NTRs regarding soil measurements and processes

[celineaubert]

Hi @pbuttigieg could you please add the following terms?

• [ ] wind soil erosion: A soil erosion process caused by wind

• [ ] water soil erosion: A soil erosion process caused by water

• [ ] soil color: color 'inheres in' some soil

• [x] concentration of organic material in soil: 'concentration of' and 'inheres in' some ('organic material' and 'part of' some soil)

• [ ] acidity of soil ENVO:09200010: could you please add exactsyn: soil pH

• [ ] humidity in soil ENVO:09200015 could you please add exactsyn soil moisture

Thanks!

[pbuttigieg]

@celineaubert

humidity in soil ENVO:09200015 could you please add exactsyn soil moisture

Humidity is usually linked to water vapour (e.g. in the pore space of soils) and moisture to the general water content. Do you have a source that shows these as interchangeable?

[kaiiam]

@pbuttigieg if you want I can add the terms humidity of soil and color of soil terms using the entity_attribute DOSDP module (without the synonyms), if you that covers these cases.

[pbuttigieg]

Thanks @kaiiam I think all of the above except the erosion classes and humidity can be handled with the DOSDP

We have to get a definition / clarification on humidity before we add it.

[celineaubert]

@celineaubert

humidity in soil ENVO:09200015 could you please add exactsyn soil moisture

Humidity is usually linked to water vapour (e.g. in the pore space of soils) and moisture to the general water content. Do you have a source that shows these as interchangeable?

@pbuttigieg indeed, after reading literature it seems that those two terms are not interchangeable. Thanks for pointing that out! I have asked help to define soil moisture (related to the issue #946). Hope to be able to come back to you soon!

[kaiiam]

@cmungall regarding concentration of organic material in soil Is it OK to use an ENVO term (organic material) in the CHEMICAL slot rather than a CHEBI term? In the DOSDP the slot is declared to be CHEBI:chemical entity. Is this strictly enforced somehow that it must be a subclass? Or is it more like a suggestion?

@pbuttigieg Even if we can do this do we want to use an ENVO term over a more precise CHEBI one? ENVO:organic material is 'composed primarily of' some biomacromolecule would it be better to use the CHEBI:biomacromolecule term? This issue will come up again (for MIxS and Planet Microbe) with measurements of env materials such as particulate organic carbon (POC) like concentrations of POC in soil or water. We should clarify if we allow ENVO materials to be used in the chemical slot, or if we mandate use of a CHEBI term in the chem conc DOSDP.

[kaiiam]

@celineaubert regarding humidity of soil, it seems what you need here is moisture of soil I think we can do as I suggested in 946 using PATO:water composition, to precompose water composition of soil.

[marieALaporte]

@kaiiam can we help adding these terms?

[kaiiam]

Hey @celineaubert and @marieALaporte (cc @cmungall @ddooley @wdduncan) sorry for the long slow response, unfortunately we have very little time to dedicate relative to the amount of terms incoming I hope you can understand.

We've been working on some strategies to move things along faster. Depending on the term type we have different mechanisms for bringing them in. The three mechanisms which are relevant to your efforts are:

1. The entity_attribute.csv pattern for generating terms like water composition of soil which pairs a PATO quality term (e.g. water composition with an environmental material (e.g. soil). Note for some requests a new pato term e.g. salinity needs to be created as well, see https://github.com/pato-ontology/pato/issues/345 and https://github.com/pato-ontology/pato/pull/352 for my attempts to get it in there.

2. The chemical_concentration.csv pattern for concentration terms e.g. concentration of methane in liquid water Which pairs a chebi chemical term (e.g. methane) with an environmental material (e.g. liquid water).

3. The ENVO-Robot-template-and-merge-workflow for other terms which don't fit the two above design patterns, e.g. something like wind soil erosion. This new protocol (hopefully) explains all the steps needed to prepare such term requests.

I know @celineaubert has made many term requests over the years many of which we have yet to respond to. In order to rectify this situation I propose the following. If @celineaubert @marieALaporte or someone on your team could consolidate/prepare all the new term requests (from the dozens of issues started by @celineaubert :P) into three google docs formatted like the 1) entity_attribute.csv 2) the chemical_concentration.csv and 3) the shared template from the ENVO-Robot-template-and-merge-workflow. You can do so by following the instructions in the merge workflow, as well as the patterns described for entity-attribute and chemical concentrations. By consolidating all your relevant terms into the appropriate formats (and following the instructions about how to prepare them), it is much easier for us to review as well as integrate your requests into our system.

Much obliged, Kai

[marieALaporte]

Hi @kaiiam. Thanks for the response. If that's ok I will create a PR directly for you to review. Which ID range should I be using for that? One of the ID ranges already created or should I request some ID range for myself?

[kaiiam]

@marieALaporte great question. You are most welcome to make one or several pull requests. We can review your terms either as a pull requests (perhaps better for the design patterns?) or as a google sheet from the merge workflow (perhaps better for the other terms?).

I'd say you're welcome to add yourself an id range in a pull request. I'd suggest you make yourself idrange 23 from [>= 3530000 , <= 3539999]

I note in the envo-idranges.owl file that there is:

Datatype: idrange:7

    Annotations:
        allocatedto: "ENVO-P, E-A"

    EquivalentTo:
        xsd:integer[>= 9200000 , <= 9299999]

for the entity attribute pattern and

Datatype: idrange:13

    Annotations:
        allocatedto: "chemical_concentration.yaml yaml design pattern"

    EquivalentTo:
        xsd:integer[>= 3200001 , <= 3300000]

for the chemical conc pattern. I presume you can use those for the design patterns? Or @cmungall would it be better if @marieALaporte uses her own ID range for those as well?