Figure 3.

Building network process. A: Input provided by the user of PhenUMA. Gene-Gene network building allows a set of genes or diseases as input (OMIM or Orphan diseases). In case of providing a disease list, genes associated with each disease (OMIM or Orphanet associations) are use to create the gene-gene network in the building network stage. Disease-Disease network can relate OMIM diseases or Orphan diseases and in both cases the input type are similar: a list of diseases or a set of genes. Phenotype query network building require of a set of phenotypes (HPO) as input, which is taken as a phenotype profile. B: Building network stage is divided in two parts: the seed network building that contains the relationships between de input set (genes, diseases or phenotypes) and the rest of elements included in the database and the network enrichment that consist in the addition of the rest of relationships included in the knowledge base (see Figure 1) between the elements related in each network.