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AgroPortal : a vocabulary and ontology repository for agronomy, plant sciences, biodiversity and nutrition

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Presentation to the SemanDiv working group in Montpellier, July 11th 2017. Similar presentation at IN-OVIVE 2017 and EFITA 2017 in June.

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AgroPortal : a vocabulary and ontology repository for agronomy, plant sciences, biodiversity and nutrition

  1. 1. AgroPortal a vocabulary and ontology repository for agronomy, plant sciences, biodiversity and nutrition Clément Jonquet, Anne Toulet jonquet@lirmm.fr SemanDiv Montpellier, July 11th 2017 http://agroportal.lirmm.fr
  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 AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017
  3. 3. 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
  4. 4. 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 ? AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017
  5. 5. 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 AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017
  6. 6. Two years ago • Mid 2014, we started the AgroPortal project with the vision of offering a vocabulary & ontology repository for agronomy and related domains such as biodiversity, plant sciences and nutrition • The prototype found a good adoption and growing interest • Advanced prototype platform • v1.4 was released in June 2017 • Hosts 64 public ontologies or vocabularies including 38 not present in any such ontology repository • We have identified around 90 candidates (still some work to do!) AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017
  7. 7. 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 AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017
  8. 8. 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) AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017
  9. 9. 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 AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017 Potential interest for biodiversity: ENVO PATO ANAEE TO PO … soon BCO TDWG TAXREF TOP …
  10. 10. Ontology groups and categories AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017 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/
  11. 11. AgroPortal: an ontology repository for agronomy Publish, search, download Browse, visualize Peer review Versioning Annotation Recommendation Mapping Notes Projects AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017 64 ontologies, 95 candidates 5 driving use cases ~60 registered users http://agroportal. lirmm.fr
  12. 12. Browse and select ontologies • Allows to search, order and select ontologies using a facetted search approach, based on the metadata • 4 additional ways to filter ontologies in the list • 2 new options to sort this list (name, released date). AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017
  13. 13. Align ontologies one another AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017 concept by concept
  14. 14. AgroPortal Annotator identifies ontology concepts within plain text for semantic indexing
  15. 15. AgroPortal Recommender get the most relevant ontologies for your data
  16. 16. 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). AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017
  17. 17. Structural information about ontologies AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017
  18. 18. Information about the community AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017
  19. 19. Information about the ontology network AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017
  20. 20. Future ontologies on the list AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017 Title Organization CAB Thesaurus CABI Wine Ontology INRA Oat, Barley, Brachiaria, Potato (etc.) trait ontologies Crop Ontology Agronomy Ontology CGIAR Agriculture Activity Ontology CAVOC IC-FOODS Ontologies (12) UC Davis agINFRA Soil Vocabulary FAO, GFAR Plant-Pathogen Interactions Ontology CBGP Biological Collections Ontology OBO Foundry Plant Phenology Ontology OBO Foundry Thesaurus Of Plant characteristics CEFE
  21. 21. Postdoc LINGUA AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017
  22. 22. LINGUA 12-month postdoc (NUMEV) • One of the challenges when dealing with multiple ontologies is the overlap and mappings between these ontologies. Within the LINGUA project, we will address specifically this aspect by developing ontology mapping capabilities to align AgroPortal ontologies and define a lingua franca for the domain. We will make AgroPortal a state-of-the-art platform for mapping extraction, generation, validation, evaluation, storage and retrieval by adopting a complete semantic web and open linked data approach and engaging the community for curation. We will first focus on the research topics of the Montpellier community (agronomy, food, biodiversity) and second join the international Global Agricultural Concept Scheme (GACS) project (integration of Agrovoc, NALt & CABt) to integrate the 3 main vocabularies to help build the new concept scheme and align GACS to other vocabularies & ontologies in AgroPortal. AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017
  23. 23. AgroPortal mapping life cycle AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017 • align the ontologies within AgroPortal with one another and with the GACS • make YAM++/AgroPortal the reference platform to extract, generate, validate, evaluate, store and retrieve ontology alignments by developing a state-of-the-art ontology alignment framework
  24. 24. AgroPortal • A platform for ontology publication (≠edition or curation) • Need for the biodiversity community? • We expect it to become a reference platform • Reuse NCBO technology and focus on customization and new science Sign up and join us with your ontologies, feedback! http://agroportal.lirmm.fr
  25. 25. Conclusion • The first 2 years of the project have been very productive • Analysis of the portal content helps to figure out what are some of the main domain of interests as well as common development practices when creating an ontology in agronomy • Continue our metadata edition and curation effort to be sure to provide the community with the best descriptions for ontologies available • Converge with the Map of standards for food and agriculture effort (Godan Action) AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017

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