add taxon restriction to "viral process"

[ValWood]

can "only in virus" taxon restriction be added here?

thanks

val

[ukemi]

Concerned about this if host proteins play roles in these processes. Also does it mean that the process can only take place in a virus? That is certainly not true. I think we need to be careful about putting these on symbiotic processes.

[ValWood]

But if the host protein plays a role, it isn't a normal process for the host (you would never annotate a host protein to a viral process would you?)

[ukemi]

13233

[ukemi]

We need to check with the annotators who annotate viral processes:

• Is the definition of viral process specific enough? Right now the definition and the logical definition are such that they would include host processes including the host's response to the virus. If this is not narrow enough, should we modify the definition to only include the processes that are required for the viral life cycle or should we obsolete the term?

• If we decide that the viral process term only refers to those processes that are concerned with the life cycle of the virus, should host proteins that are utilized or co-opted in the viral life cycle be annotates with these terms? If this is the case, we cannot put a taxon restriction on the viral process term.

• If we decide that the viral process term only refers to those processes that are concerned with the life cycle of the virus, we need to go through the children and sort out those that are part of the host's response to the virus and those that are part of the virus' life cycle.

[jimhu-tamu]

My initial reactions are:

• Host response to virus is not a viral process
• There has to be a way to annotate host proteins that are co-opted for the normal function of the viral process.

For the second issue, I think a distinction should be made between the virus using a normal host process and co-option. My instinct is that I would not annotate every host protein involved in host translation or transcription to an equivalent viral process unless there is some differentia. Some examples:

• E. coli thioredoxin is used as a processivity factor by T7 DNA polymerase. trxA mutations do not support growth of T7. I would annotate the host thioredoxin to Viral DNA replication
• Viruses use a variety of strategies for transcription, ranging from encoding their own RNAP with no shared subunits to using their own regulators of host RNAP. In between those extremes there are viruses that replace specific subunits (e.g. viral sigma factors). I'm not sure how I would want to handle the host proteins in these cases.

[ValWood]

@pgaudet should viral process only apply to viral genes?