epilimnion and hypolimnion

[kaiiam]

The current epilimnion and hypolimnion terms are in the astronomical body part hierarchy as subclasses of lake layer. In order to properly axiomatize the GOLD/EBI lentic Epilimnion and Hypolimnion terms, we need to refer to epilimnion and hypolimnion which are not in lakes but rather in any more general water body. @pbuttigieg would it make sense to move these epilimnion and hypolimnion classes away from lake layer to water body under aquatic layer or perhaps to leave the lake layer terms and create new water body classes? Or perhaps something else as I understand we are trying to move away from environmental feature classes?

[pbuttigieg]

Hmm, could you provide some examples of non-lake hypo/epilimnia?

[stevenchong]

Or perhaps something else as I understand we are trying to move away from environmental feature classes?

Can you clarify what you mean by moving away from environmental feature classes?

[kaiiam]

@pbuttigieg the examples from the EBI biomes are the following:

from both the root > Environmental > Aquatic > Freshwater > Lentic as well as root > Environmental > Aquatic > Non-marine Saline and Alkaline > Saline hierarchies we have Epilimnion and Hypolimnion terms. The former refers specifically to a lentic water body, there is another term for freshwater lakes hence why I believe the epi and hyplimnion terms may be meant to apply more general water bodies than just lakes.

The latter hierarchy is a bit more ambiguous where in additional to the Epilimnion and Hypolimnion terms they also have Athalassic (away from the sea) and Thalassic (by the sea). From the few examples of annotated data it looks like these epi and hyp terms refer only to saline lakes layers, the Athalassic to a saline lake itself and Thalassic to a saline lagoon. Given this, it is fair to assume that these Epilimnion and Hypolimnion terms are meant to refer only to saline lakes not general saline water bodies? They have a separate term for saline evaporation pond.

[kaiiam]

@stevenchong my understanding is that as an environmental feature is a bit ambiguous and hard to define, Pier has stated that he would prefer we try to eventually move toward rooting the environmental feature terms under different sub-hierarchies possibly emergent ones if we can get reasoners to help us figure out what more "natural" groupings could be.

[pbuttigieg]

Cross link to #672

from both the root > Environmental > Aquatic > Freshwater > Lentic as well as root > Environmental > Aquatic > Non-marine Saline and Alkaline > Saline hierarchies we have Epilimnion and Hypolimnion terms. The former refers specifically to a lentic water body, there is another term for freshwater lakes hence why I believe the epi and hyplimnion terms may be meant to apply more general water bodies than just lakes.

@kaiiam we'd need real world examples rather than a category scheme to justify generalising this class (e.g. is there an instance of a water body that is not a lake that has a hypolimnion?) . Lakes are lentic water bodies and there can be saline lakes, so this may just be a mild confusion due to forcing things into a category scheme with low expression (thus why the ontologising is needed)

The latter hierarchy is a bit more ambiguous where in additional to the Epilimnion and Hypolimnion terms they also have Athalassic (away from the sea) and Thalassic (by the sea). From the few examples of annotated data it looks like these epi and hyp terms refer only to saline lakes layers, the Athalassic to a saline lake itself and Thalassic to a saline lagoon. Given this, it is fair to assume that these Epilimnion and Hypolimnion terms are meant to refer only to saline lakes not general saline water bodies? They have a separate term for saline evaporation pond.

Yes, my feeling is that they still apply to lakes. Are those thalassic/athalassic attributes something of interest? Perhaps qualities?

[pbuttigieg]

@stevenchong, in response to your comment above, @kaiiam summarised it quite well.

The environmental feature was a convenience category created very early on. We're trying to be a bit more strict and link to the astronomical body part branch, eventually obsoleting the env feature. This takes time as it's such a high level term.

[diatomsRcool]

trying to think of things with hypo- and epilimnion that aren't lakes.....
ponds?
still areas of rivers or streams?
reservoirs?
vernal pool?
bayous or marshlands?
Just spit balling here.....

[kaiiam]

@diatomsRcool I was postulating that it maybe theoretically possible for a pond to have an epilimnion, however, I think @pbuttigieg is correct when he says:

this may just be a mild confusion due to forcing things into a category scheme with low expression (thus why the ontologising is needed).

I will adjust accordingly for the purposes of the creation of the EBI/JGI GOLD microbiome classes, by making both the root > Environmental > Aquatic > Freshwater > Lentic > Epilimnion and Hypolimnion classes be subclasses of root > Environmental > Aquatic > Freshwater > Lake. I believe this is fitting as all the data associated with such categories in JGI gold are lakes.

My understanding of the thalassic athalassic attributes in regard to saline water bodies is that they describe whether or not a water body is marine. I suppose they could be made into quality terms. Perhaps in ENVO as subclasses of physical quality sister classes to sea state?

[pbuttigieg]

Could be, I think these qualities are specific enough to be hosted by ENVO, rather than PATO proper.

The strategy for the limnia sounds reasonable. We can change things if we ever find a solid example that's not in a lake.

[pbuttigieg]

@kaiiam could you close this if it's resolved, and add a separate issue for the thalassic qualities?

[kaiiam]

@pbuttigieg yes, thanks for the response, see issue #801.