NTR: whole plant qualities

[pbuttigieg]

@leechuck @ramonawalls @cooperl09 @cmungall

Following some conversation with those tagged above on the topic of plant growth forms, I'd like to request a few qualities that would make it easier to express that we're talking about plants with growthforms tree, shrub, etc.

This would prevent us having to awkwardly handle the phenotype-level semantics which currently do this job. It would also allow better axiomatisation of the subclasses of FLOPO's whole plant phenotype, which is axiomatised as:

has_part some ((part_of some whole plant) and (has quality some quality))

However, the 'quality' part of that is not specified in the subclasses.

As trees, shrubs, etc are quite important to wide communities, I think we should start with qualities for the subclasses of whole plant growth form

• whole plant herbaceous
  • whole plant graminoid
  • whole plant forbacious
• whole plant arborescent
• whole plant frutescent
• whole plant lianescent

For "herbaceous", PATO:0002352 is present. I'm assuming that is satisfactory. That leaves us with:

• graminoid (grass-like)
• forbacious (forb-like)
• arborescent (tree-like)
• frutescent (shrub-like)
• lianescent (climber- or liana-like)

I could propose some definitions, but I think this would be better coming from plant scientists. There are no definitions in the FLOPO classes, it seems.

PS: Would it be better to add these in PO itself, below PATO's structure?

[ramonawalls]

I think these belong in PATO rather than PO, just because PO does not currently define any qualities. Last I checked, PO was not importing any PATO qualities to define structures, but that might happen some day.

These classes will be very helpful for many use cases. Once the qualities are in PATO, TO could add corresponding trait classes and FLOPO's terms could be more fully logically specified.

[ramonawalls]

I'm willing to give some input on these definitions, but can't commit as to when I'll have time.

I don't like PATO's definition of herbaceous, which has to do with the plant dying back after a growing season. Herbaceous plants should be defined as not having wood above ground. See https://en.wikipedia.org/wiki/Herbaceous_plant.

[cooperl09]

Another, related issue with herbaceous: PATO:0002352 is that it is a subclass of "shedability"

shedability (PATO_0001729): An organismal quality inhering in a bearer by virtue of the bearer's disposition to lose an entitity (sic) by natural process. [database_cross_reference: PATOC:GVG]

Suggest a new class to group these under: growth form Proposed def'n: An organismal quality which is the pattern of growth of an organism displayed in a particular environment. synonyms: life form, growth habit

Siblings of herbaceous could also moved under this

[marieALaporte]

I would suggest to look at this reference paper from the functional ecology domain to get the definitions of growth form and subclasses. I don't think that life form and growth form are synonyms (at least in the ecology community). https://www.eeb.ucla.edu/Faculty/Sack/publications/Lawren%20Papers/Perez-Harguindeguy_etal_2013_AusJB_TraitHandbook.pdf

I would also argue that those classes should be in TO instead of PATO are they are plant specific.