Figure 5 .

Association of template bricks with terms using the main, narrow and alternate relations. A. A template brick representing the term ‘translation’ (SBO:0000184). It fully represents this term, and is associated with it using the main relation. B. Two template bricks representing the term ‘stimulatory activity’ (BKO:0000003). The top brick represents the stimulation of an irreversible process, while the bottom one represents the stimulation of a phenotype. Since each brick only represents a subconcept of the concept described by the term, it is associated with the term using the narrow relation. C. Another template brick representing the term ‘translation’. It fully represents the term, but there is another template brick that also fully represents the term and that is more appropriate (see A). Hence it is associated with this term with the alternate relation. This template brick was only added to the set for compatibility with translation processes of CellDesigner [11]. Since this representation is not fundamentally correct with respect to the semantics of SBGN PD, it should not be used in template-based construction, but it is relevant for annotation of maps, for example.