Résumé
The AgroLD Knowledge Graph is a semantic framework designed to integrate and explore data relevant to plant sciences, particularly focused on plant genomics. AgroLD contains around 900M triples created by combining more than 100 datasets from 15 data sources. Our objective is to offer a domain-specific knowledge platform to answer complex biological and plant sciences questions related to the implication of genes in, for instance, plant disease resistance or adaptative responses to climate change. In this poster, we present some results which currently focused on genomics, genetics, and trait associations.
AgroLD is built incrementally spanning vast aspects of plant molecular interactions. The current phase covers information on genes, proteins, predictions of homologous genes, metabolic pathways, plant trait associations, and genetic studies. At this stage, we have integrated data from several resources such as Ensembl plants, TAIR, and Gene Ontology Annotation. The choice of these sources has been guided by the biological community, as they are widely used and have a strong impact on the user’s confidence. We have also integrated resources developed by the local SouthGreen platform such as TropGeneDB, a tropical plant genetics database, Rice Genome Hub, a rice genomics database, GreenPhylDB, a comparative genomics database for tropical plants, OryzaTagLine, a rice phenotype database and SniPlay, a rice genomic variation database. These resources bring together experimental data produced by research groups in Montpellier and the South of France. The online documentation provides an overview of the integrated data sources.
The conceptual framework of AgroLD is based on well-established ontologies in the plant field such as Gene Ontology, Plant Ontology, or Plant Trait Ontology. Furthermore, we developed a dedicated schema that creates links between the imported ontologies and introduces new classes and properties. The online documentation shows the complete list of the used ontologies. The majority of these ontologies are hosted by the OBO Foundry project.