Ecological functions

[pbuttigieg]

@diatomsRcool

❗ All terms with ⚠️ symbols suggest more involved semantics

Add terms covering organismal functional roles such as:

• host
• prey
  • preferred prey ⚠️
  • alternative prey ⚠️
• heterotroph
  • omnivore
  • primary consumer
    • herbivore
      • graminivore
      • folivore
      • root herbivore (org that eats roots, rhizovore)
    • algivore
  • parasite
    • parasitoid
    • internal parasite
    • external parasite
  • fungivore
  • carnivore
    • predator
      • insectivore
      • secondary consumer
      • tertiary consumer
      • quarternary consumer
      • apex predator
      • ambush predator
    • scavenger
  • detrivore (syn: detritivore)
    • litter transformer
  • decomposer
  • bacteriovore
  • top consumer (related syns: top predator, tertiary consumer)
• autotroph
• mixotroph
• chemolithotroph
• photoautotroph

[diatomsRcool]

@pbuttigieg Can I go ahead and add these classes or are we waiting for NBO?

[diatomsRcool]

I would not put insectivore, secondary, tertiary, or quaternary consumer under predator.

[diatomsRcool]

On second thought, maybe this is ok

[diatomsRcool]

@pbuttigieg I see that there is already a host and a parasite, but they are from IDO and the definitions are not good. Would it be ok to make new classes? Should we ask for a change in IDO?

[pbuttigieg]

Best to ask IDO to revise. State that we'll need to create the terms in 2 weeks if they can't resolve the issue. Perhaps it would be best for them to import from ECOCORE anyway, in aid of modularity

…

On Mon, 30 Jul 2018, 02:51 diatomsRcool, ***@***.***> wrote: @pbuttigieg <https://github.com/pbuttigieg> I see that there is already a host and a parasite, but they are from IDO and the definitions are not good. Would it be ok to make new classes? Should we ask for a change in IDO? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACK7Mrl3TFgqyEgFSteCg21FvyTJUekqks5uLliHgaJpZM4O24V3> .

[cmungall]

+1

[diatomsRcool]

Terms with checks are in ecocore-edit

[diatomsRcool]

infectious-disease-ontology/infectious-disease-ontology#2

[diatomsRcool]

Terms with checks are in latest release v2018-09-11

[cmungall]

it looks like the functions are not axiomatized?

You know my thoughts - I don't think you need 3 cognate hierarchies, for Xtrophy, Xtrophic function, Xtroph organism

However, if you do I recommend articulating your DPs and choose one hierarchy (I think process; with these having DPs defined by inputs) as base and derive everything from that

• het function: A function which inheres in a living entity by virtue of that entity being able to feed on living or once-living (dead) material. subClassOf realizedin some heterotrophy
• heterotrophy (process): A trophic interaction process during which a living entity acquires food and energy by consuming another organism or organism part, living or dead.

I'd recommend generating the shadow text defs so they are consistent

also the function def is the horrible (I can say that as I am responsible) verbiage from PATO which is intended for qualities. I don't think it makes so much sense for a BFO function

How is the function hierarchy intended to be used?