Fig. 1

Design of the PathMe framework. The PathMe software package facilitates the transformation of pathway content into BEL. The initial step consists of extracting, parsing, and/or querying content from each pathway database to retrieve entities, concepts, interactions and reactions, and their associated metadata. Subsequently, database specific identifiers for all entities are unified to stable and consistent ones, where possible. Data are then directly mapped into equivalent BEL nodes and edges, translating all human pathways from the databases into BEL. Finally, an interactive pathway viewer is implemented such that any combination of pathways, represented as BEL networks, can be explored and the consensus surrounding pathway knowledge can be directly compared