[Ontology-editors] forward and reverse transcription

[Karen Christie]

Hi,

I have had some correspondance with Caroline Kane, my PhD advisor, and 
posted it in the SF item (url below). She suggested a couple other people 
to contact, so I will do that too and post any relevant responses I get 
to the SF item.

https://sourceforge.net/tracker/index.php?func=detail&aid=2354289&group_id=36855&atid=440764

Regarding the basic ontology structure I suggested to Caroline, I think we 
need to think a little harder about the viral nucleic acid synthesis from 
RNA templates, so just take what I have in the SF item as a basic idea, 
not a final proposal, of what might be a better way to go. Note that 
synonyms are not in final form either.

Please post any further comments to the SF item, rather than by response 
to this email.

thanks,

-Karen


On Thu, 4 Dec 2008, Midori Harris wrote:

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