envo NTRs: concentration of... in soil and in water

Hi Pier Luigi, Could you please add the following terms under PATO_0000033 Concentration of?

[ ] concentration of sulfur in soil
[ ] concentration of sulfur in water
[x] concentration of potassium in soil
[ ] concentration of potassium in water
[ ] concentration of phosphate in soil
[x] concentration of phosphate in water
[x] concentration of sulfate in soil
[ ] concentration of sulfate in water
[x] concentration of sulfur in soil
[x] concentration of sulfur in water
[ ] concentration of bicarbonate in soil
[ ] concentration of bicarbonate in water
[ ] concentration of available phosphorus in soil
[ ] concentration of available phosphorus in water
[x] concentration of phosphorus in soil
[ ] concentration of phosphorus in water
[ ] concentration of total nitrogen in soil
[ ] concentration of total nitrogen in water
[x] concentration of calcium in soil
[x] concentration of magnesium in soil
[x] concentration of iron in soil
[ ] concentration of zinc in soil
[ ] concentration of copper in soil
[ ] concentration of boron in soil
[ ] concentration of molybdenum in soil
[x] concentration of manganese in soil
[ ] concentration of chlorine in soil
[ ] concentration of calcium in water
[ ] concentration of magnesium in water
[ ] concentration of iron in water
[ ] concentration of zinc in water
[ ] concentration of copper in water
[ ] concentration of boron in water
[ ] concentration of molybdenum in water
[ ] concentration of manganese in water
[ ] concentration of chlorine in water
[x] concentration of salt in soil (exactsyn: soil salinity)
[ ] concentration of salt in water
[x] concentration of water in soil (exactsyn: soil moisture)

@marieALaporte

May 14 '20 15:05 celineaubert

Hey @kaiiam thanks for self-assigning

I think we have most of the ingredients, but we may need some more CHEBI imports

Jun 02 '20 18:06 pbuttigieg

@celineaubert Thanks for the request, we have a chemical_concentration DOSDP pattern to automate this. I can make these for you, however, I'd like to draw attention to concentration of salt in soil (exactsyn: soil salinity) and concentration of water in soil (exactsyn: soil moisture).

For the former giving it that exact synonymy depends on the definition of salinity, if we make it using sodium chloride then it's not necessarily salinity, a quality concept that can include more than just NaCl, which I'll try to add to PATO and import into ENVO, see #883.

For the latter the synonymy depends on the definition of soil moisture I know there are several, but we can easily make `concentration of CHEBI:water in soil.

Finally in regard to the concentration of available phosphorus terms. As far as I understand "biologically available phosphorus is not well defined" ref. We currently have concentration of phosphate in liquid water. @celineaubert you'd have to pin down exactly what you mean by biologically available phosphate. For example some 1, 2 cite Orthophosphate (represented by CHEBI:phosphate(3−)) as a common part of the biologically available phosphate, but does that fully represent your terms?

Let me know if this suffices for you purposes, and let me know if you could help pin what exactly you mean by "available phosphate".

Jun 02 '20 19:06 kaiiam

We'd also need to make total nitrogen separately as I understand its the sum of nitrate (NO3), nitrite (NO2), organic nitrogen and ammonia ref. I presume CHEBI:organic nitrogen anion is sufficient to represent organic nitrogen, but we'd have to double check.

Jun 02 '20 19:06 kaiiam

I also noticed that concentration of phosphate in liquid water is incorrect, I used phosphate in the axiom rather than phosphate(3−). The latter has the synonym Orthophosphate and refers to the dissolved ions, which is what people measure, rather than the former (which are organic phosphates and nucleoside phosphates). I'll need to fix the axiom in http://purl.obolibrary.org/obo/ENVO_3100026. I think it's more appropriate to fix the axiom then to make a new term because as far as I'm aware there isn't a usecase of people measuring salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues in water and soil, and I don't want to confuse the community by having both terms but the other being a distraction from the common usage.

Jun 02 '20 23:06 kaiiam

xref to https://github.com/UA-SRC-data/srpdio/issues/1

Jun 03 '20 01:06 kaiiam

@kaiiam many thanks for taking this issue.

For the former giving it that exact synonymy depends on the definition of salinity, if we make it using sodium chloride then it's not necessarily salinity, a quality concept that can include more than just NaCl, which I'll try to add to PATO and import into ENVO, see #883.

The term I would like to add is soil salinity. Therefore, if the PATO term ''salinity'' is created, I would rather prefer to have a ''soil salinity'' term created than ''concentration of salt in soil''.

