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wording changes to terms for parts of bacterial-type flagellum, #14283 #14377

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Oct 18, 2017
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wording changes to terms for parts of bacterial-type flagellum, #14283 #14377

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32 changes: 16 additions & 16 deletions src/ontology/go-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -113982,7 +113982,7 @@ is_a: GO:0044443 ! pilus part
id: GO:0009420
name: bacterial-type flagellum filament
namespace: cellular_component
def: "The long (approximately 20 nm), thin external structure of the flagellum, which acts as a propeller. Examples of this component are found in bacteria." [GOC:mtg_sensu, PMID:10572114, PMID:12624192]
def: "The long (approximately 20 nm), thin external structure of the bacterial-type flagellum, which acts as a propeller." [GOC:cilia, GOC:mtg_sensu, PMID:10572114, PMID:12624192]
subset: gosubset_prok
synonym: "flagellar filament" EXACT []
synonym: "flagellin-based flagellum filament" EXACT []
Expand All @@ -113992,7 +113992,7 @@ is_a: GO:0044461 ! bacterial-type flagellum part
id: GO:0009421
name: bacterial-type flagellum filament cap
namespace: cellular_component
def: "The proteinaceous structure at the distal tip of the flagellar filament. Examples of this component are found in bacteria." [GOC:mtg_sensu, PMID:10572114, PMID:12624192]
def: "The proteinaceous structure at the distal tip of the bacterial-type flagellar filament." [GOC:cilia, GOC:mtg_sensu, PMID:10572114, PMID:12624192]
subset: gosubset_prok
synonym: "flagellar filament cap" EXACT []
synonym: "flagellin-based flagellum filament cap" EXACT []
Expand All @@ -114003,7 +114003,7 @@ relationship: part_of GO:0009420 ! bacterial-type flagellum filament
id: GO:0009422
name: bacterial-type flagellum hook-filament junction
namespace: cellular_component
def: "The region of the flagellum where the hook and filament meet. Examples of this component are found in bacteria." [GOC:mah, GOC:mtg_sensu, PMID:10572114, PMID:12624192]
def: "The region of the bacterial-type flagellum where the hook and filament meet." [GOC:cilia, GOC:mah, GOC:mtg_sensu, PMID:10572114, PMID:12624192]
subset: gosubset_prok
synonym: "flagellar hook-filament junction" EXACT []
is_a: GO:0044461 ! bacterial-type flagellum part
Expand All @@ -114027,7 +114027,7 @@ intersection_of: has_output CHEBI:29748 ! chorismate(2-)
id: GO:0009424
name: bacterial-type flagellum hook
namespace: cellular_component
def: "The portion of the flagellum that connects the filament to the basal body. Examples of this component are found in bacteria." [GOC:mtg_sensu, PMID:10572114, PMID:12624192]
def: "The portion of the bacterial-type flagellum that connects the filament to the basal body." [GOC:cilia, GOC:mtg_sensu, PMID:10572114, PMID:12624192]
subset: gosubset_prok
synonym: "flagellar hook" EXACT []
synonym: "flagellin-based flagellum hook" EXACT []
Expand All @@ -114047,7 +114047,7 @@ is_a: GO:0044461 ! bacterial-type flagellum part
id: GO:0009426
name: bacterial-type flagellum basal body, distal rod
namespace: cellular_component
def: "The portion of the central rod of the flagellar basal body that is distal to the cell membrane; spans most of the distance between the inner and outer membranes. Examples of this component are found in bacteria." [GOC:mtg_sensu, PMID:10572114, PMID:11133968, PMID:12624192]
def: "The portion of the central rod of the bacterial-type flagellar basal body that is distal to the cell membrane; spans most of the distance between the inner and outer membranes." [GOC:cilia, GOC:mtg_sensu, PMID:10572114, PMID:11133968, PMID:12624192]
subset: gosubset_prok
synonym: "flagellar basal body, distal rod" EXACT []
synonym: "flagellin-based flagellum basal body, distal rod" EXACT []
