Flexible Integration and Visualisation of Drosophila Melanogaster Datasets

The challenge in bioinformatics is not integration by itself, which could be achieved with ad-hoc scripting, but to do so in a manner that is repeatable, customisable, and enables powerful queries and visualisations. Here we present a case study which should provide some valuable insights. We set out to integrate public datasets from Drosophila melanogaster, including pathway data from BioCyc and tissue expression profiles from FlyAtlas. Cytoscape and PathVisio were used for visualisation of networks and pathways. We used existing ontologies, such as BioPAX, where possible. We found situations where the existing standard had to be amended, for example we inferred new Xref classes using Identifiers.org IRI’s. For the purposes of repeatability and provenance, we made every aspect of our system fully scripted. We discovered that Cytoscape visualisations work best to answer questions about the whole dataset, such as “Which submodules of the data are primarily active in one tissue?”. The PathVisio tool is more adept at answering detail-oriented questions, such as “Which enzymes are gatekeepers to the glycolysis, and in which tissues are they active?”. Our position is that semantic technologies provide more flexibility; repeatability through scripting is of utmost importance; and multiple visualisation tools can be combined to address a broader range of biological questions. Availability: The integrated data is available as RDF dumps, cytoscape session and a SPARQL endpoint at http://fly.cloud.generalbioinformatics.com