liquid water salinity

[kaiiam]

Similarly to #882, I would like to make a liquid water salinity class with the entity_attribute design pattern, however I would first need a PATO:salinity class for which I propose the definition:

An osmolarity quality inhering in a bearer by virtue of the bearer's amount of solute, composed primarily of dissolved ionic compounds, per volume of solution.

subclass of PATO:osmolarity

dbxref

Reasonable starting definition? Should I make a PATO issue for this?

[pbuttigieg]

Distinctions arise in the units and focus on osmotic pressure (osmoles) vs amount of solute per volume solvent.

Any sources explaining the difference clearly?

[diatomsRcool]

would it help if I brought in one of my chemical or physical oceanography friends?

[kaiiam]

@pbuttigieg

Any sources explaining the difference clearly?

Not at the moment, I can look into it.

@diatomsRcool

would it help if I brought in one of my chemical or physical oceanography friends?

Yes any expertise we can leverage here would be helpful.

[pbuttigieg]

Well, check out the International Council for the Exploration of the Sea's definition of salinity of seawater:

Total amount of solid materials in grams dissolved in one kilogram of sea water when all the carbonate has been converted to oxide, the bromine and iodine replaced by chlorine and all organic matter completely oxidized.

I'd say that's an ENVO:'ICES salinity' subclass of a more simple PATO:salinity

[cmungall]

It's been a year since this issue was opened.

I would suggest to move faster that some terms are simply added to the edit file with clear well-sourced textual definitions.

I think it's a really good idea to strictly follow design patterns when concepts are trivially compositional. For example PATO:quality and inheres-in some material. But this may not be a trivial case. How would the proposed PATO class relate to what is being used to measure sodium chloride levels in blood? Different concepts like marine salinity, lakewater salinity, blood salinity, and soil salinity may be more nuanced than the composition.

We should definitely explore these things further and bring in experts who can tell us more about measurement techniques used in different disciplines. But we can also just go ahead and add concepts with reasonable text definitions and asserted parents with a note that this is ultimately expected to conform to a pattern but we are not there yet.

Re: different definitions, such as ICES. I am sympathetic to the position that it is hard to disentangle the concept from the measurement, I think this should be represented as different assays that all provide measurements of the same concept, and we should avoid proliferating quality/characteristc concepts in ENVO

[kaiiam]

Thank you for weighing in @cmungall I agree with you on all points.

From the NERC VS P02 we have: Salinity of the water column with the not super useful definition:

Parameters quantifying the concentration of sodium chloride in any body of water at any point between the bed and the atmosphere

From the wiki salinity page we have:

... [the] amount of salt dissolved in a body of water.

and

[S]alinity is the quantity of dissolved salt content of the water. Salts are compounds like sodium chloride, magnesium sulfate, potassium nitrate, and sodium bicarbonate which dissolve into ions.

From Handbook of Smart Coatings for Materials Protection 2014 (found via sciencedirect.com they have:

Salinity is defined as the total amount of salts dissolved in seawater expressed by the following equation:[1.3]Salinity=1.80655×chlorinity

From Treatise on Geochemistry

[salinity] is a measure of the total amount of salts dissolved in the water/brine, and brine, ... measured using many different units and in a number of ways. The absolute salinity, S, as defined by Forschhammer (1865), is the mass of dissolved salts in seawater, brackish water, brine, or other saline solution per mass of that solution and is given in dimensionless units: g per kg, ‰ (per mill), or ppt (parts per thousand).

The resource describes how it is difficult to actually measure, so there are many proxies used

density, i.e., specific gravity, optical refraction index, electrical conductivity, ... the concentration (contents) of some conservative elements ... .

A long time ago I took a course on marine (geo)chemistry Unfortunately I no longer have the notes, but there was much discussion about the Major and minor ions that constitute seawater and therefore salinity. I found similar material on this page from Rodger Williams University

All of the salts and that dissolve in seawater contribute to its overall salinity.

This resource and Treatise on Geochemistry (above) list tables of salts which are included as either minor or major elements in seawater. They go on to describe various different authors' values for various dissolved ions in seawater. I don't think that level of precision is needed for our definition of seawater salinity, let alone a more general salinity quality.

Attempting to summarize all of this into a consensus definition, (without considering the specific method/protocol/device used, or units), still as a subclass to PATO:osmolarity, I propose the following definition:

An osmolarity quality inhering in a bearer by virtue of the total amount of ionic salts dissolved in the bearer.

dbxref1, dbxref2, dbxref3, dbxref4, and dbxref5

Thoughts?

[cmungall]

Good summary - do you want to make a PATO PR?

[kaiiam]

@cmungall just made a PATO issue for this here. Like I said on that thread, I'd be happy to make a PR in PATO. It would be easier with editor permission, but if needed, I could probably figure out how to do it from a branch of a fork without permission. I have more terms that I'll want to push to PATO in the future so I'd be happy to become an editor there if possible.

[cmungall]

Related ticket on units: https://github.com/bio-ontology-research-group/unit-ontology/issues/31