{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Evaluating the degree of overlap between equivalent pathways in KEGG, Reactome, and WikiPathways\n", "\n", "This notebook outlines the process of evaluating the overlap between the equivalent representations in the three databases. First, we calculate a similarity index by using a variation of the Szymkiewicz–Simpson/Overlap coefficient (Equation 1) calculated for the shared amount of molecular nodes in the graph. This variation sums the three coefficients obtained for each individual pairwise comparison to generate the similarity index.\n", "Second, Venn diagrams illustrates the degree of overlap in a more visual way. The notebook was generated with data parsed on the 26th of January, 2019." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "$$overlap(X,Y))=\\frac{\\left | X \\cap Y \\right |}{min(\\left |X \\right |,\\left |Y \\right |))}$$\n", "