[Esip-soil-informatics] FW: Followup questions from 5 May GLOSIS presentation

Gary Berg-Cross gbergcross at gmail.com
Tue May 11 12:05:18 EDT 2021


Raul et al,

Thank you for the follow up response.  I hope that some of the issues and
understandings will
be helpful down the road.
I can understand the idea that a definition is implied in the collection
axioms such as
you have for   BulkDensityWholeSoil using the axioms


   - is a subclass of *sosa:Observation*
   - hasFeatureOfInterest a Layer or a Horizon
   - the observedProperty is bulkDensityWholeSoilProperty
   - and the expected values are numeric (float) measured in
   KiloGM-PER-DeciM3

I do see some issue with the variance here to what is in typical
definitions of  Bulk Density
<http://soilquality.org/indicators/bulk_density.html>

What it is: Bulk density is an indicator of* soil compaction*. It is
calculated as the dry weight of soil divided by its volume. This volume
includes the volume of soil particles and the volume of pores among soil
particles. Bulk density is typically expressed in g/cm3.
Adding definitions like this is helpful to human understanding.
This also suggests, of course,  that definitions promote the idea some
additional axioms including the relation to soil compaction (soil has part
compaction process) and a calculation process.
EnvO, for example, has this definition for: compaction process which might
be used as context:

def: "A physical process during which atoms, molecules, or other
constituents of a material entity are forced closer together."


On the 2nd issue of how the soil domain is represented, I see that, as you say:

"So, the domain knowledge is there but is not modelled as subclasses
of soil concepts, but as types of observations of soil concepts"

I wonder if people would agree that there is an understood soil domain
which includes features (of interest) and that based on this integrated
understanding observations are made to investigate the domain. Particular
observations may be of interest for different types of soil and for
purposes such as - "is this soil compact enough, healthy enough or too
acidic to support this type (X) of farming?"


Gary Berg-Cross
Potomac, MD
240-426-0770


On Fri, May 7, 2021 at 12:35 PM Todd-Brown, Kathe via Esip-soil-informatics
<esip-soil-informatics at lists.esipfed.org> wrote:

