOC:mah]
 synonym: "60S ribosomal subunit assembly" NARROW [GOC:mah]
 intersection_of: GO:0022607 ! cellular component assembly
 intersection_of: results_in_assembly_of GO:0015934 ! large ribosomal subunit
 relationship: part_of GO:0042255 ! ribosome assembly
 relationship: part_of GO:0042273 ! ribosomal large subunit biogenesis
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23886" xsd:anyURI
 
 [Term]
 id: GO:0000028
@@ -319,6 +321,7 @@ intersection_of: GO:0022607 ! cellular component assembly
 intersection_of: results_in_assembly_of GO:0015935 ! small ribosomal subunit
 relationship: part_of GO:0042255 ! ribosome assembly
 relationship: part_of GO:0042274 ! ribosomal small subunit biogenesis
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23886" xsd:anyURI
 
 [Term]
 id: GO:0000030
@@ -56343,10 +56346,12 @@ def: "The region of a cell that lies just beneath the plasma membrane and often,
 subset: goslim_candida
 subset: goslim_yeast
 synonym: "cell periphery" RELATED []
+synonym: "ectoplasm" NARROW []
 synonym: "peripheral cytoplasm" RELATED []
 xref: Wikipedia:Cell_cortex
 intersection_of: GO:0005737 ! cytoplasm
 intersection_of: part_of GO:0071944 ! cell periphery
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26298" xsd:anyURI
 
 [Term]
 id: GO:0005940
@@ -146562,9 +146567,10 @@ id: GO:0019826
 name: oxygen sensor activity
 namespace: molecular_function
 def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of oxygen (O2)." [GOC:mah]
-is_a: GO:0019825 ! oxygen binding
 intersection_of: GO:0140299 ! small molecule sensor activity
 intersection_of: has_primary_input CHEBI:25805 ! oxygen atom
+relationship: has_part GO:0019825 ! oxygen binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25267" xsd:anyURI
 
 [Term]
 id: GO:0019827
@@ -186342,9 +186348,10 @@ namespace: molecular_function
 def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of a sterol." [GOC:mah]
 synonym: "sterol sensing activity" EXACT []
 synonym: "sterol-sensing domain" NARROW []
-is_a: GO:0032934 ! sterol binding
 intersection_of: GO:0140299 ! small molecule sensor activity
 intersection_of: has_primary_input CHEBI:15889 ! sterol
+relationship: has_part GO:0032934 ! sterol binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25267" xsd:anyURI
 
 [Term]
 id: GO:0032936
@@ -203062,7 +203069,7 @@ synonym: "small subunit processome assembly" EXACT []
 synonym: "SSU processome assembly" EXACT []
 intersection_of: GO:0022607 ! cellular component assembly
 intersection_of: results_in_assembly_of GO:0032040 ! small-subunit processome
-relationship: part_of GO:0000028 ! ribosomal small subunit assembly
+relationship: part_of GO:0180025 ! cytosolic small ribosomal subunit assembly
 
 [Term]
 id: GO:0034463
@@ -203071,8 +203078,8 @@ namespace: biological_process
 def: "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a 90S preribosome. The 90S preribosome represents the complex that forms on the primary rRNA transcript before it splits into the small subunit and large subunit portions." [GOC:krc, GOC:mah, GOC:tb]
 intersection_of: GO:0022607 ! cellular component assembly
 intersection_of: results_in_assembly_of GO:0030686 ! 90S preribosome
-relationship: part_of GO:0000027 ! ribosomal large subunit assembly
-relationship: part_of GO:0000028 ! ribosomal small subunit assembly
+relationship: part_of GO:0042256 ! cytosolic ribosome assembly
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23886" xsd:anyURI
 
 [Term]
 id: GO:0034464
@@ -218755,10 +218762,11 @@ name: nitric oxide sensor activity
 namespace: molecular_function
 def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of nitric oxide (NO)." [GOC:kmv, PMID:21491957]
 synonym: "NO sensor activity" EXACT []
-is_a: GO:0070026 ! nitric oxide binding
 intersection_of: GO:0140299 ! small molecule sensor activity
 intersection_of: has_primary_input CHEBI:16480 ! nitric oxide
+relationship: has_part GO:0070026 ! nitric oxide binding
 relationship: part_of GO:0071731 ! response to nitric oxide
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25267" xsd:anyURI
 created_by: bf
 creation_date: 2011-08-26T04:32:16Z
 
@@ -243095,11 +243103,13 @@ intersection_of: part_of GO:0005576 ! extracellular region
 
 [Term]
 id: GO:0043265
-name: ectoplasm
+name: obsolete ectoplasm
 namespace: cellular_component
-def: "Granule free cytoplasm, lying immediately below the plasma membrane." [GOC:curators, PMID:12211103]
-is_a: GO:0110165 ! cellular anatomical entity
-relationship: part_of GO:0005737 ! cytoplasm
+def: "OBSOLETE. Granule free cytoplasm, lying immediately below the plasma membrane." [GOC:curators, PMID:12211103]
+comment: The reason for obsoletion is that this term was added in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24424" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0005938
 
