  Systems biology approaches to the integrative study of cells, organs and
organisms offer the best means of understanding in a holistic manner the
diversity of molecular assays that can be now be implemented in a high
throughput manner. Such assays can sample the genome, epigenome, proteome,
metabolome and microbiome contemporaneously, allowing us for the first time to
perform a complete analysis of physiological activity. The central problem
remains empowering the scientific community to actually implement such an
integration, across seemingly diverse data types and measurements. One
promising solution is to apply semantic techniques on a self-consistent and
implicitly correct ontological representation of these data types. In this
paper we describe how we have applied one such solution, based around the
InterMine data warehouse platform which uses as its basis the Sequence
Ontology, to facilitate a systems biology analysis of virulence in the
apicomplexan pathogen $Toxoplasma~gondii$, a common parasite that infects up to
half the worlds population, with acute pathogenic risks for immuno-compromised
individuals or pregnant mothers. Our solution, which we named `toxoMine', has
provided both a platform for our collaborators to perform such integrative
analyses and also opportunities for such cyberinfrastructure to be further
developed, particularly to take advantage of possible semantic similarities of
value to knowledge discovery in the Omics enterprise. We discuss these
opportunities in the context of further enhancing the capabilities of this
powerful integrative platform.
