Figure 1.

An entity/relationship diagram showing a simplified model of the Semantic PHI base OWL ontology. The three panels are color-coded such that entities shared between panels can be easily identified. (A) includes the core class—Interaction—and its primary participants of Host and Pathogen (green). The Interaction is manifested in both a wild type (red) and mutant (lavender) form of the Interaction Context OWL class. The elaboration of the wild type Interaction Context is also shown in (A) (red). (B) shows the overall structure of the mutant Interaction Context node (lavender), including the phenotypic Description, experimentalProtocol, and Citation information. Interaction Context is connected to a Host Context and a Pathogen Context, of which only the Pathogen Context (blue) is populated with useful information. (C) shows the overall structure of the Pathogen Context class, which primarily connects to genetic information via an Allele class (representing the allele carried by that pathogen in that context). An Allele is linked to a Gene, which is extensively annotated into remote databases via has unique identifier properties, the values of which are, whenever possible, the Identifiers.org URL corresponding to that data-type in a remote database such as UniProt or EMBL. Finally, the Gene class links back to the Organism class (black), shared with (A). Of importance is the fact that all “data”—that is, everything that is a value, rather than an entity, is connected to the model using the SIO property has value.