Taxon-GO Checks and Commentary - Part 4

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General points about viruses in GO

Terms that are implicitly used for both cellular organisms and invading viruses

There are a lot of processes that look, on the face of it, as though they should be specific to cellular organisms, but then they turn out also to be carried out by viruses inside of the cellular organisms. This is an interesting point to note for ontology development. Should we be using the same terms for:

a) the process that is normal for a cellular organism to carry out in its own cell.
b) the same process carried out by a virus that has invaded a host cell.

Examples include the descendents of the terms cellular component organisation and cellular component biogenesis, that do not have the word 'cellular' at the beginning.

'Cellular' terms in GO - the converse of the above situation

Since we introduced the term 'cellular process' we have also started to make terms called 'cellular x', for example in the example below we will make the term 'cellular methylation'. This creation of parallel 'cellular x' and 'x' terms enables the natural process as carried out by a cellular organism to be annotator to the 'cellular x' term, while the same process as carried out by an invading virus in the host cell can be annotated to the non-cellular 'x' term. Is this the correct way to proceed? It involved a sort of duplication of a number of terms, though it does allow us to clearly distinguish between the host and viral processes.


Do the descendents with no 'cellular' at the beginning of the name trump the 'cellular' ancestor or vice versa, and what do we do about it?

Methylation in Viruses

GO:0032259 "methylation" only_in NCBITaxon:131567 "cellular organisms" :: PDB	1L9K_A	1L9K_A
GO:0032259	GOA:interpro	IEA	InterPro:IPR002877	P			
protein_structure	NCBITaxon:11060	20090629	UniProtKB

There are virus annotations to methylation, but this is a type of cellular process. I have asked Jane and she says I need to make this the cellular methylation term and have a generic methylation term that is just under metabolic process and not under cellular process.