Figure 3

Alignments of computational models. A: Linear pathway; only the first and the last species are annotated. B: Self-alignment of the linear pathway. Depicted are the pairwise element similarities according to the three different similarity measures. Each table entry contains six numerical values. The entries in the upper line denote the direct similarity σ (blue), the similarity ψ^fp obtained by feature propagation (red), and the similarity ψ^sp from similarity propagation (green). Values between 0 and 1 are shown by colour intensities. Similarities between different types of elements (e.g. species and reactions) were set to 0, while ψ^sp values larger than 1 were set to 1. The lower three entries show the element matching obtained from these similarities. Thick boxes indicate the correct matching.