[Ontology-editors] forward and reverse transcription

[Midori Harris]

I agree completely with Karen. We need community input, and if both GO 
and SO have to change, so be it.

Before Alex chimed in, I was unaware of the virus community's usage, which 
makes it a no-GO (groan) to use DNA<->RNA conversion as the defining 
feature of transcription. That's rather unfortunate, but upon further 
reflection, it occurs to me that it would also look quite odd to count RNA 
primer synthesis during DNA replication as transcription.

That last point does also argue against defining transcription as any 
template-based RNA synthesis, though. Maybe we won't be able to have a 
single term encompassing all transcription and only transcription 
(regardless of whether the experts regard reverse transcription as 
transcription).

m

On Wed, 3 Dec 2008, Karen Christie wrote:

> and where did SO get there definition? Maybe they just assumed they "knew" 
> what transcription was too. I just think it's worth doing some due diligence 
> to make sure that we understand what the research community thinks is 
> appropriate use of the word "transcription".
>
> Then, we should make both GO and SO reflect that usage so that we are 
> consistent.
>
> -Karen
>
> On Wed, 3 Dec 2008, Harold Drabkin wrote:
>
>> I don't think there is anything arbitrary about this at all.
>> 
>> The sequence ontology defines a transcript as " An RNA synthesized on a DNA 
>> or RNA template by an RNA polymerase."
>> 
>> Shouldn't  our use of transcription  be consistent with the use of terms in 
>> SO. I The  making of a transcript is transcription. The templated making of 
>> a transcript is transcription;
>> 
>> The term reverse-transcription is the templated syntehesis of DNA from an 
>> RNA template.  It is fundamentally different. Transcription uses 
>> ribonucleotides wherease revere transcription uses deoxyribonucleotides. 
>> Reverse transcription is not a type transcription.  It is a type of 
>> templated DNA synthesis not transcription.  The "reverse" is in terms of 
>> the central dogma reversal, not the reverse of  transcription itself.  A 
>> true reverse of transcription would be the disassembly of the RNA 
>> transcript into ribonucleotide triphosphates, I suppose in the presence 
>> DNA.
>> 
>> -h
>> 
>> Karen Christie wrote:
>>> I don't think we (we being a subset of GOC editors) can arbitrarily decide 
>>> that transcription is restricted to making an RNA molecule. I agree with 
>>> Alex that we need to reflect the current usage of the research community 
>>> (and that textbooks and the Oxford Dictionary that we used for many defs 
>>> are not good sources for getting a comprehensive view of usage of a word).
>>> 
>>> Perhaps transcription is making a single stranded copy of nucleic acid, or 
>>> perhaps as Midori suggested the possibility, there may not be a cohesive 
>>> grouping term for these three things that are known to occur:
>>> 
>>> 1. making RNA copy from DNA template
>>> 2. making RNA copy from RNA template
>>> 3. making DNA copy from RNA template
>>> 
>>> I think we should do some research and/or get input from the research 
>>> community before making changes in this area.
>>> 
>>> -Karen
>>> 
>>> 
>>> On Wed, 3 Dec 2008, Harold Drabkin wrote:
>>> 
>>>> Oops, Actually I meant to question #3.
>>>> 
>>>>> 
>>>>>> 3.  transcription of DNA from an RNA template
>>>>> ?????? depends on how we define transcription. If it's making an RNA, 
>>>>> no, because of a "reverse_of " a process not being an "instance_of"  or 
>>>>> "part_of"  the  process that it's a reverse of
>>>> ........
>>>> _______________________________________________
>>>> Ontology-editors mailing list
>>>> Ontology-editors at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>> 
>> 
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>