[Ontology-editors] forward and reverse transcription

[Karen Christie]

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
>>> ........
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>