Virus call 2013-11-27

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Attendees: Jane, Becky, Chris, David O-S

1/ We need a better way to represent viral modulation of cell activity. We've used has_participant for now:

id: GO:0039671 ! evasion by virus of host natural killer cell activity
intersection_of: GO:0030683 ! evasion or tolerance by virus of host immune response
intersection_of: has_participant CL:0000623 ! natural killer cell

but what we really need to do is say e.g. natural killer cell activity = some biological process has_participant natural killer cell

and this process is the regulation of that activity.

Also CL:0000451 ! dendritic cell term

Add new relation: regulates o process o mediated_by x cell (CL:ID)

Name of relation: regulates activity of

2/ We've got lots of terms that reference a specific host protein, where the virus modulates one or more functions of that protein e.g.

id: GO:0039548 name: suppression by virus of host IRF3 activity

IRF3 has multiple activities so we wouldn't make an MF term 'IRF3 activity' but we need it somewhere to be able to say the virus modulates it.

Add new relation: regulates o process o mediated_by x protein (PR:ID)

3/ Processes where the differentia is that it involves a virus e.g.

id: GO:0039699 name: viral mRNA cap methylation

has_participant is wrong here...need to say has_participant some protein encoded_by virus

Make mini ontology in the extensions directory for viral component.

  • RNA (SO:ID) expressed by virus (NCBI taxID)
  • protein (PR:ID) expressed by virus (NCBI taxID)