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OBOFoundry / COB

An experimental ontology containing key terms from Open Biological and Biomedical Ontologies (OBO)
https://obofoundry.github.io/COB
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definition for geographic location #91

Open wdduncan opened 4 years ago

wdduncan commented 4 years ago

Is there any proposed definition for geographic location? Are we planning to use the GAZ definition?:

http://purl.obolibrary.org/obo/GAZ_00000448
A reference to a place on the Earth, by its name or by its geographical location.

This definitions implies (to me a least) that a geographic location is information / ICE.

If we want to have something like this as a subclass of bfo:site, the label 'geographic region` makes more sense. See, for example, SIO's definition for geographic region:

http://semanticscience.org/resource/SIO_000414
A geographic region is a spatial region whose boundaries are typically defined against some material frame of reference (like the earth).

The SIO definition classified geographic region under spatial region, but I think a strong case exists for geographic regions to be sites.

nataled commented 4 years ago

GEO has "geographical entity" (GEO:000000370) as: "Material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface)."

I'm not advocating one way or another; just supplying information. The GAZ term has children that are either material entities ('continent' for example') and what I presume are ICEs (countries), though I'm not sure that's the intent of the latter. @lschriml can you comment?

wdduncan commented 4 years ago

Thanks @nataled !!!
I wasn't advocating for a particular definition either :) Only that we have a definition so that the term is used properly.
Thanks for the GEO definition. Now, we have a number of senses for geographic location. It could be understood as:

lschriml commented 4 years ago

For GAZ, we have countries - defined geographic places on Earth. Not sure how 'information ' is defined here. GAZ was developed pre-bfo

Cheers, Lynn

On Sun, Aug 16, 2020 at 10:42 AM Darren A. Natale notifications@github.com wrote:

GEO has "geographical entity" (GEO:000000370) as: "Material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface)."

I'm not advocating one way or another; just supplying information. The GAZ term has children that are either material entities ('continent' for example') and what I presume are ICEs (countries), though I'm not sure that's the intent of the latter. @lschriml https://github.com/lschriml can you comment?

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-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 lschriml@som.umaryland.edu

ddooley commented 4 years ago

Recognizing that different material / immaterial semantic senses exist for geographic location, it is pretty critical that we decide what GAZ/COB "geographic location" is to prevent unsatisfiability within OBOFoundry.

Currently COB has "geographic location" as a site. But a number of ontologies are positioning geographic location as a material entity class. GAZ is moving to be composed to have (geographic and geopolitical) place names as instances of "geographic location".

(I'd say we need to have the im/material entities defined before we get to the IAO terms that are about them (e.g. list of countries before we get to "country name is about some country".)

There are two types of examples given for site. The first form is a contextual definition, "An X [of the|in the] enclosing Y" in which X and Y are classes. This sense of site depends on clearcut relation(s) with respect to an enclosing space, e.g. the interior of, the lumen of, etc. There are many instances of a given site class (e.g. many office interiors, many planet molten cores.)

The second form contains place name references, but the limit of their 3 dimensional extent is not defined by an "interior of" relation with respect to an enclosing space. As well, such a region is always defined with reference to an instance (not a class) of another continuant. I think this is why these references seem to avoid the mapping abstraction that is behind the immaterial site concept. In fact, place name region extent is defined by convention (legal or via oral history). Borders may be defined as "bounded by the 49th parallel" or " following the shoreline of ..." - but implicitly involves reference to the material entity of earth (during some epoch). So this different formulation of region boundary definition I think justifies a more direct material entity attitude towards "geographic location". @cmungall @pbuttigieg is this a good way to differentiate these things?

wdduncan commented 4 years ago

@ddooley Thanks for the comments. COB currently has geographic location has a subclass of immaterial entity, which I assume refers to BFO's immaterial entity. I agree that site would be better suited for a superclass.

A "possible" counter-example might be layers in the atmosphere, but even those implicitly reference the surface of the Earth (IMHO).

(I'd say we need to have the im/material entities defined before we get to the IAO terms that are about them (e.g. list of countries before we get to "country name is about some country".)

Agreed!

cmungall commented 4 years ago

I agree with @lschriml GAZ existed pre-BFO, we should not look to the definition of GAZ for ontological commitment to BFO upper level classes.

I like both the name ('geographic entity') and definition from GEO. But note the definition forces instances to overlap with the planetary surface. This means that a volcano will typically be a GEO:geographic-entity, but for example an undersea volcano will not be. IMO the surface clause is arbitrary from the point of view of making a useful grouping for domain scientists.

image

cc @hoganwr (GEO contact) @pbuttigieg

We already have geophysical entity in COB, this would subsume GEO:geographic entity

With these material classes it's not clear how useful a distinct geographic location class is, it could lead to confusion.

ddooley commented 4 years ago

Perhaps "geopolitical region" is introduced under COB geophysical entity to hold all (place name/proper noun) regions defined by legislation or linguistic convention (i.e. accepted by a speech community)? It holds e.g. "Argentina", and "Vancouver Heights".

