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EnvironmentOntology
#392 added classes per 'soil textures'
Added classes:
- soil texture
- loamy sand
- fine sand
- sandy loam
- silt loam
- sandy clay loam
- clay loam
- silty clay loam
- sandy clay
- silty clay
- hydrometer method
- pipette method
- feel method
- ball and ribbon method
- ball throwing method
closes #392
In the Australian context, the 'field texture' classification is intrinsically tied to the method - usually feel and ball & ribbon methods. i.e. there is a hard dependency between the texture classification and the method.
OTOH - the ternary classification (% sand-silt-clay) is based on laboratory observations.
In the Australian context, the 'field texture' classification is intrinsically tied to the method - usually feel and ball & ribbon methods. i.e. there is a hard dependency between the texture classification and the method.
Browsing through the books you kindly sent over @dr-shorthair, I see the issue. The classification is certainly strongly dependent on the outcome, but it must point to some coarse (no pun intended) physical threshold.
In fact, for the soil harmonisation work in ESIP, getting a very generic pattern here that can accommodate different instances of these methods could be very helpful.
it must point to some coarse (no pun intended) physical threshold.
There is obviously a correlation, else the field texture classification would be pointless. However, when I very recently explored this issue with the domain experts they were very clear that field-texture and particle-size-distribution determined by lab methods are distinct and should not be conflated.
Did I get that right @ljgregory @meganrwong @abhritchie ?
Yes @dr-shorthair, my understanding as well. AFAICT it comes down to precision and trust, with field texture offering little of either. Once lab (or indeed ML-based estimates from soil spectroscopy) are available, field texture estimates are either ignored or recalibrated.
Thanks @abhritchie - that tells me we should not use the methods as differentia / definitional criteria.
We'll look towards the criteria used by the more rigorous tests and reference the physical properties they reference. @marieALaporte do you have a set of these for your soil types? I see you use the USDA thresholds (which is somewhat confusing, considering your organisation) - is that what you're using across regions?
@dr-shorthair @abhritchie happy to examine other criteria list to see if we can start some early harmonisation that may interest ESIP's soil ontology cluster.
The PR is being formulated and conflicts resolved. We have a non-trivial conflict below.
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Clay"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00002982> "Particulate environmental material which 1) is composed primarily of clay particles, 2) demonstrates plasticity when wet, and 3) is capable of hardening when dried or fired."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/ENVO_00002982> "Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible."@en)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_00002982> "EcoLexicon:clay"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_00002982> "SWEETRealm:Clay"^^xsd:string)
<<<<<<< HEAD
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://en.wikipedia.org/wiki/Clay>) rdfs:comment <http://purl.obolibrary.org/obo/ENVO_00002982> "The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam. Similar mixtures with greater than 40% clay would be considered clay soils."@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_00002982> "clay"^^xsd:string)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00002982> <http://purl.obolibrary.org/obo/ENVO_01000060>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00002982> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/ENVO_01003003>))
=======
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_00002982> "https://en.wikipedia.org/wiki/Clay"^^xsd:string)
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_00002982> "Soil material that contains 40% or more clay, less than 45% sand, and less than 40% silt."@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00002982> <http://purl.obolibrary.org/obo/ENVO_00010483>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00002982> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/ENVO_06105271>))
>>>>>>> e6f6f149aa10112bb3204b65a09d6d2b4ffbc621
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00002982> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000086> <http://purl.obolibrary.org/obo/PATO_0000984>))
DisjointClasses(<http://purl.obolibrary.org/obo/ENVO_00002982> <http://purl.obolibrary.org/obo/ENVO_01000016>)
The proposed changes in e6f6f149aa10112bb3204b65a09d6d2b4ffbc621 assert that clay has a soil texture, which - along with the proposed comment, would make clay a soil.
Is this the global understanding of clay? As a type of soil? I find that quite odd. I can imagine soils rich in clay, "clay soils", but saying that clays are soils is a bit of a push.
Silt has similar issues:
Review axioms in the PR carefully.
