[Ontology-editors] [ geneontology-Curator requests-2053783 ] parentage: RNA modification

[Chris Mungall]

On Aug 20, 2008, at 2:22 PM, SourceForge.net wrote:

> Hi Chris,

Hi Karen

Hope you don't mind if I answer your points on the editors list as I  
think they cut across the whole ontology. I would hope we can come to  
a common agreement here

This relates to:
https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2053783&group_id=36855

>
>> Ideally we could appeal directly to the definitions without the need
>> for subjective interpretation.
>
> To be honest, as an annotator, the part of the definition I usually
> find most helpful is the part that Barry Smith dismissed as merely
> descriptive and ideally not part of the definition. The 'logical' part
> of the definition is rarely helpful to me.

I find it odd that you don't find this part helpful. I find the vast  
majority of parentage issues in GO can be automatically determined by  
a rigorous logical definition. I imagine the different parts of the  
definition serve different roles for different purposes, and coming  
from an annotator's perspective the descriptive part plays a different  
role from say for example determining the correct parentage in GO. But  
surely this is important to an annotator too?

I'm not sure Barry was dismissive of the "gloss" part of the  
definition. Of course, it would easy to read the wrong sense of the  
term "gloss"

I use the term this way:

---
(1) : GLOSSARY (2) : a continuous interlinear translation (3) : a  
continuous explanation or commentary accompanying a text;  
specifically : a commentary (as made at Bologna from the 12th century  
to the 14th century) on the texts of Roman or Civil law
---

And not this way:

--
2 a [probably influenced in meaning by 3gloss and 1gloze] : something  
(as a motive alleged) designed to veil or hide what would otherwise be  
objected to : plausible pretext : SHOW, PRETENSE, SEMBLANCE, DODGE,  
EXCUSE <giving national aggrandizement the gloss of moral sanction>  
b : a deceptively attractive external appearance <selfishness that had  
a gloss of humanitarianism about it>
--

I like gloss. I would happy with massive wikipedia-article sized  
pieces of gloss (structured such that the succinct summary is easily  
digested of course).

I just think it's important to distinguish between the gloss and the  
formal part of the definition, and to write the formal part of the  
definition in a different style from the gloss. The formal part of the  
definition should ideally be in genus differentia style and clearly  
and succinctly state the necessary and sufficient conditions, using  
only simpler terms, preferably using terms from the same ontology or  
other ontologies. Of course, there are some terms for which this is  
difficult : parts of the ontology on the cutting edge of science for  
example. But I would bet that for the majority of terms it is  
achievable.

I don't have such strong opinions on the gloss part of the definition.

>> The def of RNA processing introduces 2 terms that are not defined in
>> GO: primary RNA transcript and mature RNA molecule. (not sure the
>> switch between transcript and molecule). If we refer to SO here:
>>
>> SO:0000185 !  primary_transcript [DEF: "A transcript that in its
>> initial state requires modification to be functional."]
>>
>> SO:0000233 !  mature_transcript [DEF: "A transcript which has
>> undergone the necessary modifications, if any, for its function. In
>> eukaryotes this includes, for example, processing of introns,
>> cleavage, base modification, and modifications to the 5' and/or the  
>> 3'
>> ends, other than addition of bases. In bacteria functional mRNAs are
>> usually not modified."]
>
> In my reading, I'm not sure if I've ever seen it called the 'mature
> transcript'.  After maturation, it is generally referred to as a
> 'mature RNA', e.g., the mature 25S rRNA or the mature 18S rRNA. My
> sense is that the transcript is what is copied from the DNA and once
> it's been fiddled with so that it isn't a direct copy, you wouldn't
> refer to it as a transcript anymore.

I agree "mature transcript" sounds unusual, but I have heard  
"processed transcript" a lot

> So, I'm really not sure that SO's
> nomenclature is standard here, or that GO would want to follow it.

I think we want to use the same terms as much as possible, so I would  
hope that GO wouldn't just ignore SO's terms and say "we don't want to  
follow that". Instead we'd work together on the terms that are  
acceptable by all. This goes for all OBO ontologies of course. There  
is probably more we can do to facilitate this kind of inter-ontology  
discussion, beyond mutual cross-linked tracker items, ideas welcome!

Off my soapbox, I may respond to some of the specific points below  
back on the tracker...

Cheers
Chris

>
>> Then it seems there are kinds of RNA modification that are not kinds
>> of RNA processing, specifically those that involve changes entirely
>> during the pre-functional or entirely during the post-functional
>> state.
>
> Considering that changes during the pre-functional state would be part
> of converting the primary transcript to the mature RNA, those could
> probably be considered to be part of processing. However, if there are
> modifications that occur as part of catabolism, that would be a reason
> to not make the change I suggested, at least with the current def of
> RNA processing.
>
>> However, it's not entirely clear to me what a functional RNA is and
>> exactly how to apply this. So perhaps either the SO definitions or  
>> the
>> GO definition of RNA processing needs to change.
>>
>> As far as common usage goes, the PMID above supports the case that
>> "RNA processing" is used inclusively of "RNA modification" at least
>> once. Idiomatic usage of the terms processing and modification may
>> support this.
>
>> Regardless of the words used, it does seem like there is a possibly
>> important division between large scale modifications involving an
>> irreversable change of type (eg primary->spliced) and those more
>> minors ones introducing a variation on the molecule (eg editing). It
>> seems the GO graph captures the distinction, though the defs may need
>> tweaked (and possibly the names changed so that common usage is not
>> violated?)
>>
>> Whilst looking at this part of the graph I notice an extra  
>> distinction
>> between mRNA and ncRNA may be useful (not revelant to this item
>> however). For example, placing pseudouridine synthesis under ncRNA
>> modification would explicitly computationally state that this is  
>> never
>> synthesized in mRNA (as the def currently states in natural  
>> language).
>
> Actually, the def only says that mRNAs in bacteria are not
> modified. mRNAs in eukaryotes are definitely methylated
> internally. This is very common in mammals, and has also been observed
> in S. cerevisiae. So, we can't make statements that RNA modifications
> don't occur in ncRNA. If anything, it's artificial to have separate
> terms for each 'type' of RNA. Often the same processes target multiple
> different types of RNAs, e.g. rRNAs, snRNAs, and mRNAs, for a given
> modification. However, I recognize that people want to be able to
> identify the processes as they occur on 'types' of RNA, so I think we
> need those types of terms too.
>
> probably better for now to not make the change I suggested.