Figure 1

Mapping SNPs functional effects from textual descriptions to network representations. The activation of RAS by SOS1 is used as an example. In the upper part of the Figure the Reactome representation of the reaction is depicted. The textual description of the functional effect of the SNP from UniProt is presented in the lower part. In Reactome, the reaction is annotated to the GO term "Ras guanyl-nucleotide exchange factor activity". The type of reaction (catalysis of "control-type activation") is provided by the BioPAX ontology. In UniProt, the W->L mutation at position 729 of SOS1 is described with the text "promotes constitutive RAS activation", which could be mapped to the GO term "activation of Ras GTPase activity" by NER. Reactome and UniProt refer to the reaction through different perspectives impeding a mapping of the UniProt textual description of the sequence variant onto the reaction in Reactome. The direct mapping using the GO annotations is hindered as the two GO terms appear in different GO branches. An alternative would be to use the BioPAX ontology.