NTRs related to MIxS sediment checklist

[simroux]

Based on work done in the NMDC Ontology workshop. A substantial part of these terms would also apply to the MIxS soil checklist which @ukaraoz is curating. To order the different terms, we looked at which fields were most often filled in in submission to ENA (thanks to data provided by @josieburgin) for the soil and sediment checklist. The list below includes is ordered from the most frequently to least frequently used terms.

MIxS term	MIxS Values	MIxS description	ontology term label	ontology	ontology ID	ontology purl	notes
depth	key	Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples	depth in soil		to be created
salinity	key	Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater			to be created
methane	key	Methane (gas) amount or concentration at the time of sampling			to be created
tidal_stage	key	Stage of tide			to be created		Should be an ENVO process ?
tidal_stage	low tide				to be created
tidal_stage	ebb tide				to be created
tidal_stage	flood tide				to be created
tidal_stage	high tide				to be created
tot_org_carb	key	Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content			to create		Similar to ENVO_09000008, "concentration of carbon atom in soil". We need to add all of these composite terms to ENVO: DOC = dissolved organic carbon (in soil, in water), DIC = dissolved inorganic carbon (in soil, in water), TOC =total organic carbon (in soil, in water), TIC = total inorganic carbon (in soil, in water), TC = total carbon (in soil, in water)
pH	key	Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid		CHMO	CHMO:0002354	http://purl.obolibrary.org/obo/CHMO_0002354	Should be added to ENVO ?
oxy_stat_samp	key	Oxygenation status of sample			to be created
oxy_stat_samp	aerobic				to be created		add under ENVO_00002007?
oxy_stat_samp	anaerobic		anaerobic sediment	ENVO	ENVO:00002045	http://purl.obolibrary.org/obo/ENVO_00002045
oxy_stat_samp	other				to be created
nitro	key	Concentration of nitrogen (total)			to be created
sulfate	key	Concentration of sulfate in the sample			to be created		Should be added to ENVO under PATO:0000033 ?
carb_nitro_ratio	key	Ratio of amount or concentrations of carbon to nitrogen			to be created
redox_potential	key	Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential			to be created
nitrite	key	Concentration of nitrite in the sample			to be created		Should be added to ENVO under PATO:0000033 ?
phosphate	key	Concentration of phosphate			to be created		Should be added to ENVO under PATO:0000033 ?
pressure	key	Pressure to which the sample is subject to, in atmospheres			to be created		Should be added to ENVO under PATO:0000033 ?
potassium	key	Concentration of potassium in the sample			to be created
magnesium	key	Concentration of magnesium in the sample			to be created
calcium	key	Concentration of calcium in the sample			to be created
perturbation	key	Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types	exposure stressor	EXO	EXO:0000000	http://purl.obolibrary.org/obo/ExO_0000000	Should be added to ENVO ?
water content	key	Water content measurement	soil water content	EO	EO:0007259	http://purl.obolibrary.org/obo/EO_0007259	Should be added to ENVO ?
silicate	key	Concentration of silicate			to be created		Should be added to ENVO under PATO:0000033
sodium	key	Sodium concentration in the sample			to be created		Should be added to ENVO under PATO:0000033
sulfide	key	Concentration of sulfide in the sample			to be created		Should be added to ENVO under PATO:0000033
turbidity	key	Measure of the amount of cloudiness or haziness in water caused by individual particles			to be created		Add under PATO:0001018
org_carb	key	Concentration of organic carbon			to be created
org_matter	key	Concentration of organic matter			to be created
org_nitro	key	Concentration of organic nitrogen			to be created
diss_org_carb	key	Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid			to be created
diss_org_nitro	key	Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2			to be created
diss_oxygen	key	Concentration of dissolved oxygen			to be created

[pbuttigieg]

Thanks! We also should use this as an opportunity to spot dangerous semantic variation of the same label across packages.

[pbuttigieg]

@simroux when we create the ontology terms to represent these, I suppose they will be sediment specific right? So "depth" is actually "depth in the sediment"? The table above suggests this is "depth in soil" which isn't the same thing (i.e. wouldn't be the same ontology class).

