Definitions of terms - Species

[amazein]

In SBML spec, there is a definition of 'species': Species: A pool of entities of the same kind located in a compartment and participating in reactions (processes). In biochemical network models, common examples of species include ions, proteins and other molecules; however, in practice, an SBML species can be any kind of entity that makes sense in the context of a given model. We do not have it in SBGN PD spec while the term is used a few times. A more general question is about best practices of spec development, maybe aligning the language of SBML and SBGN specs.

[draeger]

The term `specie' in the SBML specification Level 1 was an error. The singular form of species is also species. This has been corrected relatively early.

[amazein]

Thank you, my mistake, the spelling is corrected

[draeger]

If wanted, we could add a sentence to the specification in SBGN stating that the concept of entity pool nodes roughly corresponds to that of species in SBML.

[draeger]

We could even add a brief rationale to this stating why the choice was made not to name it "species" but "entity pool node". The rationale was that the term "species" in SBML has been introduced at a very early development phase of that language when SBML was primarily targeting biochemical networks. When SBGN has been developed 10 years later, it was noticed that this term was too restrictive and also sometimes confused with the synonym for "organism".

[cannin]

A current sentence mentioning SBML is "The current solution is consistent with other Systems Biology representations such as SBML and BioPAX" (do something equivalent). Replace species with entity.

[hasanbalci]

Based on @draeger's comments, I thought we could modify the third paragraph in Section 2.1 Overview (the term "entity pool nodes" is first mentioned in this section in Figure 2.1) as follows:

The essence of the Process Descriptions is the change: it shows how different entities in the system process from one form to another. The entities themselves can be many different things. In the example of Figure 2.1, they are pools of either macromolecules or simple chemicals, but as will become clear later in this chapter, they can be other conceptual and material constructs as well. The concept of "entity pool nodes" roughly corresponds to "species" in SBML. However, the term "entity pool node" was chosen in SBGN instead of "species" to avoid the limitations of the latter term. When SBML was first developed, "species" was introduced in the context of biochemical networks, but over time, it was recognized as too narrow, especially for more generalized or diverse types of networks. Additionally, "species" can be confused with its use as a synonym for "organism." SBGN, developed later, adopted the broader term to ensure flexibility and clarity in describing a wider range of networks. Note also that we speak of entity pools rather than individuals; this is because, in biochemical network models, one does not focus on single molecules, but rather collections of molecules of the same kind. The molecules in a given pool are considered indistinguishable from each other. The way in which one type of entity is transformed into another is conveyed by a process node and links between entity pool nodes, and process nodes indicate influence by the entities on the processes.

@adrienrougny @cannin I think we also decided to replace all "species" in the specification with "entity", right?