# Class: <http://purl.obolibrary.org/obo/ENVO_01000016> (silt)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://en.wikipedia.org/wiki/Silt>) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01000016> "Particulate environmental material which is primarily composed of silt particles."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/ENVO_01000016> "Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible."@en)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_01000016> "EcoLexicon:silt"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_01000016> "SWEETRealm:Silt"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_01000016> "https://en.wikipedia.org/wiki/Silt"^^xsd:string)
<<<<<<< HEAD
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://en.wikipedia.org/wiki/Silt>) rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01000016> "In the Udden-Wentworth scale (due to Krumbein), silt particles range between 0.0039 to 0.0625 mm, larger than clay but smaller than sand particles. ISO 14688 grades silts between 0.002 mm and 0.063 mm. In actuality, silt is chemically distinct from clay, and unlike clay, grains of silt are approximately the same size in all dimensions; furthermore, their size ranges overlap. Clays are formed from thin plate-shaped particles held together by electrostatic forces, so present a cohesion. According to the U.S. Department of Agriculture Soil Texture Classification system, the sand-silt distinction is made at the 0.05 mm particle size. The USDA system has been adopted by the Food and Agriculture Organization (FAO). In the Unified Soil Classification System (USCS) and the AASHTO Soil Classification system, the sand-silt distinction is made at the 0.075 mm particle size (i.e., material passing the #200 sieve). Silts and clays are distinguished mechanically by their plasticity."@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01000016> "silt"^^xsd:string)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000016> <http://purl.obolibrary.org/obo/ENVO_01000060>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000016> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/ENVO_00000343>))
=======
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://sis.agr.gc.ca/cansis/glossary/t/index.html") rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01000016> "Soil material that contains 80% or more silt and less than 12% clay."@en)
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01000016> "https://en.wikipedia.org/wiki/ In the Udden-Wentworth scale (due to Krumbein), silt particles range between 0.0039 to 0.0625 mm, larger than clay but smaller than sand particles. ISO 14688 grades silts between 0.002 mm and 0.063 mm. In actuality, silt is chemically distinct from clay, and unlike clay, grains of silt are approximately the same size in all dimensions; furthermore, their size ranges overlap. Clays are formed from thin plate-shaped particles held together by electrostatic forces, so present a cohesion. According to the U.S. Department of Agriculture Soil Texture Classification system, the sand-silt distinction is made at the 0.05 mm particle size. The USDA system has been adopted by the Food and Agriculture Organization (FAO). In the Unified Soil Classification System (USCS) and the AASHTO Soil Classification system, the sand-silt distinction is made at the 0.075 mm particle size (i.e., material passing the #200 sieve). Silts and clays are distinguished mechanically by their plasticity."^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01000016> "silt"^^xsd:string)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000016> <http://purl.obolibrary.org/obo/ENVO_00010483>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000016> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/ENVO_06105271>))
>>>>>>> e6f6f149aa10112bb3204b65a09d6d2b4ffbc621
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000016> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000086> <http://purl.obolibrary.org/obo/PATO_0000984>))
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000016> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000086> <http://purl.obolibrary.org/obo/PATO_0001759>))
DisjointClasses(<http://purl.obolibrary.org/obo/ENVO_01000016> <http://purl.obolibrary.org/obo/ENVO_01000017>)
Similar issues for sand:
# Class: <http://purl.obolibrary.org/obo/ENVO_01000017> (sand)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Sand"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01000017> "Particulate environmental material which is composed primarily of particles of sand."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/ENVO_01000017> "Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible."@en)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_01000017> "EcoLexicon:sand"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_01000017> "LTER:484"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_01000017> "SWEETRealm:Sand"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_01000017> "https://en.wikipedia.org/wiki/Sand"^^xsd:string)
<<<<<<< HEAD
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01000017> "sand"^^xsd:string)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000017> <http://purl.obolibrary.org/obo/ENVO_01000060>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000017> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/ENVO_00000340>))
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000017> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0001000> ObjectUnionOf(<http://purl.obolibrary.org/obo/ENVO_00001995> <http://purl.obolibrary.org/obo/OBI_0100026> <http://purl.obolibrary.org/obo/UBERON_0006612>)))
=======
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/ENVO_01000017> "ENVO"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/ENVO_01000017> "ENVO:01000017"^^xsd:string)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://sis.agr.gc.ca/cansis/glossary/t/index.html") rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01000017> "Soil material that contains 85% or more sand; the percentage of silt plus 1.5 times the percentage of clay does not exceed 15. coarse sand (sable grossier) 25% or more very coarse and coarse sand, and less than 50% any other one grade of sand."@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000017> <http://purl.obolibrary.org/obo/ENVO_00010483>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000017> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/ENVO_06105271>))
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000017> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0001000> <http://purl.obolibrary.org/obo/ENVO_00001995>))
>>>>>>> e6f6f149aa10112bb3204b65a09d6d2b4ffbc621
clay, silt, and sand are definitely not kinds of soil. They can be constituents (partOf) soil.
There is obviously a correlation, else the field texture classification would be pointless. However, when I very recently explored this issue with the domain experts they were very clear that field-texture and particle-size-distribution determined by lab methods are distinct and should not be conflated.
Simon's point about not conflating texture and particle-size-distribution is important even if lab methods are a secondary concern (e.g. intrinsic in Australia, less so in NZL).
Despite sharing three labels ('sand', 'silt' and 'clay'), the texture classes and particle size distribution classes describe different concepts. They can be confused because the strong functional relationship they have (texture depends on size distribution), and because texture is often used as a proxy for size distribution. Nevertheless, they are different.
(Apologies for any egg sucking lessons here.)
Using 'sand' as an example: in a particle size distribution, the 'sand' size fraction refers to the abundance of particles of size 0.063-2.0mm (ISO scale). The size distribution covers the 'fine earth fraction ' (clay, silt and sand) and 'coarse fragments' (gravel, boulders). This maps to a the broad understanding of 'sand' among earth scientists and why Steve points out 'sand' isn't a type of soil, it is a constituent of a particular size.
Soil texture classes compare the relative abundance of sand, silt and clay and assign a class. 'Sand' is the label given a class where sand dominates the fine earth fraction. The soil scientist I spoke to says 'sand' and 'sandy soil' can be used interchangeably - in this context. As a class assigned to a soil (horizon) it is arguably describes type of soil.
All a long-winded way of saying that a common label can't be used to infer a match.