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EnvironmentOntology / envo

A community-driven ontology for the representation of environments
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NTRs regarding soil properties and qualities for MIxS key mappings and some others #896

Open ukaraoz opened 4 years ago

ukaraoz commented 4 years ago

@cmungall @kaiiam

Regarding soil property/quality mapping from MIxS-soil package, we could maybe work with the following class/subclass structure. For definitions, I propose using USDA Soil Survey Manual and/or USDA National Soil Survey Handbook. I am not a soil scientist, just dealt extensively with metadata from soil omics datasets.

Requires some fine tuning based on your inputs and not sure what is the best way to make these additions.

chemical properties: NCIT_C17771

physical properties: PATO:0001241

geomorphological properties (not sure whether these should be properties OR realizable entities)

kaiiam commented 4 years ago

Great @ukaraoz, thanks for for proving an initial mapping for these MIxS-soil terms. We'll wrap this into the ongoing overall effort to ontologize MIxS. If you have any more soil terms to add to this please do so in this issue thread.

We typically wouldn't used the NCI Thesaurus for these kinds of mappings, but this is useful for us to create the appropriate terms.

soil texture [MIxS-soil: texture] Reading the PATO_0000150, I'd think soil texture shouldn't be a subclass.

@ukaraoz Why not? Texture is a quality which can inhere in a variety of materials, fabric soil etc.

cmungall commented 4 years ago

PATO texture is pretty vague, and the definition only talks about surface, which seems wrong not only for soil but for other things too, e.g. food texture

On Sun, Oct 27, 2019 at 11:29 AM Kai Blumberg notifications@github.com wrote:

Great @ukaraoz https://github.com/ukaraoz, thanks for for proving an initial mapping for these MIxS-soil terms. We'll wrap this into the ongoing overall effort to ontologize MIxS. If you have any more soil terms to add to this please do so in this issue thread.

We typically wouldn't used the NCI Thesaurus for these kinds of mappings, but this is useful for us to create the appropriate terms.

soil texture [MIxS-soil: texture] Reading the PATO_0000150, I'd think soil texture shouldn't be a subclass.

@ukaraoz https://github.com/ukaraoz Why not? Texture is a quality which can inhere in a variety of materials, fabric soil etc.

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kaiiam commented 4 years ago

@cmungall would changes to the PATO:texture be in scope:

def:

A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics.

Or perhaps a more specific subclass be made?

cmungall commented 4 years ago

The issue is that 'surface' may be too restrictive. Perhaps the existing class could be renamed 'surface texture' or similar and a broader class introduced...?

On Mon, Oct 28, 2019 at 10:20 AM Kai Blumberg notifications@github.com wrote:

@cmungall https://github.com/cmungall would changes to the PATOtexture http://purl.obolibrary.org/obo/PATO_0000150 be in scope:

def:

A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics.

Or perhaps a more specific subclass be made?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/EnvironmentOntology/envo/issues/896?email_source=notifications&email_token=AAAMMOJ4J2NUGJ4LA2Z2VCTQQ4NO5A5CNFSM4JFK3P6KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECNWJLY#issuecomment-547054767, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOL7RANOJG77SSINXFLQQ4NO5ANCNFSM4JFK3P6A .

smrgeoinfo commented 4 years ago

Arrgh-- the term 'texture' is so fuzzy and subject to multiple interpretations ... It caused IMMENSE trouble working on descriptive vocabularies for rocks (vocabs at http://resource.geosciml.org/def/voc/).
I'd recommend first getting clear about what you mean by texture (grain size? grain sorting? grain shape? grain alignment? pore space? mineralogy? consolidation?...) and then work on the more clearly defined vocabularies.

kaiiam commented 4 years ago

@smrgeoinfo I agree, it would be great if we could get some soil scientists who have perhaps helped in the MIxS process to provide a more specific definition of what they mean by soil texture, then it would be more clear what term would go into ENVO or perhaps another ontology.

ukaraoz commented 4 years ago

@smrgeoinfo I agree, it would be great if we could get some soil scientists who have perhaps helped in the MIxS process to provide a more specific definition of what they mean by soil texture, then it would be more clear what term would go into ENVO or perhaps another ontology.

For soil, there is "apparent texture" and "lab measured texture". They don't correlate well. Apparent texture fits into the PATO texture but the lab measured texture seems not to. That one is defined by "grain size" (reference: USDA Soil Survey Manual) and that is what MIxS refers to: "The weight proportion of the separates for particles less than 2 mm in diameter as determined from a laboratory particle-size distribution."