Merge pull request #29260 from geneontology/issue-26918-2

obsoleted term fixes #29259, fixed def fixes #29254, added references…

src/ontology/go-edit.obo

@@ -200534,11 +200534,12 @@ is_a: GO:0052041 ! symbiont-mediated suppression of host programmed cell death
 
 [Term]
 id: GO:0034055
-name: effector-mediated activation of programmed cell death in host
+name: effector-mediated activation of host programmed cell death by symbiont
 namespace: biological_process
 def: "A symbiont process in which a molecule secreted by the symbiont activates a programmed cell death pathway in the host to suppress the host innate immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
 comment: Note that this term is used to annotate gene products of the symbiont.
 synonym: "activation by symbiont of host defense-related programmed cell death" NARROW [GOC:pamgo_curators]
+synonym: "effector-mediated activation of programmed cell death in host" EXACT []
 synonym: "effector-mediated induction of programmed cell death in host" EXACT []
 synonym: "enhancement by symbiont of host defense-related programmed cell death" NARROW [GOC:pamgo_curators]
 synonym: "positive regulation by symbiont of host defense-related PCD" EXACT [GOC:pamgo_curators]
@@ -200548,9 +200549,7 @@ synonym: "up regulation by symbiont of host defense-related programmed cell deat
 synonym: "up-regulation by symbiont of host defense-related programmed cell death" EXACT [GOC:pamgo_curators]
 synonym: "upregulation by symbiont of host defense-related programmed cell death" EXACT [GOC:pamgo_curators]
 is_a: GO:0034053 ! symbiont-mediated perturbation of host defense-related programmed cell death
-is_a: GO:0052042 ! symbiont-mediated activation of host programmed cell death
 is_a: GO:0052170 ! symbiont-mediated suppression of host innate immune response
-is_a: GO:0140418 ! effector-mediated perturbation of host process by symbiont
 intersection_of: GO:0140418 ! effector-mediated perturbation of host process by symbiont
 intersection_of: positively_regulates_in_another_organism GO:0012501 ! programmed cell death
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20284" xsd:anyURI
@@ -230191,6 +230190,7 @@ synonym: "negative regulation by virus of host mRNA nuclear export" BROAD [GOC:b
 synonym: "suppression by virus of host mRNA export from nucleus" NARROW []
 synonym: "suppression of host mRNA nuclear export by virus" NARROW []
 xref: VZ:902 "Inhibition of host mRNA nuclear export by virus"
+is_a: GO:0039657 ! symbiont-mediated suppression of host gene expression
 intersection_of: GO:0044003 ! symbiont-mediated perturbation of host process
 intersection_of: negatively_regulates_in_another_organism GO:0006406 ! mRNA export from nucleus
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26922" xsd:anyURI
@@ -258846,7 +258846,6 @@ namespace: biological_process
 def: "A process in which a symbiont initiates, promotes, or enhances the normal activation of plasminogen, the pathway resulting in the processing of inactive plasminogen to active plasmin in the host organism. This can facilitate the dissemination of the symbiont into host tissues. It can also be used to destroy complement, opsonins as well as antibacterial proteins like histones." [PMID:18070889, PMID:27533300, PMID:34305859]
 synonym: "plasminogen activation in another organism" BROAD []
 synonym: "plasminogen activation in other organism" BROAD []
-is_a: GO:0052031 ! symbiont-mediated perturbation of host defense response
 intersection_of: GO:0044003 ! symbiont-mediated perturbation of host process
 intersection_of: positively_regulates_in_another_organism GO:0031639 ! plasminogen activation
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26812" xsd:anyURI
@@ -326755,7 +326754,6 @@ def: "Reactions triggered in response to the presence of a virus that act to pro
 synonym: "antiviral response" EXACT []
 synonym: "defence response to virus" EXACT []
 synonym: "defense response to viruses" EXACT []
-is_a: GO:0140546 ! defense response to symbiont
 intersection_of: GO:0006952 ! defense response
 intersection_of: has_primary_input NCBITaxon:10239 ! Viruses
 
@@ -331560,7 +331558,7 @@ def: "A process in which a symbiont alters or subverts the normal execution of t
 synonym: "modulation by organism of inflammatory response of other organism involved in symbiotic interaction" BROAD []
 synonym: "modulation by symbiont of host inflammatory response" EXACT []
 synonym: "perturbation by symbiont of host inflammatory response" EXACT []
-is_a: GO:0052031 ! symbiont-mediated perturbation of host defense response
+is_a: GO:0052167 ! symbiont-mediated perturbation of host innate immune response
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25016" xsd:anyURI
 
