amazein
commented
6 years ago This should be discussed via [sbgn-discuss], voted on etc. For L1V2 we should act on what we already have so we can do it quickly. If you would like to change names of the glyphs in L1V2 we should start the discussion via [sbgn-discuss] soon. I think we can postpone this. I agree, there are inconsistencies there, they should be fixed, but they are not critical for the use of the notation.
On the topic itself, I understand the motivation for renaming the process glyph. On the other hand, generic process assumes specific processes. if in the future we remove association and dissociation glyphs, there would not be any specific processes over which we would have generic process. This might not be a problem though.
For modulation, stimulation, catalysis and inhibition arcs, the term could be regulatory arcs?
adrienrougny
hasanbalci
The ontologies in section 3.3 "The conceptual model" mix glyphs and concepts, which doesn't seem correct. Indeed, in those ontologies, nodes are classes of glyphs, and arcs _isa relationships shared among concepts (and not glyphs): For example, in Figure 3.1, the Process and Omitted process classes refer to the process and the omitted process glyphs respectively (as they are subclasses of the SBGNGlyph class), and the Omitted process class is a subclass of the Process class. In a given map, all instances of the omitted process glyph are not instances of the process glyph (simply because the glyphs are different), but in terms of biological concepts, all instances of omitted processes are instances of processes (i.e. a process is an omitted process). Hence the relationship Omitted process _isa Process only holds if those classes refer to the biological concepts (and not to the glyphs used to represent these concepts). In general, I believe an ontology organizing the relationships shared between glyphs is not interesting, because its structure would have to be horizontal: all classes of processes (referring to the process glyph, the omitted process glyph, the association glyph, etc.) would have to be sister classes (i.e. share the same parent class); and it would be the same for all other types of glyphs (modulations, EPNs, etc.). That is of course not the case for ontologies organizing the represented concepts (see SBO).
Another related issue is whether the process glyph can replace any other type of process glyph (the omitted process glyph, the dissociation glyph, etc.), i.e. whether the process glyph can be used to represent any process (and possibly losing some information doing so), or not. The same question arises for the modulation glyph. I also believe that, interestingly, it is relevant for the unspecified entity glyph. The alternatives are illustrated in the following PDF.
Finally, it would be good to rename the process glyph and the modulation glyph: currently, when talking of "process grlyphs", we do not know if we're talking about "all instances of the process glyph" or all instances of glyphs that represent processes (i.e. all instances of the process glyph, together with those of the dissociation, association, ..., glyphs). In Stuart's version of the specification L1V2, the process glyph was renamed to the generic process glyph. The same could be done for the modulation glyph.