This is a presentation of the AgroPortal project.

1. AgroPortal
ontology repository for
agronomy
Clément Jonquet
jonquet@lirmm.fr
November 2016
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2. Clement Jonquet
Anne Toulet
Vincent Emonet
Pierre Larmande
Marie-Angélique Laporte
Elizabeth Arnaud
Valeria Pesce
Esther Dzalé-Yeumo
Sophie Aubin
and
Cyril Pommier (URGI)
Pascal Neveu (MISTEA)
Patrice Buche (DIADE)
Odile Hologne (DIST)
Mark Musen
John Graybeal
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3. Context
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4. Big
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Open
Linked

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6. Why ontologies?
Why an ontology repository?
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7. Biologist have adopted ontologies
• To provide canonical representation of scientific
knowledge
• To annotate experimental data to enable interpretation,
comparison, and discovery across databases
• To facilitate knowledge-based applications for
• Decision support
• Natural language-processing
• Data integration
But ontologies are: spread out, in
different formats, of different size,
with different structures
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8. 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 ?
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9. Why don’t have a portal like the NCBO
BioPortal for agronomy?
• The is definitively such a need in the
community
• We listed 120+ candidate vocabularies/
ontologies
• Maybe listed in OBO Foundry or not
• NCBO BioPortal is specific for health and biomedical ontologies
• Overlap exists
• Some ontologies are not really biomedical ones
• But many plant/agro related ontologies are not covered
• NCBO technology is domain-independent and open source
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10. 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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11. An ontology repository… who’s
gonna use it?
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12. 5 Driving Agronomic Use Cases
• IBC Rice Genomics & AgroLD project
• data integration and knowledge management related to rice
• RDF data integrated from a variety of plant resources and ontologies
• Pierre Larmande
• RDA Wheat Data Interoperability working group
• common framework for describing, representing, linking and publishing wheat data with
respect to open standards
• Esther Dzalé-Yeumo
• INRA Linked Open Vocabularies, LovInra
• publish vocabularies produced or co-produced by INRA scientists and foster their reuse
beyond the original researchers
• Esther Dzalé-Yeumo & Sophie Aubin
• Crop Ontology project
• publishes ontologies required for describing crop germplasm, traits and evaluation trials
• Elizabeth Arnaud & Marie-Angélique Laporte
• GODAN global map of agri-food data standards
• http://vest.agrisemantics.org
• Valeria Pesce
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13. Other projects interested
• FAO Agricultural Information Management Standards (http://aims.fao.org)
• GACS project (merge CABt, NALt and Agrovoc)
• Research Data Alliance (https://rd-alliance.org)
• New AgriSemantics group
• New Rice Data Interoperability WG
• Planteome (www.planteome.org)
• Development and enrichment of new and existing reference ontologies for plants
• Data annotation, mapping to reference ontologies
• Elixir (www.elixir-europe.org)
• US and EU cyberinfrastructure for life science and plants
• IFB platforms (www.france-bioinformatique.fr)
• (SouthGreen, URGI, PlantNode, etc.)
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14. How does it looks?
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15. http://agroportal.lirmm.fr
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17. Ontologies already included
• Already 55 ontologies…
• 33 are not included in the NCBO BioPortal
• 2 privates
• 77 other candidates ontologies
• Ontologies are organized
in Groups and Categories
• Specific slices display/use only the
ontologies of a group
• http://inra.agroportal.lirmm.fr/
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21. Community based
functionalities
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22. REST Web Service API:
http://data.agroportal.lirmm.fr/documentation
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SPARQL endpoint:
http://sparql.agroportal.lirmm.fr

23. New features (already included)
• New groups & categories
• New mappings management (enable interportal & external
mappings)
• New scoring methods for the AgroPortal Annotator
• Working to support specific ontology format (SKOS, trait dictionary)
• New metadata model & automatic parsing of 300+ properties from
common semantic web languages
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24. Conclusion
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25. AgroPortal
• A platform for ontology publication (≠edition or curation)
• We expect it to become a reference platform
• Reuse NCBO technology and focus on customization and new science
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Sign up and join us with your ontologies, feedback!
http://agroportal.lirmm.fr