[Ontology-editors] forward and reverse transcription

[Harold Drabkin]

Midori Harris wrote:
> Wait, I'm confused now about what you guys favor. RNA-dependent 
> synthesis of RNA isn't transcription at all; it's RNA replication.

As it is described above, you do not know if it is replication or 
transcription (note, in my original post, is some cases a "transcript" 
is made by copying RNA, not DNA. (as is the case for some viruses).
Reverse transcription as originally coined in the literature by Temin 
and Baltimore was refering to the synthesis of a DNA strand using an RNA 
template.

>
> Transcription is the interconversion of DNA and RNA by synthesizing 
> one on a template made of the other. Synthesis of RNA on a DNA 
> template is considered "forward" because it's by far the more common 
> direction.
I don't think that was the idea. Forward is more because it fits the 
paradigm

In the case of the single-stranded viral genome life cycles, a 
transcript is made by copying RNA.
1. do we limit the definition of "transcript" to only an RNA made from a 
DNA template or
2. does labeling something a transcript imply ultimate usage (mRNA, 
functional RNA, etc.).

Thus:
Is the product of  the RNA dependent generation of an mRNA (certain 
viruses)  a transcript or not? If is is read by ribosomes to translate a 
protein product, then is it not an mRNA?
SO, are all mRNAs transcripts?

My original post was looking at the term name and it's def, which did 
not agree.
id: GO:0006410
  name: transcription, RNA-dependent
  namespace: biological_process
  def: "The synthesis of DNA on a template of RNA."

Synthesis of DNA from RNA is a reverse of transcription (Temin, 
Baltimore), it is NOT a type of transcription; it makes DNA, not RNA.
>
> m
>
> On Mon, 1 Dec 2008, David Hill wrote:
>
>> I agree with Harold.  Reverse transcription refers to the process of 
>> reversing the transcription process, not a type of transcription.
>>
>> Harold Drabkin wrote:
>>> Hmm, from  the def of 64101, the term name really doesn't fit, since 
>>> to me, RNA -dependent transcription would be a process whereby an 
>>> RNA template is transcribed to create another RNA molecule. As it's 
>>> defined, it is "reverse" transcription.
>>> Based on the def, I would vote to merge them.
>>> Posted to SF also
>>>
>>>
>>> Midori Harris wrote:
>>>> Hi,
>>>>
>>>> A couple of questions have come up in SF 2354289:
>>>>
>>>> 1. Should these terms be merged?
>>>>
>>>>   id: GO:0006278
>>>>   name: RNA-dependent DNA replication
>>>>   def: "The process whereby new strands of DNA are synthesized, 
>>>> using RNA
>>>>   as a template for RNA-dependent DNA polymerases (e.g. reverse
>>>>   transcriptase) that synthesize the new strands."
>>>>
>>>>   id: GO:0006410
>>>>   name: transcription, RNA-dependent
>>>>   namespace: biological_process
>>>>   def: "The synthesis of DNA on a template of RNA."
>>>>
>>>> 2. Should reverse transcription be considered part of gene 
>>>> expression (at present it is, by transitivity, but if it shouldn't 
>>>> be, it's easy to change)?
>>>>
>>>> Comments here or on the SF item much appreciated.
>>>>
>>>> https://sourceforge.net/tracker/index.php?func=detail&aid=2354289&group_id=36855&atid=440764 
>>>>
>>>> Midori