[Ontology-editors] What does the MF ontology represent?

[Karen Christie]

For me, it's not so much the actual phrase, as the impression that the 
biological perspective is being dismissed as less important that the 
ontological one. I'm sure Barry could have been equally dismissive of the 
non-logical part of the definition, regardless of what he called it. I was 
left with the impression that he wanted to remove that part entirely.

Agreeing with Jen, I think that making more of an effort to explain the 
ontological terms and give appropriate background will help, especially 
since many of the people listening will not have the background in the 
ontological terms and issues. I think we want to present the case for how 
complying with the ontological formalisms will help the biology, and not 
leave people with the impression that we're implementing various 
ontological formalisms regardless of how that affects the representation 
of the biology.

-Karen


On Tue, 16 Sep 2008, Jennifer Deegan (nee Clark) wrote:

> Hi,
>
> I don't mind the derogatory phrases that much. I just find often I am lacking 
> background information. It's quite easy to get behind in a consortium meeting 
> discussion if you're not steeped to the gills in it.
> Now the group is so big it's not possible to ask for the background 
> information without holding things up. For example, if I can't quite remember 
> what 'occurent' means, then a whole discussion can be lost on me. I think if 
> we could aim to explain terms like that as we go along then fewer good 
> suggestions would get stone-walled.
>
> Jen
>
>
>
> Amelia Ireland wrote:
>> Back in Gotham City on 16 Sep 2008, at 09:08, Chris Mungall wrote:
>> 
>>> And can we just drop the "dirty function" thing? The term has been used 
>>> once since St Croix in a clearly ironic context, it's not like there is a 
>>> gang of ontologists trying to force this term down poor biologists 
>>> throats.
>> 
>> I can't remember if I was the evil mind responsible for the term in the 
>> first place, but I apologize if I was. I've always used the phrase as a 
>> joke, and would certainly not advocate its use in any formal context. I 
>> have the misfortune of a dry sense of humour and a deadpan manner, so 
>> things said ironically or as a joke are often misinterpreted as being 
>> serious (especially since this is the opposite of the way Americans act). 
>> Ah, the burdens of being British (or maybe just of having a crap sense of 
>> humour...)! ;) ;)
>> 
>> If, at some point in the future, this topic gets broached with the 
>> consortium, perhaps we can use some nomenclature that is accurate without 
>> sounding derogatory; maybe something like 'functional role'? I do think 
>> much of the confusion surrounding the issue is due to 'function' having a 
>> number of different possible meanings. If there were some way of describing 
>> the different classes of term in the MF ontology without using the word 
>> 'function', it would make explaining things much easier. Well, possibly...
>> 
>> A.
>> 
>> -- 
>> Amelia Ireland
>> GO Editorial Office
>> http://www.ebi.ac.uk || http://www.berkeleybop.org
>> BBOP Plant Project: http://bbopgarden.blogspot.com
>> 
>> 
>> 
>> 
>> 
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