Re: [Obo-relations] transformation relation

[David Osumi-S. <da...@eb...>]

I'm very much in favor of keeping 'transformation of', as it allows us to distinguish changes to a continuant that involve a change in identiy from those that do not.  Please see my comments on the derives from ticket:

https://code.google.com/p/obo-relations/issues/detail?id=42#c7

It would also be good if we could keep discussion on tickets as far as possible.

James: Looks like there is not yet a ticket for transformation_of ?

Cheers,
On 7 Feb 2015, at 17:34, Barry Smith <phi...@bu...> wrote:

> is-transformation-of was originally included in RO for cases of what are called substantial change; these occur where some x is an instance of some universal U1 at time t1 and an instance of some universal U2 at time t2.
> 
> the classical examples were 
> 
> fetus transformation-of embryo
> corpse transformation-of human organism
> 
> Since most people prefer viewing those cases not as substantial change, but rather as a change in qualities or phenotypes, with an underlying substantial identity (identify of bearer); thus there seems to be no room for the transformation-of relation
> BS
> 
> On Fri, Feb 6, 2015 at 5:31 PM, Melanie Courtot <mco...@gm...> wrote:
> Hi,
> 
> Following up on the case of methylation of a protein, it was recommended to use transformation instead of derivation [1].
> However, the definition of “transformation of” is very circular and doesn’t really clarify what is a transformation "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships”
> 
> It also is a sub property of "developmentally related to”, which definition reads "A relationship that holds via some developmental process (GO:0032502)”, and where GO:0032502 is developmental process defined as “A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.” [2].
> 
> It therefore seem that this may not be suitable for a methylation process - should I just use something along the lines of output of a methylation process, or is there another relation that would work?
> 
> Cheers,
> Melanie
> 
> [1] https://code.google.com/p/obo-relations/issues/detail?id=42
> [2] http://amigo.geneontology.org/amigo/term/GO:0032502
> 
> -- 
> Mélanie Courtot
> Post-doctoral research associate
> Brinkman Lab, MBB Department, Simon Fraser University, 
> Hsiao lab, BC Public Health Microbiology & Reference Laboratory,
> Rm SSB7121, 8888 University Drive
> Burnaby, BC, Canada, V5A 1S6
> 
> 
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