>
>
> *From: *Raul Palma <rpalma at man.poznan.pl>
> *Date: *Friday, May 7, 2021 at 5:13 AM
> *To: *"Egmond, Fenny van" <fenny.vanegmond at wur.nl>, Luís de Sousa <
> luis.desousa at isric.org>, Tomáš Řezník <tomas.reznik at sci.muni.cz>, Kathi
> Schleidt <kathi at datacove.eu>, "Bulens, Jandirk" <jandirk.bulens at wur.nl>,
> Bogusz Janiak <bogusz.janiak at gmail.com>
> *Cc: *"Todd-Brown, Kathe" <kathe.toddbrown at essie.ufl.edu>
> *Subject: *Re: [Esip-soil-informatics] Followup questions from 5 May
> GLOSIS presentation
>
>
>
> Hi,
>
> Sure, from my side I can say a few words.
>
> Regarding question 1.
>
> Indeed, the concepts are not having a textual description, apart from the
> codelists:
> https://github.com/rapw3k/glosis/blob/master/glosis_cl_v1.0.0.ttl
>
> The definition is at the owl level, so for example,
>
> BulkDensityWholeSoil we can see that
>
>    - is a subclass of *sosa:Observation*
>    - hasFeatureOfInterest a Layer or a Horizon
>    - the observedProperty is bulkDensityWholeSoilProperty
>    - and the expected values are numeric (float) measured in
>    KiloGM-PER-DeciM3
>
> Nevertheless, I agree having also textual descriptions would be a good
> addition.
>
> This would require, though, to go through documentation and excels of the
> GLOSIS, but should be done.
>
>
>
> Regarding question 2.
>
> I think the view on this is a bit reverse.
>
> The main concept taxonomy of the soil domain is derived from the ISO28258,
> as you can see in the picture attached.
>
> Then all the observation types that we have defined in GloSIS are
> connected to those soil concepts (via the hasFeatureOfInterest property).
>
> So, the domain knowledge is there but is not modelled as subclasses of
> soil concepts, but as types of observations of soil concepts.
>
> To make it more explicit, we could make a superclass for all those
> observations, e.g., , something like “SoilObservation” (as a subclass of
> sosa:Observation) and then make all our observations subclasses of that
> superclass (instead of being subclass of sosa:Observation). This way it
> could be clear that these are observations of soil concepts, but in terms
> of explicit semantics is not really adding much.
>
> Perhaps others here have some opinions in this regard?
>
> Cheers,
> Raul
>
>
>
> *From: *"Egmond, Fenny van" <fenny.vanegmond at wur.nl>
> *Date: *Friday, 7 May 2021 at 10:38
> *To: *Raul Palma <rpalma at man.poznan.pl>, Luís de Sousa <
> luis.desousa at isric.org>, Tomáš Řezník <tomas.reznik at sci.muni.cz>, Kathi
> Schleidt <kathi at datacove.eu>, "Bulens, Jandirk" <jandirk.bulens at wur.nl>
> *Cc: *"Todd-Brown, Kathe" <kathe.toddbrown at essie.ufl.edu>
> *Subject: *FW: [Esip-soil-informatics] Followup questions from 5 May
> GLOSIS presentation
>
>
>
> Hi,
>
>
>
> I don’t know if you receive the emails on the emailstring below, so just
> to be sure I forward to you. Would one of you like to answer to Gary
> through the mailing list?
>
>
>
> Thanks!
>
>
>
> Fenny
>
>
>
>
> -----------------------------------------------------------------------------------------------------------------------------------------------------
>
> Fenny van Egmond
>
> Wageningen Environmental Research (and ISRIC – World Soil Information)
>
> Postbus 47, 6700 AA, Wageningen
>
> Wageningen Campus, Gebouw 101 (Gaia), Room G.C.010 (mon, tu, fr) and Room
> C.111 (wed, th, fr)
>
> Droevendaalsesteeg 3, 6708 PB, Wageningen
>
> T. +31(0)317 480406
>
> E. fenny.vanegmond at wur.nl
>
> [image: cid:image001.jpg at 01D74331.E2044C70]
>
> *www.wur.nl/environmental-research
> <http://www.wur.nl/environmental-research>*
>
>
>
> *From:* Esip-soil-informatics <
> esip-soil-informatics-bounces at lists.esipfed.org> *On Behalf Of *Gary
> Berg-Cross via Esip-soil-informatics
> *Sent:* Thursday, May 06, 2021 19:38
> *To:* Todd-Brown, Kathe <kathe.toddbrown at essie.ufl.edu>
> *Cc:* ESIP, soil info <esip-soil-informatics at lists.esipfed.org>
> *Subject:* Re: [Esip-soil-informatics] Followup questions from 5 May
> GLOSIS presentation
>
>
>
> Raul,Et al.
>
> I have two  followup questions from the GLOSIS ontology presentation that
> there wasn't time
>
> to cover during our hour session.
>
>
>
> 1. Are there definitions in the GLOSIS ontology?
>
> When I look at a class in the ontology like " BulkDensityWholeSoil" I
> don't see definitions.
>
> I used the link:
>
> http://w3id.org/glosis/model/layerhorizon#BulkDensityWholeSoil
> <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fw3id.org%2Fglosis%2Fmodel%2Flayerhorizon%23BulkDensityWholeSoil&data=04%7C01%7Cfenny.vanegmond%40wur.nl%7C595735a6b14c4eb2735108d910b5fd78%7C27d137e5761f4dc1af88d26430abb18f%7C0%7C0%7C637559196823096956%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=5ErI2RUedWHG89qwam7bQAn3jOdlfRBQK%2BkJbIPMhwY%3D&reserved=0>