For the other terms I will ask the view of agronomists and come back to you.

Jun 03 '20 07:06 celineaubert

Hi @kaiiam ,

After asking more information about Soil moisture and Available phosphorus, here are the elements I gathered:

Soil moisture definition: the water that is held in the spaces between soil particles xref: https://www.drought.gov/drought/data-maps-tools/soil-moisture The term soil moisture would be prefer to concentration of water in soil.

Instead of concentration of available phosphorus in soil, would it be possible to have available phosphorus content in soil? Reading this paper from NCBI, I wonder if it's appropriate to have concentration of ... in soil since soil is a solid. What do you think? Also content is the term used by agronomists.

A definition for available phosphorus content in soil would be ''portion of soil phosphorus that can be utilized by plants or become mobilised to soil water''. xref: https://pubs.usgs.gov/fs/2012/3004/pdf/fs20123004.pdf

Let me know what your think! thanks

Jun 10 '20 14:06 celineaubert

In regard to content v.s. concentration, PATO defines the latter as A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. that definition seems to more similar to the definition of content in the paper you cite: content is an amount of any type per mass of liquid or gas or solid system. Hence I think PATO concentration is sufficient. @pbuttigieg thoughts? We can always add synonyms if necessary.

In regard to moisture, PATO has the class water composition, def: A composition quality inhering in an bearer by virtue of the quantities or relative ratios of water of the inhering entity.. Perhaps we use this to pre-compose terms like water composition of soil.

In regard to phosphorus: @celineaubert based on your reference and my background knowledge, I'm getting the impression that there are two measured types of phosphorus, dissolved phosphorus, which is in the form of orthophosphate, and total phosphorus, which "includes dissolved phosphorus plus the phosphorus found in particles or bound to sediment". My understanding is that it's the former, the ionic orthorphosphate, which is available to organisms.

However, @celineaubert you have requested 3 different types of phosphorus related terms: 1) concentration of phosphate, 2) concentration of available phosphorus, and 3) concentration of phosphorus.

My understanding is that 1) and 2) (above) are both dissolved phosphorus, or concentration of orthophosphate aka CHEBI:phosphate(3−), while 3) is perhaps more like concentration of elemental phosphorus or perhaps phosphorus molecular entity. @pbuttigieg and @celineaubert let me know if this makes sense to you and if @celineaubert having those two term types would satisfy your use cases. Otherwise We'd need to pin down a more accurate definition of available phosphorus in terms of the chemical entities involved.

Jun 10 '20 17:06 kaiiam

Hi @kaiiam,

What you proposed for soil moisture looks good.

I searched in literature to try clarifying the definition of phosphorus and all its forms in soil. This what I found, let me know if it helps!

soil phosphorus= concentration of total phosphorus in soil= inorganic phosphorus+organic phosphorus.

concentration of total phosphorus in soil: all forms of P in soil, inorganic+organic. syn: total phosphorus content in soil
inorganic phosphorus= concentration of available phosphorus + labile phosphorus (sorbed)+ mineral phosphorus (non-labile, bound) https://www.aces.edu/blog/topics/crop-production/understanding-phosphorus-forms-and-their-cycling-in-the-soil/
organic P= the sum of HCO3 Po (C22) and OH Po (C24). https://www.nature.com/articles/sdata2018166
concentration of available phosphorus in soil= concentration of orthophosphate aka CHEBI:phosphate(3−) (H2PO4–, HPO42-). Syn:concentration of soil solution phosphorus in soil, concentration of plant-available phosphorus in soil, available phosphorus content in soil, available inorganic phosphorus content in soil, concentration of readily-available phosphorus in soil https://www.aces.edu/blog/topics/crop-production/understanding-phosphorus-forms-and-their-cycling-in-the-soil/ https://www.ag.ndsu.edu/publications/environment-natural-resources/phosphorus-behavior-in-the-environment
concentration of phosphorus in soil: seems to be a broad term used to define all the possible measurements of phosphorus. It might be a broadsyn of concentration of total phosphorus in soil
concentration of phosphate: could we use the [CHebi term phosphate]?(https://www.ebi.ac.uk/ols/ontologies/chebi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_26020)? Agronomists measure both phosphate and phosphorus in soil, so it would be good to have 2 different terms (if it makes sense).

Jun 11 '20 09:06 celineaubert

Hi @kaiiam would you have any update on this request? Thanks!

Jan 02 '23 11:01 celineaubert