Would COB "geophysical entity" have classes of things like "cave", or would they best be over under COB/BFO "site"?

cmungall commented 4 years ago

@ddooley I think a BFO treatment of caves would be as follows.

This is pretty much the standard treatment of chambers in anatomy e.g FMA.

So the answer to your question is in one part terminological: which of the above classes should get the primary label 'cave'. I would strongly argue for the material entity, but this is essentially terminology.

However, I would go further. In contrast to classic BFO modeling I would say that the "cave space" is not a very useful class, and immaterial entities are typically less useful than at first they seem. Consider a concept like "cave temperature". This would typically be read as shorthand for temperature of the inside of the cave (not the walls). An immaterial entity cannot have a temperature, as an immaterial entity has no mass. Of course, there is a material entity inside the cave. The precise material entity may be in flux more than say the walls (e.g. flooding replaces the air content with water content).

My treatment would be:

i.e everything is material. If someone really has a need for an abstracted 'cave space immaterial entity' then they can form it via a class expression. e.g immaterial entity and occupies some cave space.

ddooley commented 4 years ago

That sounds fine to me. I agree, linguistic use of terms like 'cave' usually lines up with references to material parts (at some time T or duration), regardless of how many fiat boundaries are involved.

(Come to think of it, abstract immaterial sites for which there are material-world instances in fact depend on material world instance references for their fiat boundaries, so are a kind of specifically dependent continuant in that respect. Hmm.)

wdduncan commented 4 years ago

Agreed. There is a material entity sense of 'cave'. I do not know how well this will cover all the use cases. If I collect an air sample from inside the cave, is it important to represent that the air was contained within the cave's cavity or is it enough to just say that the air was contained within the cave?

cmungall commented 3 years ago

@wdduncan it is sufficient to state that it is a portion of air that is part of a cave

alanruttenberg commented 3 years ago

There is also the sense of geographical location as being a boundary, for instance the north pole, or the border between US and Canada, or the water-line of the Nile. I've been thinking about this for another project and my current view is that the english sense of geographical location can be any independent continuant other than a spatial region, i.e. a site, a boundary, a material entity (mount Everest). In the cave example both the senses of it as a site or as a material entity+site sum are used. In FMA the lumen of an artery is an immaterial entity and doesn't include the vessel walls. Similarly, tooth socket.

Alan

On Wed, Sep 9, 2020 at 12:22 PM Bill Duncan @.***> wrote:

Agreed. There is a material entity sense of 'cave'. I do not know how well this will cover all the use cases. If I collect an air sample from inside the cave, is it important to represent that the air was contained within the cave's cavity or is it enough to just say that the air was contained within the cave?

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wdduncan commented 3 years ago

I agree with @alanruttenberg, there are lots of senses for 'geographical location'. For purposes of this discussion, I think it would be reasonable to separate geographical locations from anatomical locations. Although there are interesting collararies between geographical and anatomical locations (e.g., canyon vs tooth cavity), trying to come up with a general solution for both might be too difficult.

@alanruttenberg following your proposal would make geographical location a defined class?

alanruttenberg commented 3 years ago

On Tue, Jun 22, 2021 at 6:34 AM Bill Duncan @.***> wrote:

I agree with @alanruttenberg https://github.com/alanruttenberg, there are lots of senses for 'geographical location'. For purposes of this discussion, I think it would be reasonable to separate geographical locations from anatomical locations.

@wdduncan They are at least separated in that one is about places on the planet and the other places in / on a person. How would you see them being different otherwise?

Although there are interesting collararies between geographical and anatomical locations (e.g., canyon vs tooth cavity), trying to come up with a general solution for both might be too difficult.

Not following. Maybe lay out one or two of the problems you see?

@alanruttenberg https://github.com/alanruttenberg following your proposal would make geographical location a defined class?

I hadn't thought in those terms, but maybe I haven't thought enough. Could you say what about it suggests defined class?

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wdduncan commented 3 years ago

@wdduncan They are at least separated in that one is about places on the planet and the other places in / on a person. How would you see them being different otherwise?

I think the distinction of "places on planet" vs "places on person" is fine for now. I was just trying to keep the discussion clear. Above @cmungall also mentions cases that we may call geographic entities/features (e.g., caves). I agree that there is a sense in which a cave is a geographic location, but do we want to restrict this class to "named" geographic locations (e.g, Europe, Pacific Ocean) or named coordinates (e.g., identified by latitude and longitude)?

I hadn't thought in those terms, but maybe I haven't thought enough. Could you say what about it suggests defined class?

EnvO has a geographic feature [ENVO_00000000] class that might be of use here: image