Prepping pull request 3 for project cryophile

[kaiiam]

from #476

In last pull request I added geographic basin In response to @pbuttigieg:

Please link with appropriate axioms to planetary crust. I'm not sure if located in or part of is more appropriate here: topology is somewhat slippery in that regard. Invoking something like 'geographic scale' is not something I'm a huge fan of, but it is used by physical geographers.

I've added the subclass axiom:

'adjacent to' some 'planetary crust'

from #482

@mschecht addressing @pbuttigieg's concerns:

change the label of marine sediment to "deep marine sediment" Please also change the synonym type to "has related synonym". Add a new superclass marine sediment with a similar definition, just not requiring it to be in the deep. Add a class, shallow marine sediment, (subclass of marine sediment, sibling to deep marine sediment) with a synonym "neritic marine sediment". Again, similar def, but this time the sediment should be on a shelf, slope, or rise.

To sediment I added the comment:

It is recommended to use a combination of sediment terms to describe a more specific sediment type.

I renamed marine sediment to deep marine sediment changed: has_exact_synonym pelagic sediment to has_related_synonym pelagic sediment def changed to:

Sediment that accumulates in the flat or very gently sloping areas of the deep ocean basin floor. The three main types of deep marine sediment, also known as pelagic sediment, are siliceous oozes, calcareous oozes, and red clays.

added Class marine sediment (super class to deep marine sediment):

Sediment which accumulates within an ocean basin.

added class: shallow marine sediment

Marine sediment which accumulates within shallow regions of the oceanic basin close to continents, such as the continental shelf, or continental slope.

with has_related_synonym neritic marine sediment

I also added subclass axiom: 'adjacent to' some ('continental shelf' or 'continental slope')

from #475

I've added: supraglacial lake

A water body which is located in a depression within the surface of a glacier.

as far as I can tell by definition these lakes are strictly located in a glacier so I added the subclass axiom:

'located in' some glacier

[pbuttigieg]

Hi @kaiiam - this seems to be a normal issue and not a PR. Could you validate? [Edit: issue title updated to reflect it's not a confusion]

Other comments below:

from #476

In last pull request I added geographic basin In response to @pbuttigieg:

Please link with appropriate axioms to planetary crust. I'm not sure if located in or part of is more appropriate here: topology is somewhat slippery in that regard. Invoking something like 'geographic scale' is not something I'm a huge fan of, but it is used by physical geographers.

I've added the subclass axiom:

'adjacent to' some 'planetary crust'

Not sure this works, the basin is actually a topological conformation of the crust. Perhaps we can use overlaps.

from #482

@mschecht addressing @pbuttigieg's concerns:

change the label of marine sediment to "deep marine sediment" Please also change the synonym type to "has related synonym". Add a new superclass marine sediment with a similar definition, just not requiring it to be in the deep. Add a class, shallow marine sediment, (subclass of marine sediment, sibling to deep marine sediment) with a synonym "neritic marine sediment". Again, similar def, but this time the sediment should be on a shelf, slope, or rise.

[...]

added Class marine sediment (super class to deep marine sediment):

Sediment which accumulates within an ocean basin.

Please add a comment here briefly describing on how the sediment is formed/transported (e.g. particles formed in the water column or transported by rivers or wind) and that it originates at the surface.

added class: shallow marine sediment

Marine sediment which accumulates within shallow regions of the oceanic basin close to continents, such as the continental shelf, or continental slope.

As above, add a comment on formation/transport processes, noting that this sediment type has more terrestrial inputs than deep sediments.

[....]

I also added subclass axiom: 'adjacent to' some ('continental shelf' or 'continental slope')

This may not be right - this implies that every portion of shallow marine sediment is adjacent to the shelf or slope, which isn't the case (you could have sediment on top of sediment or sediment in the lab). I think we should defer this until we add sedimentation processes so we can then say it was the output of a sedimentation process that occurred in a neritic biome, or similar. This should be noted in a comment.

from #475

I've added: supraglacial lake

A water body which is located in a depression within the surface of a glacier.

as far as I can tell by definition these lakes are strictly located in a glacier so I added the subclass axiom:

'located in' some glacier

Not sure about located in here. If the lake was intraglacial (in the glacier with no exposure to the atmosphere) then it would be correct.

