Foodie Ontology and Satellite API

This document is part of a project that has received funding
from the European Union’s Horizon 2020 research and innovation programme
under agreement No 732064. It is the property of the DataBio consortium and shall not be distributed or
reproduced without the formal approval of the DataBio Management Committee. Find us at www.databio.eu.
1
This project has received funding from
the European Union’s Horizon 2020
research and innovation programme
under grant agreement No 732064
This project is part
of BDV PPP
FOODIE ONTOLOGY AND SATELLITE DATA API
Karel Charvát2 Raul Palma1, Tomáš Řezník2,, Karel Charvat Jr,
Vojtech Lukas, Soumya Brahma1, Dmitrij Kozuch2, Raitis
Berzins2,
1Poznan Supercomputing and Networking Center, Poland
2Lesprojekt, Czech Republic
FREE WEBINAR // JANUARY 10,
2019 // 4PM CET
An Introduction to Semantics +
FOODIE Ontology and Satellite
Data API

2
Motivation
• Farm management context
• Multiple activities and stakeholders
• Multiple applications, tools and devices
• Multiple data sources, data types and
data formats
• Challenge
• To combine/integrate those different
and heterogeneous data sources in
order to make economically and
environmentally sound decisions

3
STILL A POORER FARMER IN CLOUD AGE
IOF2020 PARTNER AND STAKEHOLDER EVENTS 3
??????

4
FOODIE Data Models
Machinery fleet monitoring Management zones
Fertilizers/pesticides informationSensor measurements
Obrázkypřevzaty z: http://gillinstruments.com, http://wisegeek.com, http://www.dbta.com/

