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

Thu May 13 12:32:52 EDT 2021

Kathi et al,

A few more thoughts.  I hope they are useful.
On your point:
>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.

Moving the data representation to the richer OWL form but in alignment with
the original DB is useful, but I would note from Raul's presentation this
which does use the concept of an ontology:

"The presentation will provide an overview of the process for transforming
the Glosis UML data model into an OWL ontology."

Point (or question) #1 raised the idea that one might refine, harmonize and
add to this initial ontology over time with additional, but relevant
concepts.  These might come from and align with other soil DBs.  There may
be some definitional differences to resolve if this is attempted and the
ontology can serve as an integration point and a conceptual basis for such
growth.

This does also touch on point #2,
It is true that no one ontology may be suitable.  There may be several but
to avoid silos the possibility term and axiom reuse
should be considered.    Glosis UML may not be the only basis for common
and useful concepts in at least one larger ontology.
To enable this some common soil ontology design patterns (SSO is one such)
might be considered.  Unlike SSO this would be more soil-centric.

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

On Tue, May 11, 2021 at 1:01 PM Kathi Schleidt via Esip-soil-informatics <
esip-soil-informatics at lists.esipfed.org> wrote:

> 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 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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