The GraphML files contain the sequence networks and annotated metadata for protein sequences.

The GraphML attributes for the edges comprise the edge weights (pairwise sequence identity, "weight"). The GraphML attributes for the nodes comprise the identifiers from the ExED ("sequence_id", "protein_id", "hfam_id", and "sfam_id" for sequence, protein, homologous family and superfamily identifiers, respectively), the NCBI taxonomy ID ("tax_id"), the annotated (organism) source name ("tax_name"), the taxonomic lineage of the source organism ("lineage", with taxa separated by "<--"), and the length of the amino acid sequence ("sequence_length"). In addition, suggested color names are given for both fill color and border color of each node ("color" and "color_border").