AgroPortal 1.0 beta released - a portal for ontology in agronomy and plant sciences

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AgroPortal 1.0 beta released - a portal for ontology in agronomy and plant sciences

Clement Jonquet-2

We are pleased to publicly announce the first release of the AgroPortal: http://agroportal.lirmm.fr/

This is still a beta, but this is 1.0!

 

AgroPortal is an ontology repository dedicated to the agronomic and plant domains. The platform reuses the NCBO BioPortal infrastructure and customizes it. As of today, it includes 38 ontologies which come mainly from external users, NCBO BioPortal, or driving agronomic use-cases including :

·         IBC Rice Genomics & AgroLD project: rice data integration & linked RDF data from a variety of plant resources and ontologies (contact: P. Larmande)

·         RDA Wheat Data Interoperability working group: a common framework for describing, representing, linking and publishing wheat data with respect to open standards (contact: E. Dzalé-Yeumo)

·         INRA Linked Open Vocabularies: vocabularies produced or co-produced by INRA scientists (contacts: E. Dzalé-Yeumo & P. Buche)

·         The Crop Ontology project: a set of ontologies developed to compile validated concepts/relations on anatomy, structure and phenotype of Crops. (contacts: E. Arnaud & M-A. Laporte)

 

As the original BioPortal the platform enables to:

·         Store ontology metadata

·         Search within ontologies

·         Store and retrieve mappings between ontologies

·         Visualize ontology content

·         Comment about ontologies, concepts and mappings

·         Annotate text data with ontology concepts

·         Get a recommendation about which ontology use for a text corpus or set of keywords

·         Store projects which use ontologies

·         And many other features!!

 

We are currently working on new features, that will be announced regularly.

 

The content of the platform is accessible via REST API and SPARQL endpoint:

http://data.agroportal.lirmm.fr/documentation

http://sparql.agroportal.lirmm.fr/test/

 

The  main objective of the AgroPortal project is to enable straightforward use of agronomic related ontologies, avoiding data managers and researchers the burden to deal with  complex  knowledge  engineering  issues. We want to offer a “one-stop-shop” for ontologies that will arise awareness, avoid duplicated efforts, and foster adoption of common practices. The AgroPortal  project  will specifically pay attention to respect the requirements of the agronomic/plant community. So your feedbacks are welcome!

 

AgroPortal is the result of a collaboration between: LIRMM, INRA, IRD, Bioversity International, CIRAD and of course the National Center for Biomedical Ontologies (NCBO) @ Stanford Univ.

The project acknowledge the support of: French ANR, Univ. of Montpellier, CNRS, IBC of Montpellier, NUMEV.

 

Please, refer to the project with:

Clement Jonquet, Esther Dzalé-Yeumo, Elizabeth Arnaud & Pierre Larmande. AgroPortal : a proposition for ontology-based services in the agronomic domain, In 3ème atelier INtégration de sources/masses de données hétérogènes et Ontologies, dans le domaine des sciences du VIVant et de l’Environnement, IN-OVIVE'15. Rennes, France, June 2015. pp. 5. [PDF]

 

Please try out or contact us at [hidden email]


Information: AgroPortal was presented at the PAG meeting in San Diego January 9th and 11th (poster).

 

The AgroPortal team.

 

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Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor

Coordinator of the SIFR and AgroPortal projects

Visiting faculty, Stanford University

 

[hidden email]

http://www.lirmm.fr/~jonquet

 

                University of Montpellier                          Tel:                   +33/4 67 14 97 43

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