 [Term]
 id: GO:0043266
@@ -351205,10 +351215,10 @@ id: GO:0061157
 name: mRNA destabilization
 namespace: biological_process
 def: "Any process that decreases the stability of an mRNA molecule, making it more vulnerable to degradative processes. Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [GOC:dph, GOC:jh]
-is_a: GO:0017148 ! negative regulation of translation
 is_a: GO:0043488 ! regulation of mRNA stability
 is_a: GO:0050779 ! RNA destabilization
 relationship: positively_regulates GO:0006402 ! mRNA catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26342" xsd:anyURI
 created_by: dph
 creation_date: 2010-06-22T08:42:10Z
 
@@ -359262,9 +359272,10 @@ id: GO:0061891
 name: calcium ion sensor activity
 namespace: molecular_function
 def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of calcium ions (Ca2+)." [PMID:16005298, PMID:17020874, PMID:28151650]
-is_a: GO:0005509 ! calcium ion binding
 intersection_of: GO:0140299 ! small molecule sensor activity
 intersection_of: has_primary_input CHEBI:29108 ! calcium(2+)
+relationship: has_part GO:0005509 ! calcium ion binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25267" xsd:anyURI
 created_by: dph
 creation_date: 2017-06-01T23:37:01Z
 
@@ -362890,9 +362901,10 @@ name: carbon monoxide sensor activity
 namespace: molecular_function
 def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of carbon monoxide (CO)." [GOC:ecd]
 synonym: "carbon monoxide sensing activity" EXACT []
-is_a: GO:0070025 ! carbon monoxide binding
 intersection_of: GO:0140299 ! small molecule sensor activity
 intersection_of: has_primary_input CHEBI:17245 ! carbon monoxide
+relationship: has_part GO:0070025 ! carbon monoxide binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25267" xsd:anyURI
 
 [Term]
 id: GO:0070028
@@ -408313,9 +408325,10 @@ id: GO:0097063
 name: cadmium ion sensor activity
 namespace: molecular_function
 def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of cadmium (Cd++)." [GOC:rs, PMID:19456862]
-is_a: GO:0046870 ! cadmium ion binding
 intersection_of: GO:0140299 ! small molecule sensor activity
 intersection_of: has_primary_input CHEBI:63063 ! cadmium cation
+relationship: has_part GO:0046870 ! cadmium ion binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25267" xsd:anyURI
 created_by: pr
 creation_date: 2011-06-08T09:46:14Z
 
@@ -408464,9 +408477,10 @@ id: GO:0097077
 name: copper ion sensor activity
 namespace: molecular_function
 def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+)." [GOC:rs, PMID:19928961]
-is_a: GO:0005507 ! copper ion binding
 intersection_of: GO:0140299 ! small molecule sensor activity
 intersection_of: has_primary_input CHEBI:23378 ! copper cation
+relationship: has_part GO:0005507 ! copper ion binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25267" xsd:anyURI
 created_by: pr
 creation_date: 2011-06-17T09:57:11Z
 
@@ -437016,9 +437030,10 @@ id: GO:0106219
 name: zinc ion sensor activity
 namespace: molecular_function
 def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of zinc." [GOC:vw, PMID:31239353]
-is_a: GO:0008270 ! zinc ion binding
 intersection_of: GO:0140299 ! small molecule sensor activity
 intersection_of: has_primary_input CHEBI:63056 ! zinc cation
+relationship: has_part GO:0008270 ! zinc ion binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25267" xsd:anyURI
 created_by: hjd
 creation_date: 2019-08-15T16:45:43Z
 
@@ -444281,10 +444296,11 @@ name: tyrosine sensor activity
 namespace: molecular_function
 def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of tyrosine." [GOC:krc, PMID:31498992]
 synonym: "tyrosine sensing activity" EXACT []
-is_a: GO:0072545 ! tyrosine binding
 intersection_of: GO:0140299 ! small molecule sensor activity
 intersection_of: has_primary_input CHEBI:18186 ! tyrosine
+relationship: has_part GO:0072545 ! tyrosine binding
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20181" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25267" xsd:anyURI
 created_by: krc
 creation_date: 2020-11-18T01:19:42Z
 
@@ -444294,10 +444310,11 @@ name: tryptophan sensor activity
 namespace: molecular_function
 def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of tryptophan." [GOC:krc, PMID:31498992]
 synonym: "tryptophan sensing activity" EXACT []
-is_a: GO:0120284 ! tryptophan binding
 intersection_of: GO:0140299 ! small molecule sensor activity
 intersection_of: has_primary_input CHEBI:64554 ! tryptophan zwitterion
+relationship: has_part GO:0120284 ! tryptophan binding
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20181" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25267" xsd:anyURI
 created_by: krc
 creation_date: 2020-11-18T01:25:01Z
 