5
Core Data Model class Foodie Core Data Model v4.1 proposal
«featureType»
Agricultural and
Aquaculture Facilities
Model::Holding
«featureType»
Agricultural and Aquaculture Facilities Model::
Site
+ code :Identifier
+ geometry :GM_Object
+ activity :EconomicActivityNACEValue [1..*]
+ validFrom :DateTime
+ validTo :DateTime [0..1]
+ beginLifespanVersion :DateTime
+ endLifeSpanVersion :DateTime [0..1]
«voidable»
+ includesAnimal :FarmAnimalSpecies [0..*]
«dataType»
FarmAnimalSpecies
«voidable»
+ livestock :LivestockSpeciesValue [0..*]
+ aquaculture :AquacultureSpeciesValue [0..*]
«featureType»
Activity Complex::ActivityComplex
+ inspireId :Identifier
+ thematicId :ThematicIdentifier [0..*]
+ function :Function [1..*]
+ userId :CharacterString
«voidable»
+ name :CharacterString [0..1]
«voidable, lifeCycleInfo»
+ endLifespanVersion :DateTime [0..1]
«featureType»
Plot
+ code :Identifier
+ beginLifeSpanVersion :DateTime
+ geometry :GM_Object [1..*]
+ description :CharacterString [0..1]
+ originType :OriginTypeValue
«featureType»
Treatment
+ quantity :Measure [1..*]
+ tractorId :CharacterString [0..*]
+ machineId :CharacterString [0..*]
+ motionSpeed :Measure [0..1]
+ pressure :Measure [0..1]
+ flowAdjustment :Measure [0..1]
+ applicationWidth :Measure [0..1]
+ areaDose :DoseUnit [0..1]
+ formOfTreatment :FormOfTreatmentValue [1..*]
+ treatmentPurpose :TreatmentPurposeValue [0..*]
+ treatmentDescription :CharacterString [0..1]
«dataType»
NutrientsType
+ N :Measure [0..1]
+ P2O5 :Measure [0..1]
+ K2O :Measure [0..1]
+ MgO :Measure [0..1]
+ CaO :Measure [0..1]
+ S :Measure [0..1]
+ Zn :Measure [0..1]
+ Cu :Measure [0..1]
+ Fe :Measure [0..1]
+ B :Measure [0..1]
+ Mn :Measure [0..1]
+ Mo :Measure [0..1]
«codeList»
TreatmentPurposeValue
+ weed
+ pest
+ disease
«featureType»
CropSpecies
+ beginDate :Date
+ endDate :Date [0..1]
+ cropArea :GM_Object
+ cropSpecies :CropType [1..*]
+ production :ProductionType [0..*]
«featureType»
Product
+ productCode :CharacterString [0..*]
+ productName :CharacterString [1..*]
+ productType :CharacterString
+ productSubType :CharacterString [0..*]
+ productKind :ProductKindValue
+ manufacturer :CI_ResponsibleParty [1..*]
+ nutrients :NutrientsType [0..*]
+ safetyInstructions :CharacterString [0..1]
+ storageHandling :CharacterString [0..1]
+ registrationCode :CharacterString [0..*]
+ registerUrl :URL [0..*]
«featureType»
SoilNutrients
+ nutrientName :GenericName
+ nutrientAmount :Measure
+ nutrientMeasure :CharacterString
«codeList»
ProductKindValue
+ organic
+ mineral
«dataType»
SoilTextureType
+ clay :Percent
+ silt :Percent
+ sand :Percent
«dataType»
ProductionType
+ productionDate :Date
+ variety :CharacterString
+ productionAmount :Measure
+ productionAnalysis :ProductionAnalysisType [0..*]
«dataType»
ProductionAnalysisType
+ productionAnalysisDate :Date
+ property :Measure
«codeList»
OriginTypeValue
+ manual
+ system
«featureType»
Alert
+ code :Identifier
+ type :CharacterString [1..*]
+ checkedByUser :Boolean
+ alertDate :Date
+ alertGeometry :GM_Object
«featureType»
Intervention
+ type :CharacterString
+ description :CharacterString
+ notes :CharacterString [0..1]
+ status :CharacterString
+ creationDateTime :DateTime
+ interventionStart :DateTime
+ interventionEnd :DateTime [0..1]
+ interventionGeometry :GM_Object [1..*]
+ supervisor :CI_ResponsibleParty [0..1]
+ operator :CI_ResponsibleParty [0..*]
+ evidenceParty :CI_ResponsibleParty [1..*]
«featureType»
TreatmentPlan
+ treatmentPlanCode :CharacterString [0..*]
+ description :CharacterString [1..*]
+ campaign :TM_Period [1..*]
+ treatmentPlanCreation :DateTime
«featureType»
ProductPreparation
+ productQuantity :Measure
+ solventQuantity :Measure [0..*]
+ safetyPeriod :TM_Period
«dataType»
ActiveIngredients
+ code :CharacterString [0..1]
+ ingredientName :CharacterString
+ ingredientAmount :Measure
«codeList»
DoseUnit
+ minimumDose :Measure
+ maximumDose :Measure
«codeList»
FormOfTreatmentValue
+ manual
+ applicationMachine
+ aerial
«featureType»
ManagementZone
+ code :Identifier
+ validFrom :DateTime [0..1]
+ notes :CharacterString
+ dateOfAnalysis :DateTime [0..*]
«featureType»
SoilType
+ soilType :CharacterString [1..*]
«featureType»
SoilTexture
+ soilTexture :SoilTextureType [1..*]
«featureType»
pH
+ pH :Measure [1..*]
«featureType»
OrganicMatter
+ organicMatter :Percent
«featureType»
ElectricConductivity
+ electricConductivity :Measure [1..*]
«featureType»
ZonePolygon
+ area :Measure
«dataType»
CropType
+ name :CharacterString
+ scientificName :CharacterString
+ seedingAdvice :CharacterString
+ harvestingAdvice :CharacterString
0..*
1..*
+contains
1..*
HoldingSites
1..*
0..*
+containsZone
0..*
+HoldingPlot
0..*
+containsPlot 1..*
HoldingPlots
0..*
0..1 0..1
0..*
0..*
+crop 0..*
Holding attribute Value
Identifier http://foodie-project.eu/CZ/MJM/Trsicka
Function agriculture
User identifier 47674814
Name Tršická zemědělská, a.s.
Valid From 1993-12-13
Begin Lifespan 2015-03-11

