[Ontology-editors] forward and reverse transcription

[Karen Christie]

I was going to say that it's too bad that we don't have the has_part 
relationship. I could go with biding our time till we can use the more 
appropriate relationship type.

-Karen


On Tue, 2 Dec 2008, Midori Harris wrote:

> response to latest comment; other stuff snipped for clarity
>
> On Tue, 2 Dec 2008, Karen Christie wrote:
>
>> one further comment inline
>> 
>>>> 1. Based on the current defs of "RNA-dependent DNA replication" (which 
>>>> includes the phrase 'RNA-dependent DNA polymerases (e.g. reverse 
>>>> transcriptase)' and of "transcription, RNA-dependent" which has 'reverse 
>>>> transcriptase' as a synonym, these two terms do seem to be identical.
>>>> 
>>>> However, it seems to me that the reverse transcription (txn) step is only 
>>>> half of "RNA-dependent DNA replication" because reverse txn only makes a 
>>>> ssDNA copy. This ssDNA then serves as the template for production of 
>>>> dsDNA (going off my old biology book). So, perhaps the def of 
>>>> "RNA-dependent DNA replication" needs to be broader to encompass the 
>>>> whole process, and "transcription, RNA-dependent" could have a part_of 
>>>> relationship to such a redefined/new term.
>>> 
>>> That's an interesting point, and one that hadn't occurred to me, since I 
>>> was going by just the existing GO defs. Your proposed changes sound like 
>>> they would work well, assuming that reverse transcription always happens 
>>> in the context of dsDNA synthesis (I don't know of any non-experimental 
>>> exceptions). Perhaps the broader process should be named RNA-dependent DNA 
>>> synthesis or something to that effect, rather than use 'DNA replication' 
>>> -- DNA replication seems a bit odd for a process that doesn't start with 
>>> DNA.
>> 
>> Julie and I both sort of thought that reverse txn occurs both in the 
>> contects of DNA replication and mRNA production. Neither of us is a viral 
>> expert, so we could be wrong. But if our current sense is right, then we 
>> probably can't have the only 'reverse transcription' term be part_of 
>> 'RNA-dependent DNA replication'. We might need to have a general term and 
>> child terms that can receive appropriate parentage under DNA replication 
>> etc. So, it seems that we need to get a better sense of the biological 
>> contexts of reverse transcription before proceeding.
>
> Fair enough. To deal with the current SF item I can move transcription out 
> from under gene expression, and put DNA-dependent txn in; that will err on 
> the side of caution to avoid one path that might be false.
>
> As for where 'reverse transcription' should go, another option is to bide our 
> time until we've deployed the has_part relationship type (which I hope won't 
> be too long now ...), and then say that RNA-dependent RNA replication 
> has_part reverse transcription, and likewise viral mRNA production.
>
> m
>