Turning a genome annotation into a RDF knowledge graph.
Introduction In this article, I will describe the steps taken to generate a RDF (Resource Description Format) datastructure starting from a gff3 formatted genome annotation file. The annotation file in question is the new reference annotation for Pseudomonas fluorescens strain SBW25.
Required packages I will make use of the following python packages:
gffutils to read the gff3 file into a sqlite database. rdflib to construct the rdf graph. requests to fetch data (e.
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