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term total nitrogen concentration (tot_nitro) is water specific, should be general #680

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mslarae13 opened this issue Oct 20, 2023 · 3 comments · May be fixed by #751
Open

term total nitrogen concentration (tot_nitro) is water specific, should be general #680

mslarae13 opened this issue Oct 20, 2023 · 3 comments · May be fixed by #751
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1-TermUpdate Update suggestion for existing term, including bugs. Issues from "cig-bug" label moved here.

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@mslarae13
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Describe the bug
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The description of tot_nitro is : Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen

The specification of water is limiting, you can have total N on all samples

this is used in extension

  • HydrocarbonResourcesCores
  • HydrocarbonResourcesFluidsSwabs
  • WastewaterSludge
  • Water

To Reproduce
Steps to reproduce the behavior:

  1. Go to https://genomicsstandardsconsortium.github.io/mixs/0000102/

Expected behavior
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Terms definitions will be general, not environment specific and slot usage can be added for specific environments

@mslarae13 mslarae13 added the bug label Oct 20, 2023
@mslarae13
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Actually, it looks like a separate slot was made to be less water specific... see https://genomicsstandardsconsortium.github.io/mixs/0000530/

I recommend deprecating tot_nitro and using tot_nitro_content

@ramonawalls ramonawalls added 1-TermUpdate Update suggestion for existing term, including bugs. Issues from "cig-bug" label moved here. and removed cig-bug labels Dec 28, 2023
@mslarae13 mslarae13 linked a pull request Jan 13, 2024 that will close this issue
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@cmungall cmungall removed a link to a pull request Apr 5, 2024
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@cmungall cmungall linked a pull request Apr 5, 2024 that will close this issue
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@mslarae13 mslarae13 moved this to Todo in TWG Activity Track Jul 3, 2024
@mslarae13
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will complete when deprecation protocol is in place

@mslarae13 mslarae13 moved this from Todo to For CIG in TWG Activity Track Jul 17, 2024
@lschriml lschriml moved this from Discuss to For CIG in TWG Activity Track Jan 7, 2025
@lschriml
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lschriml commented Jan 7, 2025

The nuance of what is being measured, concentration vs % of nitrogen in the soil could be lost, if these two were combined.
In order to use a more generic term 'total nitrogen content'. The second part of the definition should include the water/soil details.
The 'new' term could just be: 'total nitrogen'

Reviewing the definitions:
for water:
Term: total nitrogen concentration (tot_nitro)
Definition:
Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen

Note: two forms of Nitrogen are measured

for soil:
Term: total nitrogen content (tot_nitro_content)
Total nitrogen content of the sample

To measure total C and N, subsamples of dried, finely ground soil are weighed into small foil capsules that are combusted in an automated CHN analyzer that measures the amount of released CO2 and N2 by gas chromatography. Final values are expressed as the percentage of carbon or nitrogen in dry soil.

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Labels
1-TermUpdate Update suggestion for existing term, including bugs. Issues from "cig-bug" label moved here.
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Status: For CIG
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3 participants