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

Kathi Schleidt kathi at datacove.eu
Tue May 11 12:54:18 EDT 2021


Dear all,

a bit of background from the underlying model that Raul has so nicely
transformed to a more semantic representation - please bear in mind that
Raul's task was not to design a soil ontology, but to transform the
model for the Global Soil Information System GloSIS towards a semantic
representation thereof. For details of that data model, please go back
to the talk that Tomas Reznik and myself held for this group at the
April 7th meeting.

To point 1 and the definition of bulk density (pretty sure you'll
encounter similar issues in a lot of the concepts for with data is
foreseen) - all the requirements were extracted from the FAO Guidelines
on Soil Description as well as the available drafts towards GloSIS -
thus the semantics of these concepts should be aligned with those
sources, ideally with domain experts, which we data geeks are definitely
NOT (I just understand the structure of what you do, not the details ;) )

To point 2 representation of the soil domain - while I think the world
is still looking for ONE ontology to support all requirements, I've
become wary of this goal, as ontologies are strongly guided in their
perspective on the world by their use cases - as GloSIS was designed to
collect, harmonize, merge all available data on soil, it took a
measurement-data-centric perspective, leading to the statement of:

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

I totally get the requirement for a more user-centric perspective on
soil, but believe this should be a complementary (but interlinked)
ontology representing user concepts and thus suitable for answering
questions such as posed in your example of "is this soil compact enough,
healthy enough or too acidic to support this type (X) of farming?" - if
suitably interlinked, the user-centric system could then transpose the
question of if "farming type X can be supported" to the
measurement-data-centric perspective provided by GloSIS (accessing
information on compactness, healthiness or acidity), aggregate this
measurement data, put it in context, and return an answer.

Does this help?

:)

Kathi


On 11.05.2021 18:05, Gary Berg-Cross via Esip-soil-informatics wrote:
> 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 processwhich
> 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 enoughor 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
> <mailto:esip-soil-informatics at lists.esipfed.org>> wrote:
>
>     * *
>
>     *From: *Raul Palma <rpalma at man.poznan.pl
>     <mailto:rpalma at man.poznan.pl>>
>     *Date: *Friday, May 7, 2021 at 5:13 AM
>     *To: *"Egmond, Fenny van" <fenny.vanegmond at wur.nl
>     <mailto:fenny.vanegmond at wur.nl>>, Luís de Sousa
>     <luis.desousa at isric.org <mailto:luis.desousa at isric.org>>, Tomáš
>     Řezník <tomas.reznik at sci.muni.cz
>     <mailto:tomas.reznik at sci.muni.cz>>, Kathi Schleidt
>     <kathi at datacove.eu <mailto:kathi at datacove.eu>>, "Bulens, Jandirk"
>     <jandirk.bulens at wur.nl <mailto:jandirk.bulens at wur.nl>>, Bogusz
>     Janiak <bogusz.janiak at gmail.com <mailto:bogusz.janiak at gmail.com>>
>     *Cc: *"Todd-Brown, Kathe" <kathe.toddbrown at essie.ufl.edu
>     <mailto: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
>     <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
>     <mailto:fenny.vanegmond at wur.nl>>
>     *Date: *Friday, 7 May 2021 at 10:38
>     *To: *Raul Palma <rpalma at man.poznan.pl
>     <mailto:rpalma at man.poznan.pl>>, Luís de Sousa
>     <luis.desousa at isric.org <mailto:luis.desousa at isric.org>>, Tomáš
>     Řezník <tomas.reznik at sci.muni.cz
>     <mailto:tomas.reznik at sci.muni.cz>>, Kathi Schleidt
>     <kathi at datacove.eu <mailto:kathi at datacove.eu>>, "Bulens, Jandirk"
>     <jandirk.bulens at wur.nl <mailto:jandirk.bulens at wur.nl>>
>     *Cc: *"Todd-Brown, Kathe" <kathe.toddbrown at essie.ufl.edu
>     <mailto: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 <mailto:fenny.vanegmond at wur.nl>
>
>     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
>     <mailto: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
>     <mailto:kathe.toddbrown at essie.ufl.edu>>
>     *Cc:* ESIP, soil info <esip-soil-informatics at lists.esipfed.org
>     <mailto: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.
>
>     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
>     <mailto: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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>
>
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