@@ -455970,9 +455987,10 @@ name: glucose sensor activity
 namespace: molecular_function
 def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of glucose." [PMID:17470517]
 synonym: "glucose sensing activity" EXACT []
-is_a: GO:0005536 ! glucose binding
 intersection_of: GO:0140299 ! small molecule sensor activity
 intersection_of: has_primary_input CHEBI:17234 ! glucose
+relationship: has_part GO:0005536 ! glucose binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25267" xsd:anyURI
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25792" xsd:anyURI
 created_by: pg
 creation_date: 2023-07-24T13:39:21Z
@@ -459489,23 +459507,61 @@ creation_date: 2023-07-14T13:19:39Z
 id: GO:0180022
 name: RQC-trigger complex
 namespace: cellular_component
-def: "A ribosome disassembly complex which dissociates stalled ribsome subunits as part of the ribosome quality control pathway. RQT complex is composed of a RNA helicase-family proteiny yeast Rqt2 (human ASCC3), a ubiquitin-binding protein yeast Rqt3, (human ASCC2), and Rqt4 (Human TRIP4)." [PMID:28757607, PMID:32099016]
+def: "A ribosome disassembly complex which dissociates stalled ribsome subunits as part of the ribosome quality control pathway. RQT complex is composed of a RNA helicase-family protein yeast Rqt2 (human ASCC3), a ubiquitin-binding protein yeast Rqt3, (human ASCC2), and Rqt4 (Human TRIP4)." [PMID:28757607, PMID:32099016]
 synonym: "RQT complex" EXACT []
 is_a: GO:0032991 ! protein-containing complex
-property_value: creation_dat "2023-10-11T11:40:08Z" xsd:dateTime
+property_value: creation_date "2023-10-11T11:40:08Z" xsd:dateTime
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26239" xsd:anyURI
 created_by: vw
 
+[Term]
+id: GO:0180023
+name: cytosolic large ribosomal subunit assembly
+namespace: biological_process
+def: "The aggregation, arrangement and bonding together of a set of components to form a cytosolic large ribosomal subunit." [PMID:30467428]
+intersection_of: GO:0022607 ! cellular component assembly
+intersection_of: results_in_assembly_of GO:0022625 ! cytosolic large ribosomal subunit
+relationship: part_of GO:0042256 ! cytosolic ribosome assembly
+property_value: creation_date "2023-11-03T16:06:38Z" xsd:dateTime
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23886" xsd:anyURI
+created_by: vw
+
 [Term]
 id: GO:0180024
 name: membrane grommet activity
 namespace: molecular_function
 def: "An activity in which a protein, or group of proteins, acts to restrict the size of a fenestration in a membrane or membrane system (i.e. restrict the diameter of a hole in a membrane). An example of this is the molecular function is performed by ESCRT-III proteins at the nuclear envelope of fission yeast during anaphase B." [PMID:37783794]
 is_a: GO:0003674 ! molecular_function
-property_value: creation_dat "2023-10-30T17:11:51Z" xsd:dateTime
+property_value: creation_date "2023-10-30T17:11:51Z" xsd:dateTime
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26228" xsd:anyURI
 created_by: vw
 
+[Term]
+id: GO:0180025
+name: cytosolic small ribosomal subunit assembly
+namespace: biological_process
+def: "The aggregation, arrangement and bonding together of a set of components to form a cytosolic small ribosomal subunit." [PMID:30467428]
+is_a: GO:0000028 ! ribosomal small subunit assembly
+intersection_of: GO:0022607 ! cellular component assembly
+intersection_of: results_in_assembly_of GO:0022627 ! cytosolic small ribosomal subunit
+relationship: part_of GO:0042256 ! cytosolic ribosome assembly
+property_value: creation_date "2023-11-03T16:22:03Z" xsd:dateTime
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23886" xsd:anyURI
+created_by: vw
+
+[Term]
+id: GO:0180026
+name: mitochondrial small ribosomal subunit assembly
+namespace: biological_process
+def: "The aggregation, arrangement and bonding together of a set of components to form a mitochondrial small ribosomal subunit." [PMID:30467428]
+is_a: GO:0000028 ! ribosomal small subunit assembly
+intersection_of: GO:0022607 ! cellular component assembly
+intersection_of: results_in_assembly_of GO:0005763 ! mitochondrial small ribosomal subunit
+relationship: part_of GO:0061668 ! mitochondrial ribosome assembly
+property_value: creation_date "2023-11-03T16:24:18Z" xsd:dateTime
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23886" xsd:anyURI
+created_by: vw
+
 [Term]
 id: GO:0198738
 name: cell-cell signaling by wnt
@@ -503961,6 +504017,7 @@ synonym: "66S preribosome formation" NARROW [GOC:TermGenie]
 synonym: "preribosome, large subunit precursor formation" EXACT [GOC:TermGenie]
 intersection_of: GO:0022607 ! cellular component assembly
 intersection_of: results_in_assembly_of GO:0030687 ! preribosome, large subunit precursor
+relationship: part_of GO:0000027 ! ribosomal large subunit assembly
 created_by: tb
 creation_date: 2014-01-16T19:38:05Z