6
«featureType»
Agricultural and
Model::Holding
«featureType»
Site
+ code :Identifier
«voidable»
«dataType»
FarmAnimalSpecies
«voidable»
«featureType»
«voidable»
«featureType»
Plot
+ code :Identifier
«featureType»
Treatment
«dataType»
NutrientsType
+ N :Measure [0..1]
+ S :Measure [0..1]
+ B :Measure [0..1]
«codeList»
+ weed
+ pest
+ disease
«featureType»
CropSpecies
+ beginDate :Date
«featureType»
Product
«featureType»
SoilNutrients
«codeList»
ProductKindValue
+ organic
+ mineral
«dataType»
SoilTextureType
+ clay :Percent
+ silt :Percent
+ sand :Percent
«dataType»
ProductionType
«dataType»
+ property :Measure
«codeList»
OriginTypeValue
+ manual
+ system
«featureType»
Alert
+ code :Identifier
+ alertDate :Date
«featureType»
Intervention
«featureType»
TreatmentPlan
«featureType»
ProductPreparation
«dataType»
ActiveIngredients
«codeList»
DoseUnit
«codeList»
+ manual
+ aerial
«featureType»
ManagementZone
+ code :Identifier
«featureType»
SoilType
«featureType»
SoilTexture
«featureType»
pH
«featureType»
OrganicMatter
«featureType»
«featureType»
ZonePolygon
+ area :Measure
«dataType»
CropType
0..*
1..*
+contains
1..*
HoldingSites
1..*
0..*
+containsZone
0..*
+HoldingPlot
0..*
+containsPlot 1..*
HoldingPlots
0..*
0..1 0..1
0..*
0..*
+crop 0..*
Site attribute Value
Identifier http://foodie-project.eu/CZ/MJM/Trsicka
Activity (NACE
code)
A1.1.1 - Growing of cereals (except rice),
leguminous crops and oil seeds
Valid From 2014-03-15
Begin Lifespan 2015-04-07

7
«featureType»
Agricultural and
Model::Holding
«featureType»
Site
+ code :Identifier
«voidable»
«dataType»
FarmAnimalSpecies
«voidable»
«featureType»
«voidable»
«featureType»
Plot
+ code :Identifier
«featureType»
Treatment
«dataType»
NutrientsType
+ N :Measure [0..1]
+ S :Measure [0..1]
+ B :Measure [0..1]
«codeList»
+ weed
+ pest
+ disease
«featureType»
CropSpecies
+ beginDate :Date
«featureType»
Product
«featureType»
SoilNutrients
«codeList»
ProductKindValue
+ organic
+ mineral
«dataType»
SoilTextureType
+ clay :Percent
+ silt :Percent
+ sand :Percent
«dataType»
ProductionType
«dataType»
+ property :Measure
«codeList»
OriginTypeValue
+ manual
+ system
«featureType»
Alert
+ code :Identifier
+ alertDate :Date
«featureType»
Intervention
«featureType»
TreatmentPlan
«featureType»
ProductPreparation
«dataType»
ActiveIngredients
«codeList»
DoseUnit
«codeList»
+ manual
+ aerial
«featureType»
ManagementZone
+ code :Identifier
«featureType»
SoilType
«featureType»
SoilTexture
«featureType»
pH
«featureType»
OrganicMatter
«featureType»
«featureType»
ZonePolygon
+ area :Measure
«dataType»
CropType
0..*
1..*
+contains
1..*
HoldingSites
1..*
0..*
+containsZone
0..*
+HoldingPlot
0..*
+containsPlot 1..*
HoldingPlots
0..*
0..1 0..1
0..*
0..*
+crop 0..*
Plot attribute Value
Identifier http://foodie-
project.eu/CZ/MJM/Trsicka/Plot/001
Valid from 2015-04-09
Origin type manual
Crop species wheat
… …

