GenomicsStandardsConsortium / mixs

Minimum Information about any (X) Sequence” (MIxS) specification
https://w3id.org/mixs
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do we need new soil terms in Food package #214

Closed only1chunts closed 3 years ago

only1chunts commented 3 years ago

Current term details in ticket #201 there are 3 soil texture terms proposed for the Food package:

Term name - soil texture classification
Structured comment name - soil_texture_class
Definition - One of the 12 soil texture classes use to describe soil texture based on the relative proportion of different grain sizes  of mineral particles [sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um)] in a soil.
Expected value - enumeration
Value syntax - [clay|clay loam|loam|loamy sand|sand|sandy clay|sandy clay loam|sandy loam|silt|silty clay|silty clay loam|silt loam]
Example - silty clay loam
Term ID - MIXS:0001164
Package(s) - Food
Term name - soil texture method
Structured comment name - soil_texture_meth
Definition - Reference or method used in determining soil texture classification.
Expected value - PMID,DOI or url
Value syntax - {PMID}|{DOI}|{URL}
Example - https://uwlab.soils.wisc.edu/wp-content/uploads/sites/17/2015/09/particle_size.pdf (hydrometer method)
Term ID - MIXS:0001165
Package(s) - Food
Term name - soil type name
Structured comment name - soil_type_name
Definition - Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998).  Multiple terms can be separated by pipes.
Expected value - ENVO_00001998
Value syntax - {termLabel} {[termID]}
Example - plinthosol [ENVO:00002250]
Term ID - MIXS:0001166
Package(s) - Food

Suggested update(s) I believe these are already covered by the existing terms:

Term name - texture
Structured comment name - texture
Definition - The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.
Expected value - measurement value
Value syntax - {float} {unit}
Term ID - MIXS:0000335

and

Structured comment name - texture_meth
Term name - texture method
Definition - Reference or method used in determining soil texture
Expected value - PMID,DOI or url
Value syntax - {PMID}|{DOI}|{URL}
Term Id - MIXS:0000336

and

Term name - soil type
Structured comment name - soil_type
Definition - Soil series name or other lower-level classification
Expected value - soil type name
Value syntax - {text}
Term ID - MIXS:0000332

Additional context These terms were propsed as part of the Food package #201

ramonawalls commented 3 years ago

For soil texture - food package is a classification but existing term is a method type. Keep both but rename existing term "texture" to "soil texture measurement".

Soil texture method and texture method are the same and should be merged.

Merge soil type terms and specify ENVO classes as new CV. Need to check if any terms in the old CV are missing from ENVO.

only1chunts commented 3 years ago

Summary

Update MIXS:0000332 and use it instead of creating MIXS:0001166:

Term name - soil type
Structured comment name - soil_type
* Definition - Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998).  Multiple terms can be separated by pipes.
* Expected value - ENVO_00001998
* Value syntax - {termLabel} {[termID]}
* Example - plinthosol [ENVO:00002250]

Update name MIXS:0000336 and use it instead of creating MIXS:0001165:

* Term name - soil texture method
* Structured comment name - soil_texture_meth
Definition - Reference or method used in determining soil texture classification.
Expected value - PMID,DOI or url
Value syntax - {PMID}|{DOI}|{URL}
Example - https://uwlab.soils.wisc.edu/wp-content/uploads/sites/17/2015/09/particle_size.pdf (hydrometer method)
Term ID - MIXS:0000336

Update name of MIXS:0000335 to

* Term name - soil texture measurement
* Structured comment name - soil_text_measure
Definition - The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.
Expected value - measurement value
Value syntax - {float} {unit}
Term ID - MIXS:0000335

in MIxS v6 Term Updates sheet Updated MIXS:0000332 in package terms sheet Updated MIXS:0000335 in package terms sheet Updated MIXS:0000336 in package terms sheet Updated MIXS:0001165 to MIXS:0000336 in newFood sheet Updated MIXS:0001166 to MIXS:0000332 in newFood sheet and included all changes in v6 update log