ontology-based services and knowledge management in the agricultural domain, by pierre larmande
TRANSCRIPT
Ontology-‐based services and knowledge management in the
Agronomic Domain
Pierre Larmande Ins-tute of Research for Development (IRD)
Head of data integra-on group at the Ins-tute of Computa-onal Biology [email protected]
Outline
• Data integration challenges in the Life Sciences
• Ontologies/ Semantic Web Technologies
• AgroPortal a proposition for ontology-based services in the agronomic domain
• Agronomic Linked Data project
Data landscape in the Life Sciences
• The availability of biological data has increased
• Advancements in:• computational biology• genome sequencing• high-throughput technologies
• Integrative approaches are necessary to understand the functioning of biological systems
• Lack of effective approaches to integrate data that has created a gap between data and knowledge
• Need for an effective method to bridge gap between data and underlying meaning
• Harvest the power of overlaying different data sets
Data integration challenges
Semantic Web Technology
• An extension of the current Web technologies.
• Enables navigation and meaningful use of digital resources.
• Support aggregation and integration of information from diverse sources.
• Based on common and standard formats.
Resource Description Framework (RDF)
• Framework for representing information about resources on the Web
• Provides a labeled connection between two resources
• Uses Unique Resource Identifiers (URI)
• Statements take the form of triples:
Subject Predicate Object
<Gene_A> <codes_for> <Protein_A>
RDF Triple
• Combining the triples results in a directed, labeled graph.
<Gene_A>
<Protein_A> <has_funcFon>
<BP_A>
<MF_A>
<Gene_X>
<regulates>
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AgroPortal a proposi(on for ontology-‐based services in the agronomic domain
Clément Jonquet, Esther Dzalé-‐Yeumo, Elizabeth Arnaud, Pierre Larmande
ObjecFves of AgroPortal project
• Develop and support a reference ontology repository for the agronomic domain – One-‐stop-‐shop for plant/agronomic related ontologies – Primary focus on the agronomic & plant domain
• Reusing the NCBO BioPortal technology – Avoid to re-‐implement what has been done – Facilitate interoperability – Reusing the scien-fic outcomes, experience & methods
of the biomedical domain
• Enable straighUorward use of agronomic related ontologies – Respect the requirements of the agronomic community – Fully seman-c web compliant infrastructure
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Available ontologies
• Already 29 ontologies… and we expect around 40 soon. – (half are not included in the NCBO BioPortal)
• Ontologies are organized in Groups and Categories
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REST Web Service API: hhp://data.agroportal.lirmm.fr/documenta-on
Atelier InOvive 2015 – Rennes – 29 juin 2015 19
4 Driving Agronomic Use Cases • IBC Rice Genomics
– data integra-on and knowledge management related to rice
• RDA Wheat Data Interoperability working group
– common framework for describing, represen-ng, linking and publishing wheat data with respect to open standards
• INRA Linked Open Vocabularies, LovInra – publish vocabularies produced or co-‐produced by
INRA scien-sts and foster their reuse beyond the original researchers
• The Crop Ontology project – publishes ontologies required for describing crop
germplasm, traits and evalua-on trials.
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Each use case has a specific group in AgroPortal
• Feature to come: slices – Specific “entry” in the AgroPortal
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AgroLD The Agronomic Linked
Data project
Aravind Venkatensan, Gildas Tagny,
Nordine El Hassouni, Manuel Ruiz,
Pierre Larmande
Agronomic Linked Data (AgroLD)
• Semantic web based system that integrates data from South Green Bioinformatics node
• Aim:
• Capability to answer complex real life questions
• Efficient information integration / retrieval.
• Easy extensibility.
• Aid in holistic understanding of domain
AgroLD
• AgroLD will be developed in phases –
• Website: www.agrold.org
• Phase I: includes data on:• Rice (Oryza spp).
• Oryza barthi• Oryza brachyantha• Oryza Sativa• Oryza glaberimma
• Arabidopsis thaliana• Sorghum (Sorghum bicolor)• Maize/Corn (Zea mays)• Wheat
• Triticum astivum• Triticum urartu
Acknowledgements
Elizabeth Arnaud, Leo Vale\e, Marie-‐Angelique Laporte, Julian Pietragalla
Manuel Ruiz,
Nordine El Hassouni
Aravind Venkatesan, Gildas Tagny
Esther Dzalé-‐Yeumo, Cyril Pommier
Patrick Valduriez
Clement Jonquet
Pierre Larmande
Contact: [email protected]