- This is a list of terms (not complete) that might be useful for annotating viruses. There may be children (more specific) terms that are more suitable, but this list should get curators started.
- Don't forget that the GO (Gene Ontology) is for describing the attributes of gene products (proteins or RNAs).
- You should not annotate to any terms that aren't used to describe an attribute. (i.e. if the virus has a dsRNA or ssDNA genome, this is NOT a characteristic of a protein).
Genome Replication terms
- The reason there are no "types of viral genome replication" terms is because the synthesis of a viral DNA or RNA genome is mechanistically the same as genome replication by prokaryotes, eukaryotes or archaea. The linkage of nucleotides based on a template to synthesize a genome is not unique to virus!
- Similarly, there are few (if any) complex or activity terms that are specific to viruses due to the fact that they ultimately do the same thing. The definition of each in GO does not specify which organism is being referred to, so it is acceptable to use the existing GO terms.
Parts of the capsid, tail, etc
- I would recommend annotating to one of the child terms (more specific) of GO:0044423 virion part.
- Alternatively, you can see a list of the children on QuickGO here.
- process terms: viral genome packaging and its children
- function terms: DNA translocase activity involved in viral DNA genome packaging and its children
- cellular component terms: GO:0043493 viral terminase complex
- Lysis by viruses fits under GO:0001897 cytolysis by symbiont of host cell
- The reason for this is that the GO (Gene Ontology) Consortium considers viruses to be a symbiont of their host. Their ultimate interaction may be detrimental to the host, but they are still symbionts (parasitic, though they may be).
All the processes that happen inside an infected cell
- There are a ton of virus terms that describe what virus-encoded proteins do to the host cell.
- These might include
- GO:0030683 Evasion or tolerance by virus of host immune response
- GO:0039513 suppression by virus of host catalytic activity
- GO:0039525 modulation by virus of host chromatin organization
- GO:0039526 modulation by virus of host apoptotic process
- GO:0039611 suppression by virus of host translation initiation factor activity
- GO:0039602 suppression by virus of host transcription initiation from RNA polymerase II promoter
- GO:0039595 induction by virus of catabolism of host mRNA
- or any of their children!!!!
This category has the following 24 subcategories, out of 24 total.