GenomicsStandardsConsortium
Duplicate term: MIXS:0000102 & MIXS:0000504. Deprecate MIXS:0000504?
the term nitro as well as tot_nitro_content are both in MixS? They are defined almost synonymously, but the tot_nitro_content term allows for more units:
tot_nitro_content units: microgram per liter, micromole per liter, milligram per liter
nitro units: micromole per liter
should this term be standardized across the two packages?
To be discussed on next CIG call. It looks to make sense to replace nitro in the Misc package.
We have multiple very similar terms for nitrogen:
| URI | label | definition |
|---|---|---|
| MIXS:0000102 | total nitrogen concentration (tot_nitro) | Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen |
| MIXS:0000504 | nitrogen (nitro) | Concentration of nitrogen (total) |
| MIXS:0000338 | total nitrogen content method (tot_nitro_cont_meth) | Reference or method used in determining the total nitrogen |
| MIXS:0000744 | total dissolved nitrogen (tot_diss_nitro) | Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen |
| MIXS:0000162 | dissolved organic nitrogen (diss_org_nitro) | Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 |
| MIXS:0000205 | organic nitrogen (org_nitro) | Concentration of organic nitrogen |
| MIXS:0000530 | total nitrogen content (tot_nitro_content) | Total nitrogen content of the sample |
| MIXS:0000698 | dissolved inorganic nitrogen (diss_inorg_nitro) | Concentration of dissolved inorganic nitrogen |
| MIXS:0000719 | particulate organic nitrogen (part_org_nitro) | Concentration of particulate organic nitrogen |
| MIXS:0000745 | total inorganic nitrogen (tot_inorg_nitro) | Total inorganic nitrogen content |
Maybe its because I'm not an expert in the field, but to me it seems like over-kill to have so many possible terms to capture measurements of Nitrogen. @turbomam would it be possible to get usage stats for each of those terms? If there are quite a few that have zero usage then maybe we can simplfy the choices available!
Eitherway, I think its pretty clear that MIXS:0000504 can be deprecated as a duplicate of MIXS:0000102 as long as we make the definition of 102 more generic (i.e. not water specific.)
here are the counts of harmonized attribute assertions that contain the string "nitro" in NCBI Biosamples as of 2025-03-14
| harmonized_name | count |
|---|---|
| carb_nitro_ratio | 6919 |
| diss_inorg_nitro | 2985 |
| diss_org_nitro | 7700 |
| nitro | 15943 |
| org_nitro | 7430 |
| part_org_nitro | 4314 |
| tot_diss_nitro | 7610 |
| tot_inorg_nitro | 1431 |
| tot_nitro | 46896 |
| tot_nitro_cont_meth | 815 |
- not in @only1chunts 's list:
carb_nitro_ratio - not used as a
harmonized_nameor a verbatimattribute_namein NCBI Biosamples:tot_nitro_content
Thanks @turbomam. So another low-hanging fruit action here would be to deprecate MIXS:0000530 | total nitrogen content (tot_nitro_content) as its the same as MIX:0000102 and its never been used anyway.
What we do with the rest of them I'm not sure!
comment by @mslarae13 there is historic reason for MIX:0000102 being water specific, something to do with the expected values meant to be of the water surrounding the hydrocarbons being sampled. at the CIG call we discussed things again and its apparent that we have got a lot of terms, but we dont have enough for every eventuality (e.g. people collect ammonia, or urea or other specific compounds, not just "organic" or "inorganic"). We dont know what to do, but maybe there is a way to offer a single term for “nitrogen” content with some sort of structured value to indicate exactly what measurement(s) were done and their values and units? Perhaps that can be expanded to be a compound attribute which asks for “measured compound/chemical” & “measurement method” & “measured value” & “measured unit” where each field is taken from a controlled vocab (except the value).