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Presentation AgroPortal

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This is a presentation of the AgroPortal project.

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Presentation AgroPortal

  1. 1. AgroPortal ontology repository for agronomy Clément Jonquet jonquet@lirmm.fr November 2016 1
  2. 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 2
  3. 3. Context 3
  4. 4. Big 4 Open Linked
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  6. 6. Why ontologies? Why an ontology repository? 6
  7. 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 7
  8. 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 ? 8
  9. 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 9
  10. 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 10
  11. 11. An ontology repository… who’s gonna use it? 11
  12. 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 12
  13. 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.) 13
  14. 14. How does it looks? 14
  15. 15. http://agroportal.lirmm.fr 15
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  17. 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/ 17
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  21. 21. Community based functionalities 21
  22. 22. REST Web Service API: http://data.agroportal.lirmm.fr/documentation 22 SPARQL endpoint: http://sparql.agroportal.lirmm.fr
  23. 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 23
  24. 24. Conclusion 24
  25. 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 25 Sign up and join us with your ontologies, feedback! http://agroportal.lirmm.fr

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