Fixes to GO:0019054 modulation by virus of host process - immune sytem perturbation terms to replace virus by symbiont

[pgaudet]

• [x] GO:0039699 | viral mRNA cap methylation >> change label to "evasion of mRNA degradation by host via mRNA cap methylation" + move to is_a 'evasion of host innate immune recognition'
• [x] GO:0099016 | evasion by virus of DNA end degradation >> change label to "evasion of DNA end degradation by host" + move to is_a 'evasion of host innate immune recognition'
• [x] GO:0099018 | evasion by virus of host restriction-modification system >> change label to "evasion of host restriction-modification system" + move to is_a 'evasion of host innate immune recognition'
• [x] GO:0098672 | inhibition of host CRISPR-cas system by virus >> change label to "symbiont-mediated suppression of CRISPR-cas system" + move to is_a 'symbiont-mediated suppression of host innate immune response'
• [ ] GO:0039573 | suppression by virus of host complement activation >> obsolete & replace by GO:0042784 symbiont-mediated suppression of host complement activation

Other terms to check:

• [ ] GO:0075528 | perturbation by virus of host immune response >> has several children
• [ ] GO:0039503 | suppression by virus of host innate immune response >> has several children
• [ ] GO:0039504 | suppression by virus of host adaptive immune response >> has several children
• [ ] GO:0039673 | evasion by virus of host dendritic cell activity >> need to check with @SIBVirus Modulation of host dendritic cell activity by virus >> 4 IEAs by KW mapping
• [ ] GO:0039671 | evasion by virus of host natural killer cell activity >> need to check with @SIBVirus KW-1131 Modulation of host NK-cell activity by virus >> 8 IEAs by KW mapping + 1 IDA
• [ ] GO:0019049 | virus-mediated perturbation of host defense response >> 3 KW; check with @SIBVirus + has several children

[pgaudet]

Change label of the following terms to change label to "symbiont-mediated suppression of cytoplasmic... "

• [x] GO:0039537 suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway
• [x] GO:0039554 suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of host MDA-5 activity
• [x] GO:0039540 suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of host RIG-I activity
• [x] GO:0039724 suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity
• [x] GO:0039548 suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity
• [x] GO:0039557 suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity
• [x] GO:0039545 suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity
• [x] GO:0039723 suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity
• [x] GO:0141077 suppression of host interferon-mediated signaling pathway
• [x] GO:0039502 suppression by virus of host type I interferon-mediated signaling pathway
• [x] GO:0140884 suppression by virus of host type II interferon-mediated signaling pathway
• [x] GO:0140885 suppression by virus of host type III interferon-mediated signaling pathway
• [x] GO:0039580 suppression by virus of host PKR signaling
• [x] GO:0039560 disruption by virus of host JAK-STAT cascade via inhibition of host IRF9 activity
• [x] GO:0039574 disruption by virus of host JAK-STAT cascade via inhibition of host TYK2 activity
• [x] GO:0039576 disruption by virus of host JAK-STAT cascade via inhibition of JAK1 activity
• [x] GO:0039562 disruption by virus of host JAK-STAT cascade via inhibition of STAT activity

[pgaudet]

Obsoletions:

• [x] GO:0140886 suppression by virus of host interferon-mediated signaling pathway >> obsolete & replace by GO:0141077 symbiont-mediated suppression of host interferon-mediated signaling pathway: 0 annotations, 1 KW mapping

• [x] GO:0039573 | suppression by virus of host complement activation >> obsolete & replace by GO:0042784 symbiont-mediated suppression of host complement activation

• [x] GO:0039644 suppression by virus of host NF-kappaB cascade >> replaced by GO:0085034 'symbiont-mediated suppression of host canonical NF-kappaB cascade'

• [x] GO:0141076 symbiont-mediated suppression of host TRAF-mediated signal transduction >> replace by GO:0039527 'disruption by virus of host TRAF-mediated signal transduction' (new term, no annotations, no mappings) & rename symbiont-mediated suppression of host TRAF-mediated signal transduction

• [x] GO:0141077 'symbiont-mediated of host interferon-mediated signaling pathway' >> replace by GO:0140886 suppression by virus of host interferon-mediated signaling pathway (new term, no annotations, no mappings) & rename symbiont-mediated suppression of host TRAF-mediated signal transduction

• [x] GO:0141075 symbiont-mediated suppression of host JAK-STAT cascade >> replace by GO:0039514 disruption by virus of host JAK-STAT cascade & rename symbiont-mediated suppression of host JAK-STAT cascade

• [x] GO:0141105 symbiont-mediated suppression of host toll-like receptor signal transduction >> replace by GO:0039722 'suppression by virus of host toll-like receptor signaling pathway' (new term, no annotations, no mappings) & rename symbiont-mediated suppression of host toll-like receptor signal transduction

[pgaudet]

Created new grouping term +[Term] +id: GO:0141136 +name: symbiont-mediated perturbation of immune response-activating signaling pathway +namespace: biological_process +def: "A process in which a symbiont interferes with, inhibits or disrupts the normal execution of a signaling pathway that activates the host immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction." [] +is_a: GO:0052170 ! symbiont-mediated suppression of host innate immune response +created_by: pg +creation_date: 2023-12-21T13:56:09Z

[pgaudet]

Dear all,

The proposal has been made to obsolete Obsoletions:

• GO:0140886 suppression by virus of host interferon-mediated signaling pathway >> obsolete & replace by GO:0141077 symbiont-mediated suppression of host interferon-mediated signaling pathway
• GO:0039573 | suppression by virus of host complement activation >> obsolete & replace by GO:0042784 symbiont-mediated suppression of host complement activation
• GO:0039644 suppression by virus of host NF-kappaB cascade >> replaced by GO:0085034 'symbiont-mediated suppression of host canonical NF-kappaB cascade'
• GO:0141076 symbiont-mediated suppression of host TRAF-mediated signal transduction >> replace by GO:0039527 'disruption by virus of host TRAF-mediated signal transduction' & rename symbiont-mediated suppression of host TRAF-mediated signal transduction
• GO:0141077 'symbiont-mediated of host interferon-mediated signaling pathway' >> replace by GO:0140886 suppression by virus of host interferon-mediated signaling pathway & rename symbiont-mediated suppression of host TRAF-mediated signal transduction
• GO:0141075 symbiont-mediated suppression of host JAK-STAT cascade >> replace by GO:0039514 disruption by virus of host JAK-STAT cascade & rename symbiont-mediated suppression of host JAK-STAT cascade
• GO:0141105 symbiont-mediated suppression of host toll-like receptor signal transduction >> replace by GO:0039722 'suppression by virus of host toll-like receptor signaling pathway' & rename symbiont-mediated suppression of host toll-like receptor signal transduction The reason for obsoletion is that we are replacing the redundant 'viral' terms with their corresponding 'symbiont terms.

All annotations are by UniProt and AgBase and will be automatically remapped. UniProt Keyword mappings will be migrated.

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/26686

Thanks, Pascale