8
«featureType»
Agricultural and
Model::Holding
«featureType»
Site
+ code :Identifier
«voidable»
«dataType»
FarmAnimalSpecies
«voidable»
«featureType»
«voidable»
«featureType»
Plot
+ code :Identifier
«featureType»
Treatment
«dataType»
NutrientsType
+ N :Measure [0..1]
+ S :Measure [0..1]
+ B :Measure [0..1]
«codeList»
+ weed
+ pest
+ disease
«featureType»
CropSpecies
+ beginDate :Date
«featureType»
Product
«featureType»
SoilNutrients
«codeList»
ProductKindValue
+ organic
+ mineral
«dataType»
SoilTextureType
+ clay :Percent
+ silt :Percent
+ sand :Percent
«dataType»
ProductionType
«dataType»
+ property :Measure
«codeList»
OriginTypeValue
+ manual
+ system
«featureType»
Alert
+ code :Identifier
+ alertDate :Date
«featureType»
Intervention
«featureType»
TreatmentPlan
«featureType»
ProductPreparation
«dataType»
ActiveIngredients
«codeList»
DoseUnit
«codeList»
+ manual
+ aerial
«featureType»
ManagementZone
+ code :Identifier
«featureType»
SoilType
«featureType»
SoilTexture
«featureType»
pH
«featureType»
OrganicMatter
«featureType»
«featureType»
ZonePolygon
+ area :Measure
«dataType»
CropType
0..*
1..*
+contains
1..*
HoldingSites
1..*
0..*
+containsZone
0..*
+HoldingPlot
0..*
+containsPlot 1..*
HoldingPlots
0..*
0..1 0..1
0..*
0..*
+crop 0..*
Intervention attribute Value
Type tillage
Status ongoing
Intervention start 2015-04-22
Supervisor John First, senior manager, phone 7435
… …

9
«featureType»
Agricultural and
Model::Holding
«featureType»
Site
+ code :Identifier
«voidable»
«dataType»
FarmAnimalSpecies
«voidable»
«featureType»
«voidable»
«featureType»
Plot
+ code :Identifier
«featureType»
Treatment
«dataType»
NutrientsType
+ N :Measure [0..1]
+ S :Measure [0..1]
+ B :Measure [0..1]
«codeList»
+ weed
+ pest
+ disease
«featureType»
CropSpecies
+ beginDate :Date
«featureType»
Product
«featureType»
SoilNutrients
«codeList»
ProductKindValue
+ organic
+ mineral
«dataType»
SoilTextureType
+ clay :Percent
+ silt :Percent
+ sand :Percent
«dataType»
ProductionType
«dataType»
+ property :Measure
«codeList»
OriginTypeValue
+ manual
+ system
«featureType»
Alert
+ code :Identifier
+ alertDate :Date
«featureType»
Intervention
«featureType»
TreatmentPlan
«featureType»
ProductPreparation
«dataType»
ActiveIngredients
«codeList»
DoseUnit
«codeList»
+ manual
+ aerial
«featureType»
ManagementZone
+ code :Identifier
«featureType»
SoilType
«featureType»
SoilTexture
«featureType»
pH
«featureType»
OrganicMatter
«featureType»
«featureType»
ZonePolygon
+ area :Measure
«dataType»
CropType
0..*
1..*
+contains
1..*
HoldingSites
1..*
0..*
+containsZone
0..*
+HoldingPlot
0..*
+containsPlot 1..*
HoldingPlots
0..*
0..1 0..1
0..*
0..*
+crop 0..*
Treatment attribute Value
Intervention type herbicide application
Status ongoing
Dosing 240 litres
Application width 25 meters
Form of treatment Application machine
Product Roundup®
… …

