Where does virion sit in CORE?

[cmungall]

Question from @pgaudet

[bpeters42]

Is this specifically about the distinction of virion and virus (where virion is the extracellular form of a virus)? If not, 'virus' would be one of the children of organisms in our definition. I would argue that 'virion' is not dissimilar to a specific life stage of an organism; so it would be 'a virus in its extracellular form'

[pgaudet]

Yes that answers the question, thanks.

[bpeters42]

Question: Would you think we should virus and virion in the core? If so, we should probably include some other life stage, maybe a larval stage? And then have under organism the root levels of the NCBI taxonomy along with an 'organism in specific developmental stage' helper class that would have 'larvae' and 'virion' under it along with a design pattern?

[pgaudet]

Sounds reasonable - although I worry about scope creep here. As long as the scope or CORE is clear then it should help make such decisions.

[cmungall]

Ticket on stages here: #40

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On Mon, Aug 12, 2019 at 4:47 PM bpeters42 ***@***.***> wrote: Question: Would you think we should virus and virion in the core? If so, we should probably include some other life stage, maybe a larval stage? And then have under organism the root levels of the NCBI taxonomy along with an 'organism in specific developmental stage' helper class that would have 'larvae' and 'virion' under it along with a design pattern? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#44>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAAMMOJC3V6UEDXRPWNG3BLQEHZALANCNFSM4ILC6XJA> .

[cmungall]

See ongoing work in GO geneontology/go-ontology#17704

virion and virion part become subClass-siblings to protein complex, cell, and subcellular anatomical entity, children of GO:cellular component.

I think there has to be a core URI for virion, OR core has some kind of grouping below material entity

[yongqunh]

Since virion is a virus particle, I think we do not need to worry about virion in terms of taxonomy. However, we need to worry about where to put virus in the taxonomy. As far as I know as a microbiologist myself, the common sense is that virus is not an organism, with the main reason that virus cannot replicate by itself (or live by itself) and has to replicate inside a cell. Therefore, we cannot put virus under organism.