inappropriate cave synonyms

[GoogleCodeExporter]

[Term]
id: ENVO:00000058
name: underground lake
namespace: ENVO
def: "A lake which is formed under the surface of the Earth. Such a lake may be 
associated with caves and aquifers and springs." [Wikipedia:Lake#Types_of_lakes]
***synonym: "cave" RELATED [ADL:FTT]

really?

[Term]
id: ENVO:00000068
name: tunnel
namespace: ENVO
def: "An underground or underwater passage." [USGS:SDTS]
synonym: "TUNNEL" EXACT [USGS:SDTS]
***synonym: "cave" RELATED [ADL:FTT]

hmm. what use is this synonym? Yes they are related concepts and there may be a 
continuum

Original issue reported on code.google.com by cmung...@gmail.com on 25 Jan 2013 at 12:46

[GoogleCodeExporter]

Initial houghts: 
The first I think is an issue with choosing the parent of underground lake. It 
could be a lake but could also be a cave class.

The tunnel/cave relation is trickier. Cave systems can extend for kilometres, 
e.g. Mammoth Cave with length 628 km, and can conceivably be considered 
tunnels. On the other hand, caves usually are defined as underground spaces in 
some sort of solid material the notion that some macroorganisms (like a human) 
can enter. Tunnels need not be that big. 

Original comment by p.buttig...@gmail.com on 2 May 2013 at 3:32

• Added labels: ****
• Removed labels: ****

[GoogleCodeExporter]

Also:
Given: http://obofoundry.org/ro/#OBO_REL:part_of
cave part_of cave system doesn't hold at all times.

Briefly:
Where C and C1 are classes and c and c1 are their respective instances:
C part_of C1 means that for any c there must be a c1 at a given time

Not all caves are part_of cave systems

Further, I think the "part_of cave" relations for "phreatic zone" and "vadoze 
zone" need to be verified. Seems these are parts of aquifers.

Original comment by p.buttig...@gmail.com on 7 May 2013 at 1:49

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[GoogleCodeExporter]

Attended to "vadose zone" and "phreatic zone" in envo-edit.obo, rev 118.

Original comment by p.buttig...@gmail.com on 12 Oct 2013 at 3:15

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[pbuttigieg]

@cmungall
I removed the "cave" synonym for underground lake, but, as discussed above, this is not so clear cut with tunnel. In fact, doesn't the "passage" aspect suggest something like a disposition? That is, any cavity can realise a tunnel disposition if it is used as a passage by some material entity?

[cmungall]

Tunnel feels analogous to UBERON:0004111 ! anatomical conduit

[cmungall]

ontobee is mangling the axioms

EquivalentTo 'multicellular anatomical structure' and has_part some 'anatomical conduit space' and conduit_for some 'anatomical structure'

the idea is that the things passing through can be mixtures of permanent and spanning (nerves, roads) or non-permanent and non-spanning (portions of fluid, cells, cars, trains, schools of fish)

[pbuttigieg]

Hm, yes, I see the logic.
conduit_for seems like it does the work of the disposition-like nature of tunnels and conduits.

Draft def of the 'tunnel' class as used currently in ENVO:
EquivalentTo 'geographic feature' and has_part some 'conduit space' and conduit_for some 'material entity'
It seems just to be a generalisation and change to geographic scale. In fact, a very general "tunnel" definition may start to resemble a disposition-like definition: any 'material entity' and has_part some 'conduit space' and conduit_for some 'material entity'