Figure 1

PhenUMA knowledge base. A: Schematic representation of the PhenUMA knowledge base contents. Three types of relationships are included in the knowledge base: i) “known relationships” (solid lines) were extracted from the databases OMIM, Orphanet and STRING and also include the metabolic interactions from Veeramani and Bader [15]; ii) “inferred relationships” (dashed lines) were taken from the OMIM and Orphanet known relationships; and iii) “semantic similarity relationships” (dotted lines). For the semantic similarity relationships, scores were calculated using the HPO and GO. Genes (red triangles), OMIM diseases (yellow circles) and Orphanet diseases (blue octagons) are the components of these relationships. This schematic describes how inferred relationships were determined from known relationships; that is, how the dashed lines were deduced from the solid lines. B: Illustrative example of integration between phenotypic and functional gene-gene relationships as retrieved in PhenUMA for ornithine transcarbamylase (OTC; MIM# 300461) at a medium confidence level.