Fig. 1

Example of hierarchical (tree) structure of data in the Human Phenotype Ontology (HPO). Ophthalmic findings in a child with PHACE syndrome (posterior fossa anomalies, hemangioma, arterial lesions, cardiac abnormalities/coarctation of the aorta, eye anomalies) are shown. Ontologies consist of several distinct elements including terms (nodes in the figure) and relationships (arrows in the figure). Each term can be associated with annotated textual information known as metadata; these may include modifiers (blue squares), definitions and alternative/secondary identifiers. Modifiers can be assigned to each term and may relate to severity (mild, moderate etc.), temporal pattern (acute, episodic, etc.), age of onset (childhood onset, adult onset etc), progression (progressive, nonprogressive, etc.), laterality (right, bilateral etc) and spatial pattern (central, generalized, etc.). The user can specify if a specific phenotype (HPO term) is present or absent in an individual. When a phenotype/term is selected as present (e.g. terms corresponding to the five circles with thickened margins) then, by definition, all terms above this term (coloured circles; colours only used to enhance visualisation) have to be present; this is because each term is connected with its parent terms by an “is a” relationship. Therefore, the higher in the ontology a term is located, the more general it is and the lesser its information content (defined as the negative logarithm of its probability) will be