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EnvironmentOntology / envo

A community-driven ontology for the representation of environments
http://www.environmentontology.org
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create water material and deionized water in EnvO #1514

Open turbomam opened 3 months ago

turbomam commented 3 months ago

I had started this in OBI:

But now I'm thinking that EnvO would be a better home

The NMDC has contributors who would like to semantically capture the reagents they used in reactions like digesting proteins into peptides for LC/MS analysis. The number of reagents we would want to mode is not clear yet. I hope to limit it to reagents that have a significant influence of the results of the reaction. Deionized water isn't an examples of that, but I might want to illustrate how it could be done anyway.

My mental picture is that a scientist uses a reagent colloquially called "deionized water". They might say that they took some "other kind of water" and processed it in some way to get "deionized water". I don't think either the input into that process or the output of the process is pure CHEBI:15377, but the output is expected to contain significantly less dissolved mineral ions than the input.

Therefore, I could

  1. create "water material" as a subclass of 'environmental material', It would consist primarily of CHEBI:15377
  2. create a "deionized water material" subclass of "water material". I was thinking of just giving the textual differential above to start, but I am open to giving it an axiomatic differential too.

@cmungall @pbuttigieg

turbomam commented 3 months ago

see also https://en.wikipedia.org/wiki/Purified_water#Deionization

pbuttigieg commented 3 months ago

we already have ENVO:liquid water which is CPO CHEBI:water

you can add a subclass to that which is:

deionized water =def. liquid water which is the output of a deionization process

and define deionization in the process branch as :

a process during which ion exchange chemistry is used to replace one class of ions with another.

you can then create a subclass of that process to describe the specific ion exchange process used for the deionized water you're dealing with, I believe that's mineral-to-(H+/OH-) exchange.

and then define

mineral-to-(H+/OH-) deionized water with that process class

turbomam commented 3 months ago

liquid water