Ag package term suggestion growth_substrate MIXS:0001290

[only1chunts]

New term details

Term name - growth substrate
Term ID - MIXS:0001290
Structured comment name - growth_substrate
Definition - Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. This field accepts terms listed under http://purl.obolibrary.org/obo/EO_0007147, plant growth medium.
Expected value - free text
Value syntax - {termLabel} {[termID]}
Example - [potting media|rockwool|water]
Package(s) - Agriculture

Additional context Term suggested within the Ag package

Points for discussion:

1 - How does this relate to the existing term "host_substrate" MIXS:0000252? 2 - The definition includes a suggested ontology, the example seems to include a CV yet the expected value is listed as "free text", not sure why that is? this needs tidying up. how does this relate to the existing term "host_substrate" MIXS:0000252?

[ramonawalls]

Reuse 'plant growth medium' (MIXS:0001057) and allow both ENVO and EO as accepted.

Change the label to the more general "growth medium" which is more general.

[only1chunts]

@ramonawalls are these the changes you are suggesting?

Current 'plant growth medium' term details

Term name - plant growth medium
Term ID - MIXS:0001057
Structured comment name - plant_growth_med
Definition - Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary
Expected value - EO or enumeration 
Value syntax - {termLabel} {[termID]} or [husk|other artificial liquid medium|other artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water] 
Example - hydroponic plant culture media [EO:0007067]

Suggested update(s)

* Term name - growth medium
* Structured comment name - growth_medium
Definition - Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary
Expected value - EO or enumeration 
Value syntax - {termLabel} {[termID]} or [husk|other artificial liquid medium|other artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water] 
Example - hydroponic plant culture media [EO:0007067]

[ramonawalls]

@only1chunts Sorry I was not more specific. Upon further investigation, I find that there already exists a term for plant growth medium (MIXS:0001057) as well as culture rooting medium (MIXS:0001041), both in the plant associated package, as well a bunch of terms to describe characteristics of the rooting medium.

Since plant growth medium and rooting medium are the same thing, I suggest we merge them and replace the suggested term in the food package with MIXS:0001057. I do not know why the plant associated package created two terms, but I suspect it was because they wanted two different vocabularies for soil-like media and artificial media or to separate out tissue culture from other types of reproduction. However, there is no reason to keep them separate in the age of ontologies for vocabularies and better ways to know if your plant was grown from tissue culture or not (e.g., include a term for propagation)

Term name - growth medium Structured comment name - growth_medium Definition - Medium or media for growing plants, tissue cultured samples, or other organisms, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary Expected value - subclass of http://purl.obolibrary.org/obo/NCIT_C85504 from EO, http://purl.obolibrary.org/obo/PECO_0007147, or http://purl.obolibrary.org/obo/ENVO_00010483 Value syntax - {termLabel} {[termID]} Example - hydroponic plant culture media [EO:0007067] MIxS ID: MIXS:0001057

Note that the Ag package suggested [husk|other artificial liquid medium|other artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water] as a CV. They should work with ENVO or PECO to make sure those terms are included in the ontologies.

Suggest to delete culture rooting medium (MIXS:0001041) and not add growth substrate (MIxS:0001290).

This will need to be reviewed by the ag package.

[only1chunts]

thanks @ramonawalls , who is the point of contact for the Ag package ? i.e. who needs to review it, can we tag them here?

[lschriml]

Hello Chris, My primary contact is: JP Dundore-Arias @.***

And cc: Linda Kinkel @.***

Cheers, Lynn

Sent from my iPhone

On Aug 17, 2021, at 11:59 AM, Chris Hunter @.***> wrote:

 thanks @ramonawalls , who is the point of contact for the Ag package ? i.e. who needs to review it, can we tag them here?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[only1chunts]

Invited both to next months call (Sept 27th) and invited them to join the CIG google group

[jpdundorearias]

@only1chunts Sorry I was not more specific. Upon further investigation, I find that there already exists a term for plant growth medium (MIXS:0001057) as well as culture rooting medium (MIXS:0001041), both in the plant associated package, as well a bunch of terms to describe characteristics of the rooting medium.

Since plant growth medium and rooting medium are the same thing, I suggest we merge them and replace the suggested term in the food package with MIXS:0001057. I do not know why the plant associated package created two terms, but I suspect it was because they wanted two different vocabularies for soil-like media and artificial media or to separate out tissue culture from other types of reproduction. However, there is no reason to keep them separate in the age of ontologies for vocabularies and better ways to know if your plant was grown from tissue culture or not (e.g., include a term for propagation)

Term name - growth medium Structured comment name - growth_medium Definition - Medium or media for growing plants, tissue cultured samples, or other organisms, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary Expected value - subclass of http://purl.obolibrary.org/obo/NCIT_C85504 from EO, http://purl.obolibrary.org/obo/PECO_0007147, or http://purl.obolibrary.org/obo/ENVO_00010483 Value syntax - {termLabel} {[termID]} Example - hydroponic plant culture media [EO:0007067] MIxS ID: MIXS:0001057

Note that the Ag package suggested [husk|other artificial liquid medium|other artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water] as a CV. They should work with ENVO or PECO to make sure those terms are included in the ontologies.

Suggest to delete culture rooting medium (MIXS:0001041) and not add growth substrate (MIxS:0001290).

This will need to be reviewed by the ag package.

@only1chunts, we are supportive of the proposed changes by @ramonawalls regarding growth medium. Thanks

[only1chunts]

I am not going to make the changes suggested by @ramonawalls to the term name and definition as I feel that requires greater discussion and probably a wider reach than is currently being looked at, i.e. there is also a term "tiss_cult_growth_med" [MIXS:0001070] which needs to be considered. I will open a new ticket for discussion on this topic before v7. For the Ag package I will replace "growth_substrate" with the current " plant growth medium" term [MIXS:0001057] and close this ticket.