A web application for end-users with appropriate functions to import, query, and retrieve the data using the Apache Jena Java framework and SPARQL queries against RDF triples stored in a graph database.
Data describing biobank resources often contain unstructured textual information that is insufficiently precise for computational processes such as automated data discovery and integration. In this work, we demonstrate how semantic web technologies (e.g., SPARQL, RDF, ontologies) can be used to build an application that aims to improve the process of querying and integrating biobank specimens and specimen-derivative data, such as genomic sequences.
We developed Next-Generation Biobank Ontology NGBO, which defines precisely the meanings of biobanking related entities (terms) and relations in a computer actionable way. The ontology is used to construct semantic statements and provide rich metadata content to real-life biobanking use cases.