Expand All @@ -114058,7 +114058,7 @@ relationship: part_of GO:0030694 ! bacterial-type flagellum basal body, rod
id: GO:0009427
name: bacterial-type flagellum basal body, distal rod, L ring
namespace: cellular_component
def: "One of the rings of the flagellar basal body; anchors the basal body to the outer membrane. Examples of this component are found in bacteria." [GOC:mtg_sensu, PMID:10572114, PMID:12624192]
def: "One of the rings of the bacterial-type flagellar basal body; anchors the basal body to the outer membrane." [GOC:cilia, GOC:mtg_sensu, PMID:10572114, PMID:12624192]
subset: gosubset_prok
synonym: "flagellar basal body, distal rod, L ring" EXACT []
synonym: "flagellin-based flagellum basal body, distal rod, L ring" EXACT []
Expand All @@ -114069,7 +114069,7 @@ relationship: part_of GO:0009426 ! bacterial-type flagellum basal body, distal r
id: GO:0009428
name: bacterial-type flagellum basal body, distal rod, P ring
namespace: cellular_component
def: "One of the rings of the flagellar basal body; anchors the basal body to the peptidoglycan layer. Examples of this component are found in bacteria." [GOC:mtg_sensu, PMID:10572114, PMID:12624192]
def: "One of the rings of the bacterial-type flagellar basal body; anchors the basal body to the peptidoglycan layer." [GOC:cilia, GOC:mtg_sensu, PMID:10572114, PMID:12624192]
subset: gosubset_prok
synonym: "flagellar basal body, distal rod, P ring" RELATED []
synonym: "flagellin-based flagellum basal body, distal rod, P ring" EXACT []
Expand All @@ -114080,7 +114080,7 @@ relationship: part_of GO:0009426 ! bacterial-type flagellum basal body, distal r
id: GO:0009429
name: bacterial-type flagellum basal body, proximal rod
namespace: cellular_component
def: "The portion of the central rod of the flagellar basal body that is proximal to the cell membrane; proximal rod connects the distal rod to the flagellar motor. Examples of this component are found in bacteria." [GOC:mtg_sensu, PMID:10572114, PMID:11133968, PMID:12624192]
def: "The portion of the central rod of the bacterial-type flagellar basal body that is proximal to the cell membrane; the proximal rod connects the distal rod to the flagellar motor." [GOC:cilia, GOC:mtg_sensu, PMID:10572114, PMID:11133968, PMID:12624192]
subset: gosubset_prok
synonym: "flagellar basal body, proximal rod" EXACT []
synonym: "flagellin-based flagellum basal body, proximal rod" EXACT []
Expand All @@ -114092,7 +114092,7 @@ id: GO:0009431
name: bacterial-type flagellum basal body, MS ring
namespace: cellular_component
alt_id: GO:0009430
def: "One of the rings of the flagellar basal body; a double-flanged ring that anchors the basal body to the cytoplasmic membrane. Examples of this component are found in bacteria." [GOC:mtg_sensu, PMID:10572114, PMID:12624192]
def: "One of the rings of the bacterial-type flagellar basal body; a double-flanged ring that anchors the basal body to the cytoplasmic membrane." [GOC:cilia, GOC:mtg_sensu, PMID:10572114, PMID:12624192]
subset: gosubset_prok
synonym: "flagellar basal body, mounting plate" BROAD []
synonym: "flagellar basal body, MS ring" EXACT []
Expand All @@ -114115,7 +114115,7 @@ relationship: never_in_taxon NCBITaxon:2759 ! Eukaryota
id: GO:0009433
name: bacterial-type flagellum basal body, C ring
namespace: cellular_component
def: "Cytoplasmic ring located at the base of the flagellar basal body; acts as a rotor; includes three switch proteins, which generate torque and can change their conformational state in a bimodal fashion, so that the motor direction can switch between clockwise and counterclockwise. Examples of this component are found in bacteria." [GOC:mtg_sensu, PMID:10572114, PMID:12624192]
def: "Cytoplasmic ring located at the base of the bacterial-type flagellar basal body; acts as a rotor; includes three switch proteins, which generate torque and can change their conformational state in a bimodal fashion, so that the motor direction can switch between clockwise and counterclockwise." [GOC:cilia, GOC:mtg_sensu, PMID:10572114, PMID:12624192]
