Biology Reference
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(a)
(b)
Fig. 1. Petri net elements in HFPNe and their icons on Cell Illustrator. (a) A Petri net consists of three elements: place,
transition, and arc. In HFPNe, to bridge the gap between computer science and biology researchers, these terms are renamed
as more intuitive terms: entity, process, connector, respectively. In HFPNe, entity and process have three types - discrete,
continuous, and generic - and connector has three types - process, associate, and inhibitory. In Cell Illustrator, entity and
process can be displayed with more intuitive icons with the annotation by one of the biological pathway ontologies named CSO.
(b) The connection rules of elements in HFPNe.
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