[kaiiam]

@pbuttigieg in response:

for geographic basin I've changed the subclass axiom to

overlaps some 'planetary crust'

for your comments on sediment. It should by definition result form a transport process. So we'll make sedimentation process (subclass of precipitation process)

A precipitation process in during which solid sediment particles previously in suspension in a water body, leave suspension, and are transported downward by gravity settling at the base of the water body.

sediment transport process (subclass of material transport process)

A material transport process in which sediment is transported. This could result from lateral flow, turbulent flows, or benthic storms.

for supraglacial lake: we could axiom relaxed to either 'depends on' or 'adjacent to' thoughts?

[pbuttigieg]

A precipitation process in during which solid sediment particles in suspension in a water body are transported downward and settle at the base of the water body due to gravity.

Careful here, if they're in suspension they can't fall (strictly speaking)

A material transport process in which sediment is transported. This could result from lateral flow, turbulent flows, or benthic storms.

I think this is enough, but I'd move the second sentence to a comment.

[kaiiam]

@pbuttigieg more terms from #475 to add to this PR.

ice ablation zone ref

An ablation zone in which an ice ablation process occurs.

with subclass axiom:

'contains process' some 'ice ablation process'

cryoconite ref

A mixture of particulate matter including dust, rock, soot, and microorganisms deposited on an ice mass by an aeolian process.

cryoconite holes ref

A vertical hole which is found within an ice mass, formed by local increases in temperature due to increased absorption of solar radiation by cryoconite deposits.

water body
- melt pond: def = A small water body, which forms within a continuous mass of ice such a glacier or on sea ice.

physiographic feature
-- channel 
---brine channel def = A 

--- hole 
----melt hole: def = A continuous hole within an ice mass formed by the erosional forces of meltwater.
----- cryoconite hole: def = A vertical melt hole which is found within an ice mass, formed by local increases in temperature due to increased absorption of solar radiation by cryoconite deposits.

next we add glacial lake synonym tarn ref1, ref2 and we can encode the methane escaping lakes:

[pbuttigieg]

A mixture of 'particulate matter' including 'dust', 'rock', 'soot', and microorganisms deposited on an 'ice mass' by an 'aeolian process'

This could be very interestingly axiomatised. @ramonawalls this is a good chance to enliven/close the issue on microbial community over at PCO https://github.com/PopulationAndCommunityOntology/pco/issues/22

A vertical hole which is found within an ice mass, formed by local increases in temperature due to increased absorption of solar radiation by cryoconite deposits.

Good, but do mention melting processes in the def and axioms.

[pbuttigieg]

melt pond: def = A small water body, which forms within a continuous mass of ice such a glacier or on sea ice.

Mention that it forms through melting and link with axioms. Take a look at RO's process axioms to find a good one.

physiographic feature -- channel ---brine channel def = A

Def. appears to be missing

--- hole ----melt hole: def = A continuous hole within an ice mass formed by the erosional forces of meltwater.

Why continuous? Does meltwater have erosional force itself?

----- cryoconite hole: def = A vertical melt hole which is found within an ice mass, formed by local increases in temperature due to increased absorption of solar radiation by cryoconite deposits.

next we add glacial lake synonym tarn ref1, ref2 and we can encode the methane escaping lakes:

Cool, but go with "methane-releasing lake"

[kaiiam]

After some deliberation with @pbuttigieg about sedimentation process:

A material accumulation process during which solid particles are pulled through a water body by gravitation or centrifugal force and which ends when they settle on a solid surface.

with subclass axioms:

'has participant' some 'particulate matter' 'occurs in' some 'water body' 'has part' some 'precipitation process' ends some 'material transport process' 'occurs in' some 'water body'

[pbuttigieg]

Hi @kaiiam, we should label this "sedimentation in a water body" for absolute clarity

[kaiiam]

Continued from #475

brine channel:

A channel through which brine flows.

seawater freezing process def:

A material transformation process during which seawater freezes into sea ice,

brine rejection process def:

A material transformation process during which brine is formed due to the expulsion of salt during frazil formation or a seawater freezing process. Expelled salt accumulates in brine droplets, which remain in a liquid state due to their increased salinity.

brine channel formation process def:

A material accumulation process during which trapped brine droplets, between ice crystals formed during seawater freezing, form brine channels.

frazil def:

Small needle-like ice crystals consisting of nearly pure fresh water, which are suspended in water.

frazil formation def:

A material accumulation process in which frazil ice crystals merge, forming thin sheets of ice.

comment: Frazil formation constitutes an initial developmental stage of sea ice growth.

[kaiiam]

@pbuttigieg I've taken care of almost all of this. The remainder will continue in #487