Presentation by Clément Jonquet delivered at the 1st eROSA Stakeholder Workshop in Montpellier, 6/7/2017

1. AgroPortal
a vocabulary and ontology
repository for agronomy, plant
sciences, biodiversity and nutrition
Clément Jonquet
jonquet@lirmm.fr
eRosa stakeholder workshop
Montpellier, July 6th 2017
http://agroportal
.lirmm.fr

2. Working with vocabularies & ontologies
– a portal please!
• You’ve built an ontology, how do you let the world know?
• You need an ontology, where do you go to get it?
• How do you know whether an ontology is any good?
• How do you find data that are relevant to the domain of the
ontology (or to specific terms)?
• How could you use ontologies without managing them ?
2AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017

3. Objectives of AgroPortal project
• Develop and support a reference ontology repository for agronomy
• Primary focus on agronomy
• One-stop-shop for agronomical ontologies & services
• Reusing the NCBO BioPortal technology
• Avoid to re-implement what has been done, facilitate interoperability
• Reusing the scientific outcomes, experience & methods of biomedicine
• Enable cross domain interaction
• Enable straightforward use of agronomical ontologies
• Respect the requirements of the agronomic community
• Fully semantic web compliant infrastructure
• Focus on new enabled science
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4. 5 Driving Agronomic Use Cases
➢ IBC Rice Genomics & AgroLD project
➢ Data integration and knowledge management related to rice (P. Larmande)
➢ RDA Wheat Data Interoperability working group
➢ Common framework for publishing wheat data (E. Dzalé-Yeumo)
➢ LovInra : INRA Linked Open Vocabularies
➢ Vocabularies produced by INRA scientists (S. Aubin)
➢ Crop Ontology project
➢ Ontologies for describing crop germplasm & traits (E. Arnaud)
➢ GODAN global map of agri-food data standards
➢ VEST/AgroPortal MAP of standards (V. Pesce)
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5. AgroPortal: a
vocabulary and
ontology repository
for agronomy, plant sciences,
biodiversity and nutrition
Publish, search,
download
Browse,
visualize
Peer review
Versioning
Annotation
Recommendati
on
Mapping
Notes
Projects
64 ontologies, 95 candidates
5 driving use cases
~60 registered users
http://agroportal.
lirmm.fr
5

6. Describe ontologies with
semantic metadata
Display “per ontology”
Ontology specific properties => viewable and editable
within the ontology specific page
Display “per property”
Global presentation of the properties
Synthesis diagrams & listing
6

7. Examples of
ontologies
uploaded in
AgroPortal
Title Format Groups Size
IBP Rice Trait Ontology (CO_320) OWL CROP, RICE ~2K
IBP Wheat Trait Ontology (CO_321) OWL CROP, WHEAT ~1K
IBP Wheat Anatomy Ontology (CO_121) OBO CROP, WHEAT ~80
IBP Crop Research (CO_715) OBO CROP ~250
Multi-Crop Passport Ontology (CO_020) OBO CROP ~90
Biorefinery (BIOREFINERY) OWL LOVINRA ~300
Matter Transfer (TRANSMAT) OWL LOVINRA ~1.1K
Plant Ontology (PO) OWL WHEAT, RICE, OBOF ~2K
Plant Trait Ontology (TO) OWL WHEAT, RICE, OBOF ~4.4K
Durum Wheat (DURUM_WHEAT) OWL LOVINRA ~130
Agricultural Experiments (AEO) OWL LOVINRA ~60
Environment Ontology (ENVO) OWL WHEAT, OBOF ~6.3K
NCBI Organismal Classification (NCBITAXON) RRF WHEAT ~900K
AnaEE Thesaurus (ANAEE) SKOS LOVINRA ~3.3K
French Crop Usage (CROPUSAGE) SKOS none ~300
Agrovoc (AGROVOC) SKOS none ~32K
Food Ontology (FOODON) OWL OBOF ~10K
National Agriculture Library Thesaurus (NALT) SKOS none ~67K
Global Agricultural Concept Scheme (GACS) SKOS none ~585K
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8. Ontology groups
and categories
8
Category Number
Plant Phenotypes and Traits 18
Plant Anatomy and Development 3
Natural Resources, Earth and Environment 2
Animal Science and Animal Products 6
Agricultural Research, Technology and Engineering 9
Breeding and Genetic Improvement 1
Plant Science and Plant Products 4
Plant Genetic Resources 2
Food and Human Nutrition 4
Taxonomic Classifications of Organisms 2
Farms and Farming Systems 3
Specific slices display to use only the
ontologies of a group
http://inra.agroportal.lirmm.fr/
AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017

9. Align ontologies one
another
concept
by
concept
9

10. AgroPortal
Annotator
identifies ontology
concepts within plain
text for semantic
indexing
10

11. AgroPortal Recommender
get the most relevant ontologies
for your data 11

12. AgroPortal landscape page
Display “per property”
• Global presentation of the properties
• Synthesis diagrams & listing
• Allows to explore the agronomical ontology
landscape by automatically aggregating the
metadata fields of each ontologies in explicit
vizualizations (charts, term cloud and graphs).
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13. REST API
http://data.agroportal.lirmm.fr/documentation
SPARQL endpoint
http://sparql.agroportal.lirmm.fr/test
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14. Long term vision…
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15. 2017-2019
• Maintain the current prototype as a “community builder”
• Harvest, harvest, harvest…. Share, share, share… demonstrate
• Ontologies, Mappings, Metadata
• Harmonize (metadata) with Map of Standards, BioSharing
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16. 2020-2025
• EOSC Services vision
• Harmonization of the vocabularies and ontologies
• Reuse
• Semantic richness (not just thesaurus)
• Endorsement of GACS as a pivot vocabulary
• Thesaurus (the terms)
• Upper level ontologies (high level semantics)
• Connected to domain specific ontologies
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17. 2020-2025 (following)
• Help the community to adopt semantic Web / W3C standards to
describe their standards
• No more PDF standard descriptions
• Data, data, data…. annotations, data-lifting, etc.
AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017 17

18. 2027
• Production mode for GACS releases (new terms, concept, mappings
added with clear procedures, curation, validation, endorsement)
• Alike the UMLS releases
• Second used of data enabled by semantic interoperability, data
mining and AI
• Knowledge, knowledge, knowledge…
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19. AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017 19

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Where is
agriculture? NCBO BioPortal
data as of 2013