>
> And I can see a text version of the Owl file.
>
> For  BulkDensityWholeSoil it is this segment  info:
>
> glosis_lh:BulkDensityWholeSoil  a     owl:Class ;
>
>         rdfs:subClassOf  *sosa:Observation *;
>
>         rdfs:subClassOf [ a owl:Restriction ; owl:onProperty sosa:hasFeatureOfInterest ; owl:allValuesFrom [owl:unionOf (glosis_lh:GL_Layer glosis_lh:GL_Horizon) ] ] ;
>
>                        rdfs:subClassOf [ a owl:Restriction ; owl:onProperty sosa:hasResult ; owl:allValuesFrom glosis_lh:BulkDensityWholeSoilValue ] ;
>
>                        rdfs:subClassOf [ a owl:Restriction ; owl:onProperty sosa:observedProperty ; owl:hasValue glosis_lh:bulkDensityWholeSoilProperty ] .
>
>
>
> glosis_lh:bulkDensityWholeSoilProperty a sosa:ObservableProperty , qudt:Quantitykind ;
>
>         rdfs:label "bulkDensityWholeSoilProperty"@en .
>
>
>
> glosis_lh:BulkDensityWholeSoilValue a owl:Class ;
>
>         rdfs:subClassOf  qudt:QuantityValue ;
>
>         rdfs:subClassOf [ a owl:Restriction ; owl:onProperty qudt:numericValue ; owl:allValuesFrom xsd:float ] ;
>
>         rdfs:subClassOf [ a owl:Restriction ; owl:onProperty qudt:unit ; owl:hasValue unit:KiloGM-PER-DeciM3] .
>
>
>
> So no commented definition for this concept.  In general I don't see definitions, but would believe you have them, they are useful for understanding the model of the domain.  What am I missing?
>
>
>
> 2.  I'd like to know more about thoughts on the "domain" taxonomy and structure.
>
> I see ample organization using concepts like sites and things that Observations out of SOSA and SSN.
>
> These are bottom line useful for soil data by code etc.
>
>
>
> But there seems to be little about the soil domain itself (like sub-classes).
>
> Am I missing something or is that an issue?
>
> I've attached a portion of the WebVowl view of Glosis which might make clearer
>
> how I understand the domain organization and absence of a Soil concept as an organizer.
>
> This would be useful for a real use case and for harmonizing across efforts.
>
> Perhaps you have plans here.
>
> [image: cid:image002.png at 01D74331.E2044C70]
>
> Thanks,
>
>
>
> Gary Berg-Cross
>
> Ontolog Forum
>
> Potomac, MD
>
> 240-426-0770
>
>
>
>
>
> On Wed, May 5, 2021 at 3:31 PM Todd-Brown, Kathe via Esip-soil-informatics
> <esip-soil-informatics at lists.esipfed.org> wrote:
>
> Thank you Raul for a fantastic overview of the GloSIS ontology. If you
> missed it you can find the recording here: https://youtu.be/q79p_oA5rtU
> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyoutu.be%2Fq79p_oA5rtU&data=04%7C01%7Cfenny.vanegmond%40wur.nl%7C595735a6b14c4eb2735108d910b5fd78%7C27d137e5761f4dc1af88d26430abb18f%7C0%7C0%7C637559196823096956%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=BZXVbl%2BZXqEaJuX6ISCMKF1AFPAqL9WEKNtSE0tldlI%3D&reserved=0>
>  and Anne D took fantastic notes in the logistics document.
>
>
>
> Brief housekeeping: We now have ONE zoom room for both meetings and the
> easy and convenient calendar generating links might not auto update. Sorry
> that this information keeps changing, please double check your calendar to
> make sure it matches the information on the google document
> https://docs.google.com/document/d/1_SIm_3e9xpni_64zdAU1DZrFEd8YcIerbsihDJq4qwY/edit?usp=sharing
> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1_SIm_3e9xpni_64zdAU1DZrFEd8YcIerbsihDJq4qwY%2Fedit%3Fusp%3Dsharing&data=04%7C01%7Cfenny.vanegmond%40wur.nl%7C595735a6b14c4eb2735108d910b5fd78%7C27d137e5761f4dc1af88d26430abb18f%7C0%7C0%7C637559196823106951%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=gYlP727iDB9Nq9wW5sxXZ0XGrp1E8fk7Hb06dp98smg%3D&reserved=0>
>
>
>
>
> We will be meeting next on 19 May at 2300UTC. If no one comes forward with
> a different suggestion, on the agenda will be pulling together a soil
> semantic resource list for the ESIP Summer meeting (and ourselves!).
>
>
>
> We are looking for other presentations! If you know of anyone working with
> soil data who would be interested in presenting please send them my way!
>
>
>
> -Kathe
>
>
>
> ---------
>
> Katherine Todd-Brown, PhD
>
>
>
> Assistant Professor
>
> Environmental Engineering Sciences
>
> Engineering School of Sustainable Infrastructure & Environment
>
> Herbert Wertheim College of Engineering
>
> University of Florida
>
>
>
> Office: Rm B006, Phelps Lab, UF main campus
>
> Twitter: @KatheMathBio
>
>
>
> Mail: Dr Kathe Todd-Brown
>
> Center for Wetlands
>
> PO Box 116350
>
> Gainesville, FL 32611
>
>
>
>
>
>
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