What is a Species and a SpeciesAlias?
The Species represents, for example, proteins and other molecules in biochemical networks and genes in gene regulatory networks. The biochemical and genetic meanings of Species are distinguished by their symbols.
Species in SBML
SBML (Level 2 Version 4) specification defines the terms species type as follows:
The term species type refers to reacting entities independent of location. These include simple ions (e.g., protons, calcium), simple molecules (e.g., glucose, ATP), large molecules (e.g., RNA, polysaccharides, and proteins), and others.
Species in CellDesigner
In CellDesigner, there is a distinction between the terms Species and SpeciesAlias.
Species is identical to the species in SBML definition. It is simply a logical entity and does not have any graphical information.
SpeciesAlias is a graphical representation of a relevant Species.
So, when you create a Species, the graphic object you draw on canvas is in fact a SpeciesAlias, and not a Species.
If a new Species is created and given the same name as the existing Species, it will be regarded as the second SpeciesAlias of the same Species. Species is identified and distinguished only by its name, not by its shape.
Different SpeciesAliases having the same name belong to the same Species.