10
«featureType»
Agricultural and
Model::Holding
«featureType»
Site
+ code :Identifier
«voidable»
«dataType»
FarmAnimalSpecies
«voidable»
«featureType»
«voidable»
«featureType»
Plot
+ code :Identifier
«featureType»
Treatment
«dataType»
NutrientsType
+ N :Measure [0..1]
+ S :Measure [0..1]
+ B :Measure [0..1]
«codeList»
+ weed
+ pest
+ disease
«featureType»
CropSpecies
+ beginDate :Date
«featureType»
Product
«featureType»
SoilNutrients
«codeList»
ProductKindValue
+ organic
+ mineral
«dataType»
SoilTextureType
+ clay :Percent
+ silt :Percent
+ sand :Percent
«dataType»
ProductionType
«dataType»
+ property :Measure
«codeList»
OriginTypeValue
+ manual
+ system
«featureType»
Alert
+ code :Identifier
+ alertDate :Date
«featureType»
Intervention
«featureType»
TreatmentPlan
«featureType»
ProductPreparation
«dataType»
ActiveIngredients
«codeList»
DoseUnit
«codeList»
+ manual
+ aerial
«featureType»
ManagementZone
+ code :Identifier
«featureType»
SoilType
«featureType»
SoilTexture
«featureType»
pH
«featureType»
OrganicMatter
«featureType»
«featureType»
ZonePolygon
+ area :Measure
«dataType»
CropType
0..*
1..*
+contains
1..*
HoldingSites
1..*
0..*
+containsZone
0..*
+HoldingPlot
0..*
+containsPlot 1..*
HoldingPlots
0..*
0..1 0..1
0..*
0..*
+crop 0..*
Treatment attribute Value
Intervention type herbicide application
Status ongoing
Dosing 240 litres
Application width 25 meters
Form of treatment Application machine
Product Roundup®
… …
Product attribute Value
Product code 01475200
Product name Roundup®
Product type herbicide
Manufacturer MONSANTO®
Register URL http://agro-register.cz/?1475
Safety instructions Eye contact: may cause may cause pain,
redness and tearing based on toxicity
studies.
…

11
«featureType»
Agricultural and
Model::Holding
«featureType»
Site
+ code :Identifier
«voidable»
«dataType»
FarmAnimalSpecies
«voidable»
«featureType»
«voidable»
«featureType»
Plot
+ code :Identifier
«featureType»
Treatment
«dataType»
NutrientsType
+ N :Measure [0..1]
+ S :Measure [0..1]
+ B :Measure [0..1]
«codeList»
+ weed
+ pest
+ disease
«featureType»
CropSpecies
+ beginDate :Date
«featureType»
Product
«featureType»
SoilNutrients
«codeList»
ProductKindValue
+ organic
+ mineral
«dataType»
SoilTextureType
+ clay :Percent
+ silt :Percent
+ sand :Percent
«dataType»
ProductionType
«dataType»
+ property :Measure
«codeList»
OriginTypeValue
+ manual
+ system
«featureType»
Alert
+ code :Identifier
+ alertDate :Date
«featureType»
Intervention
«featureType»
TreatmentPlan
«featureType»
ProductPreparation
«dataType»
ActiveIngredients
«codeList»
DoseUnit
«codeList»
+ manual
+ aerial
«featureType»
ManagementZone
+ code :Identifier
«featureType»
SoilType
«featureType»
SoilTexture
«featureType»
pH
«featureType»
OrganicMatter
«featureType»
«featureType»
ZonePolygon
+ area :Measure
«dataType»
CropType
0..*
1..*
+contains
1..*
HoldingSites
1..*
0..*
+containsZone
0..*
+HoldingPlot
0..*
+containsPlot 1..*
HoldingPlots
0..*
0..1 0..1
0..*
0..*
+crop 0..*

12
Linked data publication process overview
• Simple set of principles & technologies
• URI, HTTP, RDF, SPARQL
• Involves a set of tasks
Datasets identification
Model specification
RDF data generation
Linking
Hyland et al.
Hausenblas et al.
Villazón-Terrazas et al.
Reference Linked data publication pipelines
Exploiting

