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

[pgaudet]

… for #26918

[github-actions[bot]]

Here's a diff of how these changes impact the classified ontology:

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/go.owl
• Version IRI: http://purl.obolibrary.org/obo/go/releases/2024-11-20/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-master.owl/reasoned.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/go.owl
• Version IRI: http://purl.obolibrary.org/obo/go/releases/2024-11-20/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-pr.owl/reasoned.owl

Ontology imports

Ontology annotations

defense response to virus http://purl.obolibrary.org/obo/GO_0051607

Removed

• defense response to virus SubClassOf defense response to symbiont

Added

• defense response to virus SubClassOf defense response to other organism

effector-mediated activation of programmed cell death in host http://purl.obolibrary.org/obo/GO_0034055

Removed

• effector-mediated activation of programmed cell death in host label "effector-mediated activation of programmed cell death in host"

Added

• effector-mediated activation of programmed cell death in host label "effector-mediated activation of host programmed cell death by symbiont"

• effector-mediated activation of programmed cell death in host has_exact_synonym "effector-mediated activation of programmed cell death in host"

intracellular transport of virus http://purl.obolibrary.org/obo/GO_0075733

Added

• intracellular transport of virus SubClassOf biological process involved in symbiotic interaction

regulation of intracellular transport of viral material http://purl.obolibrary.org/obo/GO_1901252

Added

• regulation of intracellular transport of viral material SubClassOf regulation of biological process involved in symbiotic interaction

symbiont-mediated activation of host anti-inflammatory cytokine signaling http://purl.obolibrary.org/obo/GO_0141184

Removed

• symbiont-mediated activation of host anti-inflammatory cytokine signaling has_related_synonym "cytokine storm"

symbiont-mediated activation of host plasminogen http://purl.obolibrary.org/obo/GO_0044542

Removed

• symbiont-mediated activation of host plasminogen SubClassOf symbiont-mediated perturbation of host defense response

symbiont-mediated activation of host programmed cell death http://purl.obolibrary.org/obo/GO_0052042

Removed

• symbiont-mediated activation of host programmed cell death SubClassOf part of some symbiont-mediated killing of host cell

symbiont-mediated perturbation of host inflammatory response http://purl.obolibrary.org/obo/GO_0052032

Removed

• symbiont-mediated perturbation of host inflammatory response SubClassOf symbiont-mediated perturbation of host defense response

Added

• symbiont-mediated perturbation of host inflammatory response SubClassOf symbiont-mediated perturbation of host innate immune response

symbiont-mediated suppression of host cytokine production http://purl.obolibrary.org/obo/GO_0140133

Removed

• symbiont-mediated suppression of host cytokine production label "symbiont-mediated suppression of host cytokine production"

• symbiont-mediated suppression of host cytokine production definition "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."

  • database_cross_reference "PMID:23083102"

• symbiont-mediated suppression of host cytokine production SubClassOf symbiont-mediated suppression of host innate immune response

Added

• symbiont-mediated suppression of host cytokine production label "obsolete symbiont-mediated suppression of host cytokine production"

• symbiont-mediated suppression of host cytokine production consider "GO:0052027"

• symbiont-mediated suppression of host cytokine production definition "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."

  • database_cross_reference "PMID:23083102"

• symbiont-mediated suppression of host cytokine production comment "This term was obsoleted because it represents a readout."

• symbiont-mediated suppression of host cytokine production term tracker item "https://github.com/geneontology/go-ontology/issues/29259"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• symbiont-mediated suppression of host cytokine production deprecated true

symbiont-mediated suppression of host inflammatory response http://purl.obolibrary.org/obo/GO_0052036

Removed

• symbiont-mediated suppression of host inflammatory response SubClassOf symbiont-mediated suppression of host defenses

symbiont-mediated suppression of host mRNA export from nucleus http://purl.obolibrary.org/obo/GO_0039522

Added

• symbiont-mediated suppression of host mRNA export from nucleus SubClassOf symbiont-mediated suppression of host gene expression

symbiont-mediated suppression of host-directed shutoff of host translation http://purl.obolibrary.org/obo/GO_0141154

Removed

• symbiont-mediated suppression of host-directed shutoff of host translation definition "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."
  • database_cross_reference "GOC:pg"

Added

• symbiont-mediated suppression of host-directed shutoff of host translation definition "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."

  • database_cross_reference "PMID:21622569"

  • database_cross_reference "PMID:20563710"

virus tail, tube http://purl.obolibrary.org/obo/GO_0098026

Removed

• virus tail, tube definition "The internal tube of the contractile tails of some viruses. The virus tail tube is the channel for DNA ejection into the host cytoplasm."

  • database_cross_reference "GOC:bm"

  • database_cross_reference "VZ:3960"

• virus tail, tube comment "Applies in particular the Myoviridae bacteriophages."

Added

• virus tail, tube definition "The internal tube of the tail of some viruses. The virus tail tube is the channel for DNA ejection into the host cytoplasm."

  • database_cross_reference "PMID:33188213"

  • database_cross_reference "VZ:3960"

• virus tail, tube 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."

• virus tail, tube term tracker item "https://github.com/geneontology/go-ontology/issues/29254"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)