Linking heterogeneous data from model plant species in a graph database
Résumé
More and more data are available nowadays due to emerging technology and tools to analyze
genomes. In this situation, it is necessary to identify or develop tools to connect all these data
together. In this context, graph database seems to be an appealing method to connect data as
nodes and relation between them as edges or links. Graph NEO4J TE contains genomic data
on two model plant species, one dicot and one monocot A.thaliana and B.distachyon. It puts
into interaction genomic coordinates between entities like structural gene annotation,
transposable elements, transcription factor binding site and other allowing to search possible
positional relation between these entities. We enrich these information with functional
annotation, phenotyping characterization data and localization data linked with our genomic
data using pivotal node like accession or gene.
Neo4J allows RDF importation into the database. We have been able to successfully import
gene ontology into our database and to import AgroLD rice gene data from turtle files (zenodo
repository) and bind these information with our own database with a simple query.
Finally we can export our own dataset in RDF format. That RDF can be imported into
other instance of neo4j database.
The database has been developed in « Graph » working group of CATI GREP. In this group 3
project are in development on different species and thematic. We have commonly defined the
modelisation of nodes and relationship to allow connections between graphs.