The PANTHER pathway dataset uses controlled vocabulary and graphical notation to describe pathway knowledge7. The graphical representation of pathways is generated by CellDesigner, a pathway-editing tool8, and is compliant with the Systems Biology Graphical Notation Process Description standard (SBGN-PD) 25 (Figure 2B). Currently, there are 176 expert-curated pathways in PANTHER. The scope of the pathways is similar to those described in textbooks or review articles, e.g., glycolysis, the PDGF signaling pathway or the p53 pathway. Each pathway contains three key classes of data (Figure 1). First is the pathway component (or molecule class), which represents a specific class of molecules that play the same mechanistic role within a pathway. It can be a protein (e.g., PDGF, Jak), a DNA region, or a simple molecule (e.g., ATP or glucose). If a pathway component is a protein, gene or transcribed RNA, it is associated with the protein sequences in the PANTHER protein library through manual curation (Figure 1 and 2). The individual protein sequences are instances of the pathway component. In these cases, a pathway component is typically a group of homologous/orthologous
