Parsing PID pathway data
نویسنده
چکیده
Pathway Interaction Database (PID) (http://pid.nci.nih.gov/) provides interaction data of pathways in several formats (XML and BioPAX). Here we parsed the PID XML format data (ftp://ftp1.nci.nih.gov/pub/PID/XML/). Data stored in PID XML file can be divided into four levels: pathway level, interaction level, node level and gene/compound level. The relationship between four levels is visualized in figure 1. Generally speaking, a pathway catalogue contains a list of pathways. Each pathway is composed of a list of interactions. Each interaction is represented as relation between an input node and an output node. Each node has different characters depending on whether it is a single protein, a complex or other non-protein molecules.
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