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A pathway is a collection of two or more proteins/molecules connected by their interactions within and around a cell. We study the informatics and evolutionary issues of pathways. Similar to the definition of homology in the comparison of nucleotide and protein sequences, we define homologous pathways as pathways that are evolved from the same ancestral pathway. We first present a survey of existing pathway databases and discuss their format of pathway representation. Then, our pathway representation, the SLIPR format, is presented. It is a semilinear graphic representation of nodes (proteins) and modes (interactions). Pathways in SLIPR format enable pathway comparisons for evolutionary relationship and large-scale pathway database searches. We also discuss how one can map out orthologous pathways, achieving a predictive power on functional assignment of novel genes, once the pathway is understood well-enough in a closely-related species.