Pathway Visualization Tools in Phytozome

We have recently begun adding metabolic pathway data to the genomes hosted in Phytozome, the Joint Genome Institute's plant genomics portal.

Our initial set of assignments is based on our in-house implementation of the Pathologic (http://pathwaytools.org/) workflow, coupled with Enzyme E.C. assignments derived from E2P2 (https://dpb.carnegiescience.edu/labs/rhee-lab/software).

We provide access to these pathway assignments via PhytoMine (http://phytozome.jgi.doe.gov/phytomine/begin.do), Phytozome's implementation of the open source genomic data warehouse InterMine (http://www.intermine.org).

While InterMine's data model can be extended to accomodate pathway information, the InterMine UI does not include any default pathway visualization capabilities. To provide access to these assignments to our users, we designed a pathway visualization tool for InterMine, based on the d3 library (http://d3js.org/). This tool supports viewing reactions and enzyme assignments in both graphical and tabular format, as well as the overlay of RNA-Seq expression data (to assist, for example, with identifying conditions under which a particular pathway is over- or under-expressed).

The InterMine data model and visualization tool capabilities will be presented.