subset: gosubset_prok
synonym: "flagellar basal body, C ring" EXACT []
synonym: "flagellin-based flagellum basal body, C ring" EXACT []
Expand Down Expand Up @@ -193800,7 +193800,7 @@ replaced_by: GO:0004197
id: GO:0030694
name: bacterial-type flagellum basal body, rod
namespace: cellular_component
def: "The central portion of the flagellar basal body, which spans the periplasm and threads through the rings. Examples of this component are found in Bacterial species." [GOC:mtg_sensu, PMID:10572114, PMID:11133968, PMID:12624192]
def: "The central portion of the bacterial-type flagellar basal body, which spans the periplasm and threads through the rings." [GOC:cilia, GOC:mtg_sensu, PMID:10572114, PMID:11133968, PMID:12624192]
subset: gosubset_prok
synonym: "flagellar basal body, rod" EXACT []
synonym: "flagellin-based flagellum basal body, rod" EXACT []
Expand Down Expand Up @@ -289916,7 +289916,7 @@ consider: GO:0044441
id: GO:0044461
name: bacterial-type flagellum part
namespace: cellular_component
def: "Any constituent part of flagellum, a 20 nm diameter filament composed of subunits of flagellin driven passively at its base by a motor powered by a transmembrane ion potential, typically a proton or sodium potential. Examples of this component are found in bacterial species." [DOI:10.1002/9780470015902.a0000744.pub4, GOC:cilia, GOC:jl, GOC:mtg_sensu, PMID:10572114, PMID:12624192, PMID:25251856]
def: "Any constituent part of the bacterial-type flagellum, a 20 nm diameter filament composed of subunits of flagellin driven passively at its base by a motor powered by a transmembrane ion potential, typically a proton or sodium potential." [DOI:10.1002/9780470015902.a0000744.pub4, GOC:cilia, GOC:jl, GOC:mtg_sensu, PMID:10572114, PMID:12624192, PMID:25251856]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: goantislim_grouping
subset: gocheck_do_not_annotate
Expand Down Expand Up @@ -476471,7 +476471,7 @@ creation_date: 2017-09-28T21:41:34Z
id: GO:0120100
name: bacterial-type flagellum motor
namespace: cellular_component
def: "A transmembrane complex embedded in the cytoplasmic membrane which is the motor force, or torque, generator of the bacterial-type flagellum. The motor consists of a membrane-anchored rotor complex surrounded by one or more stator complexes in the cytoplasmic membrane. The stator consists of a hetero-hexameric complex of 2 membrane proteins, A and B, with stoichiometry A4B2. Examples are the H+ -driven MotA-MotB stator complex of Escherichia coli and Salmonella enterica, and the Na+ -driven PomA-PomB stator complex of Vibrio and Shewanella species. The rotor complex consists of a membrane-anchored ring and the motor switch complex, which controls the direction of flagellar rotation." [DOI:10.1002/9780470015902.a0000744.pub4, GOC:cilia, PMID:10572114, PMID:12624192, PMID:24697492, PMID:25251856]
def: "A transmembrane complex embedded in the cytoplasmic membrane which is the motor force, or torque, generator of the bacterial-type flagellum. The motor consists of a membrane-anchored rotor complex surrounded by one or more stator complexes in the cytoplasmic membrane. The stator consists of a hetero-hexameric complex of 2 membrane proteins, A and B, with stoichiometry A4B2. Examples are the H+ driven MotA-MotB stator complex of Escherichia coli and Salmonella enterica, and the Na+ driven PomA-PomB stator complex of Vibrio and Shewanella species. The rotor complex consists of a membrane-anchored ring and the motor switch complex, which controls the direction of flagellar rotation." [DOI:10.1002/9780470015902.a0000744.pub4, GOC:cilia, PMID:10572114, PMID:12624192, PMID:24697492, PMID:25251856]
is_a: GO:0044461 ! bacterial-type flagellum part
relationship: part_of GO:0009425 ! bacterial-type flagellum basal body
created_by: kchris
