obsoleted terms fixes #29194

[pgaudet]

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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/2024-11-14/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/2024-11-14/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-pr.owl/reasoned.owl

Ontology imports

Ontology annotations

suppression by virus of host cytokine production http://purl.obolibrary.org/obo/GO_0046775

Removed

• suppression by virus of host cytokine production definition "Any viral process that results in the inhibition of host cell cytokine production."

  • database_cross_reference "PMID:10859382"

• suppression by virus of host cytokine production label "suppression by virus of host cytokine production"

• suppression by virus of host cytokine production SubClassOf symbiont-mediated suppression of host cytokine production

Added

• suppression by virus of host cytokine production deprecated true

• suppression by virus of host cytokine production comment "This term was obsoleted because it was an unnecessary grouping class."

• suppression by virus of host cytokine production term tracker item "https://github.com/geneontology/go-ontology/issues/29194"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• suppression by virus of host cytokine production label "obsolete suppression by virus of host cytokine production"

• suppression by virus of host cytokine production definition "OBSOLETE. Any viral process that results in the inhibition of host cell cytokine production."

  • database_cross_reference "PMID:10859382"

suppression by virus of host intracellular interferon activity http://purl.obolibrary.org/obo/GO_0046774

Removed

• suppression by virus of host intracellular interferon activity label "suppression by virus of host intracellular interferon activity"

• suppression by virus of host intracellular interferon activity definition "Any viral process that results in the inhibition of interferon activity within the host cell."

  • database_cross_reference "PMID:10859382"

• suppression by virus of host intracellular interferon activity SubClassOf symbiont-mediated perturbation of host signal transduction pathway

Added

• suppression by virus of host intracellular interferon activity term tracker item "https://github.com/geneontology/go-ontology/issues/29194"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• suppression by virus of host intracellular interferon activity label "obsolete suppression by virus of host intracellular interferon activity"

• suppression by virus of host intracellular interferon activity consider "GO:0140886"

• suppression by virus of host intracellular interferon activity definition "OBSOLETE. Any viral process that results in the inhibition of interferon activity within the host cell."

  • database_cross_reference "PMID:10859382"

• suppression by virus of host intracellular interferon activity deprecated true

• suppression by virus of host intracellular interferon activity comment "This term was obsoleted because it was overlapping with symbiont-mediated suppression of host interferon-mediated signaling pathway ; GO:0140886."

suppression by virus of host type I interferon production http://purl.obolibrary.org/obo/GO_0039501

Removed

• suppression by virus of host type I interferon production label "suppression by virus of host type I interferon production"

• suppression by virus of host type I interferon production definition "Any viral process that results in the inhibition of host cell type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families."

  • database_cross_reference "GOC:bf"

  • database_cross_reference "UniProtKB-KW:KW-1113"

  • database_cross_reference "GOC:add"

  • database_cross_reference "VZ:875"

  • database_cross_reference "GOC:sp"

• suppression by virus of host type I interferon production database_cross_reference "VZ:875"

  • label "Inhibition of host IFN-mediated response initiation by virus"

• suppression by virus of host type I interferon production EquivalentTo symbiont-mediated perturbation of host process and (negatively regulates in another organism some type I interferon production)

• suppression by virus of host type I interferon production SubClassOf symbiont-mediated suppression of host gene expression

• suppression by virus of host type I interferon production SubClassOf negatively regulates in another organism some type I interferon production

Added

• suppression by virus of host type I interferon production definition "OBSOLETE. Any viral process that results in the inhibition of host cell type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families."

  • database_cross_reference "GOC:bf"

  • database_cross_reference "GOC:add"

  • database_cross_reference "GOC:sp"

• suppression by virus of host type I interferon production term tracker item "https://github.com/geneontology/go-ontology/issues/29194"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• suppression by virus of host type I interferon production term replaced by "GO:0039502"

• suppression by virus of host type I interferon production deprecated true

• suppression by virus of host type I interferon production comment "This term was obsoleted because it represents the same process as symbiont-mediated suppression of host type I interferon-mediated signaling pathway ; GO:0039502."

• suppression by virus of host type I interferon production label "obsolete suppression by virus of host type I interferon production"

symbiont-mediated perturbation of host dendritic cell mediated immune response http://purl.obolibrary.org/obo/GO_0039673

Removed

• symbiont-mediated perturbation of host dendritic cell mediated immune response label "symbiont-mediated perturbation of host dendritic cell mediated immune response"

• symbiont-mediated perturbation of host dendritic cell mediated immune response definition "A process in which a symbiont alters or subverts the dendritic cell mediated immune response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction."

  • database_cross_reference "GOC:jl"

  • database_cross_reference "GOC:bf"

  • database_cross_reference "UniProtKB-KW:KW-1118"

Added

• symbiont-mediated perturbation of host dendritic cell mediated immune response label "symbiont-mediated suppression of host dendritic cell mediated immune response"

• symbiont-mediated perturbation of host dendritic cell mediated immune response definition "A process in which a symbiont inhibits or disrupts the dendritic cell mediated immune response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction."

  • database_cross_reference "GOC:jl"

  • database_cross_reference "GOC:bf"

  • database_cross_reference "UniProtKB-KW:KW-1118"