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eROSA Stakeholder WS1: AgroPortal: a vocabulary and ontology repository for agronomy, plant sciences, biodiversity and nutrition
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
3AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
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)
4AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
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
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
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).
12AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
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
15AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
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
16AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
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…
18AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017