Re: [Obo-envo] habitat relations

[Pankaj J. <pj...@co...>]

Barry Smith wrote:
> At 08:16 AM 1/20/2009, Norman Morrison wrote:
>> Hi Chris / OBI Group,
>>
>> In sending this post, you've actually provided a use case that
>> potentially opens up a (small) can of worms that I've also been thinking
>> about for a while.
>>
>> When including an has_habitat <-> is_habitat_of relation, I think it's
>> worth stepping back for a moment and considering whether or not an
>> has_environment <-> is_environment_of relation might be more appropriate?
>>
>> The reason being is that the definition of habitat amongst
>> biologists/ecologists - more often than not - implies the USUAL or
>> PREFERRED environment of an organism. ie If you were visiting Milwaukee
>> County Zoo, you wouldn't expect to see the habitat of 'Zero' the polar
>> bear described as 'a compound in a zoo' on his plaque, rather you would
>> expect to see something like 'Arctic ice sheets'. As you point out this
>> might make more sense for habitat to be considered as type level relation.
>>
>> I was actually considering a proposal to substitute all instances of the
>> term 'habitat' in EnvO with 'environment', in order to avoid any further
>> confusion.
> 
> Note that we need instances, too -- otherwise 
> EnvO won't work with GAZ. That is, EnvO should 
> supply the resources to state that Zero is 
> currently living in the XYZ compound in the ABC 
> zoo. I think that where Zero is living is then an 
> instance of the type environment (an organism is 
> living in it), even we are not talking here about 
> the usual environment for arctic bears
> BS
> 
> 

As I see it, I think this relationship is driven by the 
annotation/metadata rather than hard coding it. As Norman points in his 
latest mail, existence of the individuals representing a species found 
in a wild can be hard coded, but not for the individuals introduced by 
the human subject/as the climate changes, habitats move and sometimes 
new inhabitants adapt or move as well.

We can say that X-species is prevalent (is this a good word?) in a given 
GAZ location in association to a given set of Envo terms. However, for a 
given individual (accession/stock/germplasm/seed) it is all annotation 
driven. Because although it was first identified/collected from the 
original source, the later generations may have been maintained/bred at 
a different location.

Pankaj