This also raises an issue about domain conflict that @ramonawalls can perhaps help resolve with BCO:

ENVO can deal with properties of environmental entities. "Depth of sediment" is fine as are things like "nitrate concentration in sediment". However, what seems to be needed in the "depth" case (ignoring the soil/sediment conflict) is "depth of sampling event in a sediment column" which is more a BCO field. @ramonawalls thoughts?

[simroux]

@pbuttigieg : These are two good questions. For question #1: I would intuitively say sediments are a subset of soils, however this is not what is currently reflected in ENVO, where soil and sediment are two distinct classes at the same rank (under "Environmental material"), and there's certainly some very good reasons + experts opinion for this. So then yes, while I initially tried to re-use terms associated with soil (e.g. "depth in soil"), these should be adapted to sediment (i.e. "depth in the sediment").

For BCO vs ENVO, I agree that the "depth" will most often be associated with a sample or measurement (I could imagine some in situ probe measurements that would need to be associated with a "depth in sediment" information). So we may need both BCO and ENVO ??

[pbuttigieg]

Building on the above - many of these seem to be package agnostic:

"concentration of magnesium" inheres in any sampled material, not just sediment.

Two routes present themselves:

Option 1

We use BCO with its notion of "sample" to compose things like "concentration of magnesium in a sample of environmental material" axiomatised similar to

'concentration of'
 and ('inheres in' some 
    (magnesium
     and ('part of' some (BCO:sample and 'composed primarily of' some 'environmental material'))))

Where the ENVO medium/material field in the MIxS core checklist will be parsed to specify the environmental material.

Option 2

For each package, we pre-compose specific IRIs for each property described by each parameter. When we RDFise MIxS, this will mean that each field in each package will have its own IRI.

Thoughts @ramonawalls @cmungall ?

[pbuttigieg]

So then yes, while I initially tried to re-use terms associated with soil (e.g. "depth in soil"), these should be adapted to sediment (i.e. "depth in the sediment").

Thanks for the clarification @simroux - this is what I meant above by some of the 'dangerous semantic variation' in MIxS. This wasn't a big issue in the past, but now when we're trying to get more organised and precise, we'll need to clean this up.

For BCO vs ENVO, I agree that the "depth" will most often be associated with a sample or measurement (I could imagine some in situ probe measurements that would need to be associated with a "depth in sediment" information). So we may need both BCO and ENVO ??

It's likely we'll need a combination of ontologies to handle the semantics implicit in several MIxS terms, but don't worry too much - this is normal and healthy in the OBO world as we don't want to try to build one ontology that covers everything. OBO ontologies interoperate and can be spliced together as needed.

@cmungall @ramonawalls An OBO application ontology for MIxS may not be a bad idea here, so we get the IDs and RDF we need to take MIxS forward in an interoperable way.

[simroux]

Cleaning up this type of issues would be great :-) From my outsider perspective, option 1 seems the best as, once this would be in place, you could expand it to new compounds / measurements or new environments relatively "easily", but I've no idea how more complex this would be in terms of implementation.

[pbuttigieg]

From my outsider perspective, option 1 seems the best as, once this would be in place, you could expand it to new compounds / measurements or new environments relatively "easily", but I've no idea how more complex this would be in terms of implementation.

I'm leaning that way too - it's a good segue into more efficient and structured use of reference ontologies that saves the need for massive inflation.

A potential issue with my draft approach for option 1 is that there can be multiple material terms in the 3rd slot.

[cmungall]

I don't think we need to bring in BCO classes here

[dr-shorthair]

Hmm. Not all soils are sediments in the classical sense. Organic soils in particular. 'Sediment' has a genetic feel about it (related to sedimentation?) while soils are formed through a variety of processes, some involving transport, but others not.

Somewhat related is this long-outstanding NTR: https://github.com/EnvironmentOntology/envo/issues/825 the narrative for which now includes the textual definitions of the Australian soil orders.