Re: [Obo-phenotype] fixed vs living

[David Osumi-S. <dj...@ge...>]

Alan's suggestion here makes much more sense to me than treating fixed  
as a quality.

On 18 Nov 2009, at 17:47, Alan Ruttenberg <ala...@gm...>  
wrote:

> If you mean "fixed" as in has been put in fixative, for example, then
> this would be an example of something OBI has been dealing with. We
> think that there are a bunch of terms that are adjective in form, but
> which don't name qualities in the BFO (or PATO) sense. Rather what
> they mean is that the substance in question has undergone some process
> and that the annotation should be to the process, not as a quality.
> Certainly there are qualities and dispositions that arise from such a
> process, but they aren't the same as the term the adjective denotes.
>
> For example, consider "digested". One can't tell by looking at a
> substance whether it has been trypsin digested - you have to know that
> it got to be the way it is in a certain way. We annotate such entities
> in OBI by saying they are the specified output of, e.g.,  a trypsin
> digestion process as specified in some protocol.
>
> There are a number of terms in PATO that are of this nature, and
> there's a conversation been started with Chris about this. I'm curious
> about your thoughts on this, and in the short term would recommend
> that in cases where you are describing not-occurring-nature things
> like "fixing" you consider seeing if OBI has what you want, or
> submitting a term request. Information about our recent release is at
> http://obi-ontology.org/page/Releases/2009-11-06
>
> Regards,
> Alan
>
> ps. The OBI part of this conversation is at
> http://groups.google.com/group/obi-developer/browse_thread/thread/a7b3157d8f9b98fb
>
> On Mon, Nov 16, 2009 at 7:07 PM, Nicole Washington <NLW...@lb... 
> > wrote:
>> hello,
>>
>> how could i go about capturing the two status' of tissues that have
>> either been treated or untreated with a reagent, such as to render
>> them "fixed" or "living" in an assay?
>>
>> i see a term mobile, PATO:0000300, which has "fixed" as a synonym, is
>> defined as "A mobility quality inhering in a bearer by virtue of the
>> bearer's being incapable to move freely".
>>
>> think this is the right term to use?
>>
>> and how do i capture the opposite, unfixed?  should that be immobile?
>>
>> nicole
>>
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