Expand All @@ -476481,7 +476481,7 @@ creation_date: 2017-10-03T15:44:35Z
id: GO:0120101
name: bacterial-type flagellum stator complex
namespace: cellular_component
def: "A hetero-hexameric complex of 2 membrane proteins, A and B, with stoichiometry A4B2. The A and B proteins form a channel through which the ions that power the flagellum flow. They form the stator, or nonrotating portion, of the flagellum motor with the B protein apparently attached to the peptidoglycan cell wall. Examples are the H+ -driven MotA-MotB stator complex of Escherichia coli and Salmonella enterica, and the Na+ -driven PomA-PomB stator complex of Vibrio and Shewanella species." [GOC:cilia, PMID:10572114, PMID:12624192, PMID:24697492, PMID:25251856]
def: "A hetero-hexameric complex of 2 membrane proteins, A and B, with stoichiometry A4B2. The A and B proteins form a channel through which flow the ions that power the bacterial-type flagellum. They form the stator, or nonrotating portion, of the flagellum motor with the B protein apparently attached to the peptidoglycan cell wall. Examples include the H+ driven MotA-MotB stator complex of Escherichia coli and Salmonella enterica, and the Na+ driven PomA-PomB stator complex of Vibrio and Shewanella species." [GOC:cilia, PMID:10572114, PMID:12624192, PMID:24697492, PMID:25251856]
synonym: "bacterial-type flagellum motor force generator complex" EXACT [PMID:24697492]
synonym: "bacterial-type flagellum torque generator complex" EXACT [DOI:10.1002/9780470015902.a0000744.pub4]
is_a: GO:0005887 ! integral component of plasma membrane
Expand All @@ -476494,7 +476494,7 @@ creation_date: 2017-10-03T16:06:16Z
id: GO:0120102
name: bacterial-type flagellum secretion apparatus
namespace: cellular_component
def: "A structure located at the cytoplasmic side of the MS ring and composed of six membrane proteins (FlhA, FlhB, FliP, FliQ, FliR, and FliO, or orthologs thereof) and three soluble proteins (FliI, FliH, and FliJ, or orthologs thereof) in the cytoplasm. It is responsible for secretion of flagellar type III protein substrates, including the proteins of the flagellar rod, hook, and filament." [DOI:10.1002/9780470015902.a0000744.pub4, GOC:cilia, PMID:10572114, PMID:12624192, PMID:24697492, PMID:25251856]
def: "A part of the bacterial-type flagellum that is located at the cytoplasmic side of the MS ring and composed of six membrane proteins (FlhA, FlhB, FliP, FliQ, FliR, and FliO, or orthologs thereof) and three soluble proteins (FliI, FliH, and FliJ, or orthologs thereof) in the cytoplasm. It is responsible for secretion of flagellar type III protein substrates, including the proteins of the flagellar rod, hook, and filament." [DOI:10.1002/9780470015902.a0000744.pub4, GOC:cilia, PMID:10572114, PMID:12624192, PMID:24697492, PMID:25251856]
synonym: "bacterial-type flagellum export apparatus" EXACT []
is_a: GO:0044461 ! bacterial-type flagellum part
relationship: part_of GO:0009425 ! bacterial-type flagellum basal body
Expand Down Expand Up @@ -476548,7 +476548,7 @@ creation_date: 2017-10-11T22:56:44Z
id: GO:0120107
name: bacterial-type flagellum rotor complex
namespace: cellular_component
def: "The rotor complex consists of a membrane-anchored ring and the motor switch complex, which participates in the conversion of proton/Na+ energy into the mechanical work of rotation and controls the direction of flagellar rotation." [GOC:cilia, PMID:10572114, PMID:12624192, PMID:25251856]
def: "The rotor complex of the bacterial-type flagellum consists of a membrane-anchored ring and the motor switch complex, which participates in the conversion of proton/Na+ energy into the mechanical work of rotation and controls the direction of flagellar rotation." [GOC:cilia, PMID:10572114, PMID:12624192, PMID:25251856]
is_a: GO:0044461 ! bacterial-type flagellum part
relationship: part_of GO:0120100 ! bacterial-type flagellum motor
created_by: kchris
Expand Down