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

[Midori Harris]

Hi,

On Wed, 20 Aug 2008, Chris Mungall wrote:

>
> 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?

Interesting ... my initial, intuitive reaction was not to be all that 
surprised by Karen's comment. Upon further reflection I wouldn't say that 
logical definitions are useless or uninformative to biologists, but that 
"necessary and sufficient" for logical purposes sometimes doesn't equate 
to "everything a biologist would want to know" about a term or the bit of 
reality it represents.

> 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 wouldn't presume to read Barry's mind, but I do recall him saying things 
that could give the impression that he dismisses "gloss". But I don't 
think that's a major concern for us.

[snip 'gloss' defs]
> 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.

My 2-small-currency-units: Even with well-written formal definitions 
(which I agree we should have), for many terms a gloss will remain 
valuable -- for some terms, indispensable -- for annotators and other 
biologically-oriented users to understand what a term represents and how 
it should be used.

>>> 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.

I agree -- it seems obvious that we should determine what name best 
balances accuracy and community usage, and use that name (plus any 
synonyms) in both GO and SO.

> 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!

Is there any centralized forum for this sort of issue? The obo-discuss 
list seems to broad in scope (it's not restricted to content (rightly), 
and tends towards higher-level issues), whereas many of the other obo-* 
lists are specific to an ontology or to topics that are cross-ontology but 
rather technical (e.g. obo-relations, which seldom fairs to make my head 
spin).  I'm not even sure that Yet Another Mailing List is the way to go 
...

m

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