AgroPortal 1.2 (beta) Released - an Ontology Portal for Agronomy

The AgroPortal team is pleased to announce the 1.2 release of the AgroPortal: http://agroportal.lirmm.fr/

AgroPortal is an ontology repository dedicated to the agronomy. The platform reuses the NCBO BioPortal infrastructure and customizes it. As of today, it includes 56 ontologies (4 private ones) about multiple aspect of agricultural data: technologies, breeding, food, plant phenotypes and traits, anatomy, etc. Those ontologies have been uploaded in collaboration with several driving use cases including: INRA’s vocabularies, the Crop Ontology project, the AgroLD project, the RDA Wheat Data Interoperability WG and more recently the FAO VEST Registry.

Among the new content of this release the AgroPortal team includes:

  • 18 new ontologies
  • New categories for ontologies
  • The AgroPortal team has enabled specific “slice of AgroPortal” for each group of ontologies: crop, lovinra, agrold, wheat e.g.,
  • http://wheat.agroportal.lirmm.fr/ allows to see/use only the ontologies selected by the RDA Wheat Data Interoperability WG;
  • http://crop.agroportal.lirmm.fr/ allows to see/use only the ontologies developed within the Crop Ontology project.

Among the new feature of this release (and 2.1) the AgroPortal team includes:

  • The AgroPortal team has enabled the storing of:
  • Interportal mappings: between an ontology within AgroPortal and an ontology in another portal appliance (typically the NCBO BioPortal itself).
  • External mappings: between an ontology within AgroPortal and any other  ontology/vocabulary  for which URIs are available.

For instance: http://agroportal.lirmm.fr/ontologies/CO_715?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCO_715_0000165#mappings

  • Multiple relation mappings i.e., the possibility to tag a mapping with multiple semantic web properties such as skos:exactMatch, gold:translation, etc.
  • Annotations scoring. Annotations returned by the AgroPortal Annotator are now scored based (mainly) on frequencies. See [PDF] for details.
  • Annotation RDF outputs using the Annotation Ontology. See [PDF] for details.
  • A new model for ontology metadata. The AgroPortal team has reviewed 350 properties from the most standard and relevant vocabularies out-there (21 totals) to describe metadata for ontologies (such as Dublin Core, OMV, DCAT, VOID, etc.) and selected 124 properties implemented in AgroPortal. Now, when an ontology is uploaded, metadata is directly extracted from the original file and used to populate the model. The current metadata appears on each ontology page e.g., http://agroportal.lirmm.fr/ontologies/BIOREFINERY. The AgroPortal team is currently working on adding metadata to current ontologies and new visualization inside the portal. This work is still in progress if interested contact the AgroPortal team.

In addition, the AgroPortal team is pleased to announce the released of the VEST/AgroPortal unique map of standards, as the result of our collaboration with FAO within GODAN Action: http://vest.agrisemantics.org/

Every ontologies hosted in AgroPortal will automatically be included into the unique map.

AgroPortal is the result of a collaboration between: LIRMM, INRA, IRD, Bioversity International, CIRAD, FAO and the NCBO.  The project acknowledge the support of: French ANR (grant ANR-12-JS02-01001), Univ. of Montpellier, CNRS, IBC of Montpellier (grant ANR-11-BINF-0002), the NUMEV Labex (grant ANR-10-LABX-20), the EU H2020 Marie Skłodowska-Curie program (grant 701771).

Please, refer to the project with:

Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé-Yeumo, Vincent Emonet, John Graybeal, Mark A. Musen, Cyril Pommier & Pierre Larmande. Reusing the NCBO BioPortal technology for agronomy to build AgroPortal, In 7th International Conference on Biomedical Ontologies, ICBO'16, Demo Session. Corvallis, Oregon, USA, August 2016. (D203), pp. 3.

Please try out or contact the AgroPortal team at agroportal-support@lirmm.fr

AgroPortal release notes: https://github.com/agroportal/documentation/wiki/Release-notes

Information: AgroPortal was presented last week at the GODAN Summit in New York City: http://summit.godan.info/   

 


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