From Ontology for Genetic Interval (OGI) to Sequence Assembly - Ontology applying to next generation sequencing

We develop an OWL ontology: OGI (Ontology for Genetic Interval) for the formalization of the genomic elements by defining them as a Genetic Interval. Based on OGI’s definition of Genetic Interval Relations, which derived from the Allen interval calculus, we attempt to represent the relationships among contigs and sequence data from next generation sequencing. A real dataset generated from the bench has been loaded and tested by using SPARQL for validating OGI. Although the dataset is small, this semantic-based method provides a clue for assembly sequence. Evaluating this method on a bigger dataset, both harmony and conflict of definitions with current ontologies, such as SO (Sequence Ontology), need to be considered. OGI is available on NCBO’s BioPortal website.