Figure 1.

(a) Targeted relation types in RegulaTome and their relationship to each other: there are 43 relation types annotated in RegulaTome, mapped to the biological process sub-ontology of GO, and since GO lacks terms to collectively catalog all catalysis of small molecule conjugation or removal processes, we have decided to group catalysis of phosphoryl group conjugation or removal relations (i.e. catalysis of phosphorylation and catalysis of dephosphorylation) separately from the other catalysis of small molecule conjugation/removal relations, both because of their biological significance, and—most importantly—because we observed that these are discussed differently in the biomedical literature, (b) Illustration of relation representations in RegulaTome: multiple relations between a Protein (“Sir2”) and another Protein (“Foxo1”) participant are shown in the first sentence – an undirected Complex formation relation and a directed catalysis of deacetylation relation denoted with a left-to-right arrow, originating from “Sir2” with “Foxo1” as the target and a directed relation that has “Foxo1” as the target, this time originating from another Protein participant (“cAMP-response element-binding protein-binding protein”) and in the opposite direction denoted by a right-to-left arrow; relationships can arise between all entity types annotated, e.g. in the second sentence two directed relations (regulation of gene expression and positive regulation) originate from a Family (“protein kinase C”) participant and target a Protein participant and a Complex (“nuclear factor.kappa B”).