Elizabeth Arnaud MarieAngelique Laporte Caterina Caracciolo Tom Baker Ferdinando Valle What is CGIAR A n international organization that advances international agricultural research ID: 801303
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Slide1
AgroHackthonMontpellier 29 June
Elizabeth Arnaud
Marie-Angelique
Laporte
Caterina
Caracciolo
Tom Baker
Ferdinando
Valle
Slide2What is CGIAR ?
A
n
international organization that advances international agricultural research for food security.
Photo
CGIAR
15
Centers worldwide
40 years
of
research
Over
8,000
scientists, researchers, technicians, and staff
Slide3Crop Ontology
www.cropontology.org
Banana
Barley (
ICARDA, POLAPGEN
)
Cassava
Chickpea Common bean Cowpea Groundnut Lentil Maize Oat (Global Triticeae) Pearl millet Pigeon Pea Potato Soybean (IITA & USDA) Sweet Potato Rice Sorghum Vitis (INRA) Wheat Yam
Slide4Standard Variable
Method and scales are important
to capture for supporting data
comparison & interpretation
Ontologies provide sometimes brief
information on Methods but as a text in the attribute
information
A Variable is combination of
Property
(Trait) + Method + Scales/unitsIt annotates the actual value of the measurement Has a unique name -> Proposed naming convention: P_M_STrait = Entity+ Quality(Root) (Length) Average root length expressed in cm Average root length scored on a 3 level scale :1=short (<50cm)2= medium (50-100cm)3=long (>100cm)
Slide5Development of the Agronomy Ontology (
AgrO
)
Socio-
Economy
Trial Information
Person
Experimental design
Site
informations
Institute informations Agricultural operationsLand preparation SeedingFertilizerIrrigationPest controlHarvestAgricultural equipmentMonitored dataCrop OntologyGermplasmBiotic factorsAbiotic factors SoilRainfallLightTemperature Humidity AtmospherePest Ontology
Agronomy Ontology
Slide6Annotation tool
Slide7Mapping based on EQ statements
CO_321:0000056
Spike Length
TO:0000271
Inflorescence Length
?
PO:0009049
Inflorescence
Synonym
: spike
CO_321:0000056Spike LengthTO:0000271Inflorescence LengthPO:0009049InflorescenceSynonym: spike PATO:0000122LengthEntity QualityInferencePATO:0000122LengthEntity Qualityequivalent
Slide8Planteome web site
Rice
Cassava
Enabling retrieving annotations
done with CO
Slide9Some Agrisemantics group members proposition
Annotator
Improve Annotator so user can upload other type of files than text: tabular files
Store a missing concept for submissionLook at the Annotation tool on Crop Ontology web siteDiscovery of other vocabularies
Mappings Add more finer ways of mapping terms than just string exact matchTest publishing results of
Planteome mapping on EQ statements?
Slide10CIMMYT Dataverse
Slide11Adding Keywords on Dataverse
Data set sur
dataverse
=URI derriere chaque ;ots cles Agroportal
fournit les termes dans divers formats - OWL Interface utilisateurs
pour decouvrir les termesIl suffirait de prendre la traduction automatique d’une onto en OWL en
SKOS et la placer sur SKOSMOS et offrir dans le Browser pour annotation – savoir si la perte de semantique, specification
formelle est importante ou non pour ce type d’utilisation Hypothese : cette perte dans la traduction n’est pas
impactante
pour l’utilisation
décriteOffrir des mots clés Decouverte des concepts