A reference metabolic network of L. lactis IL1403 has been used to evaluate our method (discussed below). This network was also constructed for constraint-based modeling purposes and was retrieved from the authors as a flat-file, containing gene-reaction associations. Throughout the article we will refer to this published reference network as the Oliveira network [31 (link)].
To compare the automatic reconstruction of L. lactis IL1403 metabolic network by Pathologic with that of our method, we used the Genbank NCBI annotation file of L. lactis IL1403 as input for the Pathologic software [27 (link),43 ]. In addition, the same Genbank file together with two manually curated networks from the BioCyc collection (i.e. EcoCyc [16 (link)] and LacplantCyc [17 (link)]) were used as inputs for our method (discussed below).