 [Term]
@@ -331638,7 +331636,6 @@ synonym: "inhibition by symbiont of host inflammatory response" NARROW []
 synonym: "negative regulation by organism of inflammatory response of other organism involved in symbiotic interaction" BROAD []
 synonym: "negative regulation by symbiont of host inflammatory response" EXACT []
 synonym: "suppression by symbiont of host inflammatory response" EXACT []
-is_a: GO:0044414 ! symbiont-mediated suppression of host defenses
 is_a: GO:0052032 ! symbiont-mediated perturbation of host inflammatory response
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25016" xsd:anyURI
 
@@ -331723,7 +331720,6 @@ synonym: "stimulation by symbiont of host programmed cell death" NARROW []
 synonym: "upregulation by symbiont of host programmed cell death" EXACT []
 intersection_of: GO:0044003 ! symbiont-mediated perturbation of host process
 intersection_of: positively_regulates_in_another_organism GO:0012501 ! programmed cell death
-relationship: part_of GO:0001907 ! symbiont-mediated killing of host cell
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23652" xsd:anyURI
 
 [Term]
@@ -399430,6 +399426,7 @@ synonym: "intracellular virion transport" RELATED []
 synonym: "movement of virus within host cell" EXACT []
 synonym: "viral egress" RELATED []
 synonym: "viral genome transport in host cell" EXACT []
+is_a: GO:0044403 ! biological process involved in symbiotic interaction
 intersection_of: GO:0046794 ! transport of virus
 intersection_of: occurs_in GO:0043657 ! host cell
 relationship: part_of GO:0019058 ! viral life cycle
@@ -419795,12 +419792,13 @@ creation_date: 2012-07-19T14:16:51Z
 id: GO:0098026
 name: virus tail, tube
 namespace: cellular_component
-def: "The internal tube of the contractile tails of some viruses. The virus tail tube is the channel for DNA ejection into the host cytoplasm." [GOC:bm, VZ:3960]
-comment: Applies in particular the Myoviridae bacteriophages.
+def: "The internal tube of the tail of some viruses. The virus tail tube is the channel for DNA ejection into the host cytoplasm." [PMID:33188213, VZ:3960]
+comment: Applies in particular the Myoviridae bacteriophages. Many bacteriophages with dsDNA genomes, or Caudovirales, have a tail. The viral tail can be short (Podoviridae), long and non-contractile (Siphoviridae) or long and contractile (Myoviridae). The tail is the channel through which the phage genome is injected into the host bacterial cell.
 synonym: "bacteriophage tail tube" NARROW [GOC:bm]
 xref: VZ:3960 "Viral tail tube protein"
 is_a: GO:0044423 ! virion component
 relationship: part_of GO:0098015 ! virus tail
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29254" xsd:anyURI
 created_by: bm
 creation_date: 2012-07-19T14:21:28Z
 
@@ -451033,14 +451031,17 @@ creation_date: 2017-11-10T08:55:38Z
 
 [Term]
 id: GO:0140133
-name: symbiont-mediated suppression of host cytokine production
+name: obsolete symbiont-mediated suppression of host cytokine production
 namespace: biological_process
-def: "A process by which a symbiont inhibits or disrupts cytokine production in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:23083102]
+def: "OBSOLETE. A process by which a symbiont inhibits or disrupts cytokine production in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:23083102]
+comment: This term was obsoleted because it represents a readout.
 synonym: "negative regulation by symbiont of host cytokine production" EXACT []
 synonym: "suppression by symbiont of host cytokine production" EXACT []
 synonym: "suppression by symbiont of host cytokine secretion" RELATED []
-is_a: GO:0052170 ! symbiont-mediated suppression of host innate immune response
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14553" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29259" xsd:anyURI
+is_obsolete: true
+consider: GO:0052027
 created_by: pg
 creation_date: 2017-11-14T07:07:04Z
 
@@ -462030,7 +462031,7 @@ creation_date: 2024-01-30T15:48:01Z
 id: GO:0141154
 name: symbiont-mediated suppression of host-directed shutoff of host translation
 namespace: biological_process
-def: "A process in which a symbiont inhibits or disrupts the host shutoff of host translation, a host response that prevents mRNA in the cell to be translated, to prevent the symbiont from expressing its genes. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pg]
+def: "A process in which a symbiont inhibits or disrupts the host shutoff of host translation, a host response that prevents mRNA in the cell to be translated, to prevent the symbiont from expressing its genes. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:20563710, PMID:21622569]
 is_a: GO:0044414 ! symbiont-mediated suppression of host defenses
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26918" xsd:anyURI
 created_by: pg
@@ -462340,7 +462341,6 @@ id: GO:0141184
 name: symbiont-mediated activation of host anti-inflammatory cytokine signaling
 namespace: biological_process
 def: "A process in which a symbiont subverts an anti-inflammatory cytokine signaling pathway in the host organism by initiating, promoting, or enhancing its activation." [PMID:23284742, PMID:27437422, PMID:29924996]
-synonym: "cytokine storm" RELATED []
 is_a: GO:0052028 ! symbiont-mediated activation of host signal transduction pathway
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27129" xsd:anyURI
 created_by: pg