13
Linked data publication technologies overview
• Used technologies:
• D2RQ for transforming Relational Databases as
Virtual RDF Graphs
• RDF for the representation of data
• Farming ontology providing the underlying
vocabulary and relations
• Virtuoso for storing the semantic datasets
• Silk for discovery of links
• Sparql for querying semantic data
• Hslayers NG for visualisation of data
• Metaphactory for visualisation of data
D2RQ

14
Ontology for farming data - overview
• ShapeChange output
• UML featureTypes and dataTypes modelled as classes, and
their attributes as datatype or object properties
• UML codeLists modelled as classes/concepts, and their
attributes as concept members
• Cardinalities restrictions defined on properties (exactly,
min, max)
• DataType properties ranges defined according to
model/mappings
• Object properties ranges defined according to
model/mappings
• Object properties inverseOf defined
Top hierarchy
FeatureType hierarchy
Codelist hierarchy
Datatype hierarchy

15
Ontology for farming data – main classes overview
• For the purposes of FOODIE, we found the lack of a feature on a more
detailed level than Site that is already part of the INSPIRE AF data model.
• Main concept: Plot
• Represents a continuous area of agricultural
land with one type of crop species, cultivated
by one user in one farming mode
• Two kinds of data associated:
• metadata information
• agro-related information
 Next concept: Management Zone
• Enables a more precise description of the land
characteristics in fine-grained area
foodie:Plot
INSPIRE-AF:Site
foodie:Alert Foodie:InterventionFoodie:CropSpecies
Foodie:ManagementZone
containsPlot
containsManagementZone
interventionPlotspeciesPlot
alertPlot
plotAlert
Foodie:ProductionType
production
Foodie:SoilNutrients
zoneNutrients

16
Ontology for farming data – main classes overview
• The Intervention is the basic feature type for any kind of (farming)
application with explicitly defined geometry, e.g., tillage or pruning.
• Has multiple indirect associations with different concepts
Foodie:Intervention
Foodie:Treatment
Foodie:TreatmentPlan
Foodie:Product Foodie:ProductPreparation
Foodie:ActiveIngredients
is-a
plan
productPlan
planProduct
preparationProduct preparation
productTreatment
treatmentProduct
preparationPlan
ingredientProduct
Foodie:FormOfT
reatmentValue
Foodie:Treatme
ntPurposeValue
formOfTreatmenttreatmentPurpose

17
RDF data generation
• D2RQ requires a mapping file (in RDF)
specifying how to map the content of a
relational database to RDF
https://github.com/FOODIE-cloud/ontology/tree/master/mappings

18
Exploiting the Linked Data - querying
• Sparql endpoint: https://www.foodie-cloud.org/sparql

19
Exploiting the Linked Data – search & navigate
• Faceted search endpoint: https://www.foodie-cloud.org/fct

20
Example of satellite processed data yield potential
• http://foodie.lesprojekt.cz/vynosy_2017/

21
Example of satellite processed data yield potential
• http://foodie.lesprojekt.cz/vynosy_2017/

22
Exploiting the Linked Data – visualisation
• Map visualisation: http://ng.hslayers.org/examples/databio/

23
Exploiting the Linked Data – visualization (video demo)
• Map visualisation: http://ng.hslayers.org/examples/databio/

24
Hackathon tasks
• Basic steps, which we would like implement
• Find farm/field boundaries on client side (QGIS)
• Display selected data from farm/field
• Query server with satellite data for data from farm/field
• Display selected satellite data for farm/field on QGIS

25
Hackathon tasks
• Farmer data or field data (it could be eventually single field)

26
Hackathon tasks
• Processed data on hub (data could be stored as processed or process can be
calculate on demand)

27
Hackathon tasks
• What farmer need

28
Hackathon tasks
• Tasks
• How could be queried server from client side (if we are using defined
processing, probably we can use the same query for both stored or
processed data)
• we need define, how will look API for querying
• we need define data model for transfering data for single fields
• How will be send back result
• in case of vectorised data, probably will be necessary to define only format and
model
• in case of raster data?

29
Thank you for your attention!
Contact details: charvat@lesprojekt.cz
www.databio.eu

Foodie Ontology and Satellite API

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