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Global Biotic Interactions food web map

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posted on 07.02.2015, 01:47 authored by Sergey SlyusarevSergey Slyusarev, Dimitrios-Georgios Kontopoulos, William Taysom, Adrian GuzmanAdrian Guzman, Bimlesh Wadhwa

Using GloBI data archive ( accessed at June 9, 2015) we have generated a graph of predator-prey relations on species level, using R ( 'igraph' library. Then another graph with the same species was generated, with weighted edges, representing similarity of position in the original graph (modified Jaccard similarity index (with min(A,B) instead of (A ∪ B) in the denominator) was used for that). The latter graph was preliminary clustered with 'infomap' algorithm, then individual cliques were extracted from clusters and several passes of moving species from clique to clique were performed in order to increase average weight of within-clique edges. After that, these cliques were used to merge nodes and merge edges in the original graph. After labeling nodes (with data acquired using 'Reol' package) and ascribing them values corresponding to geographical metadata (using 'sp' package and ecoregion maps published at, graph went to 'Cytoscape' to be laid out with 'yFiles Organic' layout. Resulting image was post-processed in 'Adobe Illustrator'.
Visualization was made during IVMOOC 2014 (


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