6.1. hiPathDB

With heterogeneous biological pathway data sets in the diversity of potential data formats available, the integration of pathway resources has become an important issue in utilizing these resources systematically and efficiently. In order to utilize these resources to interpret and analyze genomic data using network-based analysis methods, the information stored in dispersed data repositories needs to be linked and combined in efficient ways, and strongly required to unify heterogeneous interactions in different pathway data sources into the one general network model.

Here, MONGKIE provides a built-in software module for highly interactive pathway visualization and exploration, tightly integrated with hiPathDB (Yu et al., 2012). hiPathDB is an integrated pathway database that combines curated human pathway databases of NCI-Nature PID (Schaefer et al., 2009), Reactome (Croft et al., 2010), BioCarta (Nishimura, 2001) and KEGG (Kanehisa and Goto, 2000). hiPathDB provides two different types of integration. One is the pathway-level integration - shown in Figure 3 of Yu et al., 2012 - which is conceptually a simple collection of individual pathways, was achieved by devising an elaborate model that takes distinct features of four databases into account, and subsequently reformatting all pathways in accordance with our model - shown in Figure 2 of Yu et al., 2012 - while maintaining molecular details of signaling processes. Another is the entity-level integration - shown in Figure 4 of Yu et al., 2012 - creates a single unified pathway, super-pathway, that encompasses all pathways by merging common components. Even though the detailed molecular-level information such as complex formation or post-translational modifications tends to be lost in the entity-level integration, such integration makes it possible to investigate signaling network over the entire pathways and allows identification of pathway cross-talks. Therefore, the unified super-pathway achieved by entity level integration facilitates the network-based analysis and navigation from the perspective of biological pathways.