On Jan 20, 2012, at 7:57 AM, Walls, Ramona wrote:
> We have been working on something similar with plants. We have been considering using "found_in", rather than "lives_in", because it does not carry the implication that the organism is necessarily alive. It allows the relation to be used with continuants that are not organisms.
Can you give further details? Is this the same as being located in, or is there a more dispositional aspect? E.g. If I'm walking in a spacesuit on the surface of the moon, would you say I was found_in the lunar environment at that time? I'm guessing not as you would just use a more standard locational relation.
How about some kind of adaptation-oriented relation? There could be sub-relations for natural and artificial adaptation. The range of this relation would be a high level class in ENVO.
But it wouldn't be appropriate to use this for the relationship between a newly captured tiger and the small Manhattan apartment it's living in - but I think this is getting into another category of relation altogether. Maybe raised_in and sub-relations?
> I need to describe both class level relations and instance level relations. For class level relations, I need to talk about both classes of organisms in a particular habitats (like what you have below) as well as classes of organisms that live in particular geographic regions, such as "all individuals of the species Dioscorea omiltemensis are found in Guerrero, Mexico". In this case, I think Dioscorea omiltemensis is a class, and Guerrero, Mexico is an instance, since there is only one Guerrero (perhaps instance of the class "Mexican State").
In general relations in RO are object properties (between individuals). You'd just quantify them how you like
* some instances of X are found_in instance Y
* some instances of X are found_in some instance of Y
* all instances of X are found_in instance Y
* all instances of X are found_in some instance of Y
* all instances of X are found_in only instances of Y
* n% of instances of X are found_in an instance of Y
The last can't be directly encoded in most ontology languages but that's the idea.
These limited forms of quantification may not be sufficient for your use case then there may be reason to add a class relation -- but let's see if we can capture what you require without that
> I also want to talk about individual organisms (instances of the class that describes some species) that live in either a specific habitat or in a geographic region or or at a specific locality. For example: "collection #RW107 of Dioscorea omiltemensis was collected in a pine-oak forest" or "collection #RW107 of Dioscorea omiltemensis is from Guerrero, Mexico" or ""collection #RW107 of Dioscorea omiltemensis was collected at W 99 36.147, N 17 38.296". I would like to be able to use "found_in" for all of these (except maybe the last one – not sure about that).
It would seem that "found in" implies something a bit different that "collected from".
I'm less keen on "found" in that it implies a process of finding.
> I also want to talk about, for example, "the plant disease bacterial wilt is found in Iowa, USA".
Do you want to say anything stronger than there was an observation of a plant with this disease in the wild in Iowa? If not then simple locational relationships may suffice.
> All of the examples I listed are between two continuants, so perhaps something similar to located_in will work, but I am not sure.
> Sorry I don't really have an answer for you, because I just started thinking about this, but I wanted to point out some of the other examples where such a relation could be used.
> From: Suzanne Santamaria <suesantamaria@...>
> Date: Fri, 20 Jan 2012 10:26:39 -0500
> To: <obo-relations@...>
> Subject: [Obo-relations] relation for organism living in a site
> We need a relation to associate an organism with the physical location (environment/site) where it lives in the developing ontology of practical animal classes. I see two possible relations in the newest renditions of RO: Located_in and Has_site_of. However, I’m not sure if either are suitable for this situation. Here are some examples of where this relation would be used in our ontology (“Lives_in” is used as placeholder relation for now):
> · Term: Cattle on pasture for beef production
> o Text definition: Cattle which produce beef and live on pasture
> o Synonym: Pasture beef cattle
> o Formal definition:
> § isa Cattle for beef production
> § Lives_in some pasture (ENVO term)
> · Term: Feral pig
> o Domesticated species of pig which live in the wild
> o Synonym: Feral hog
> o Formal definition:
> § isa Pig
> § Lives_in some terrestrial biome (ENVO)
> · Term: Cold-blood aquatic animal
> o Text definition: Cold-blooded animal that lives in water.
> o Formal definition:
> § Isa Cold-blooded animal
> § Lives_in some aquatic habitat (ENVO)
> Please advise on whether we should create a new relation “Lives_in” between continuants such as an Object and a Site or use one of the existing RO relations.
> Many thanks,
> Suzanne Santamaria, DVM
> Veterinary Terminologist | Veterinary Medical Informatics Laboratory
> slsantamaria@... | 540-231-4427 | http://informatics.vetmed.vt.edu
> “Information is care” ~ Donald Berwick, M.D.
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