Proposed design patterns: for study type and it's children

[cmungall]

For history see #80

current top level:

. EO:0007359 ! plant experimental condition
 % EO:0007231 ! study type
  % EO:0007255 ! laboratory study *
  % EO:0007248 ! green house study *
  % EO:0007256 ! field study *
  % EO:0007280 ! unknown study type *
  % EO:0007269 ! growth chamber study *
 % EO:0001001 ! plant treatment
  % EO:0007357 ! biotic plant treatment *
  % EO:0007191 ! abiotic plant treatment *
  % EO:0001062 ! control treatment *
  % EO:0007403 ! unknown treatment *
  % EO:0007027 ! seasonal environment *
  % EO:0007064 ! ecological environment *

study type children with defs:

• EO:0007248 ! green house study The treatment where the plants were grown under green house conditions. This may involve supplemental treatments in addition to any standard conditions.
• EO:0007255 ! laboratory study The treatment where the plants were grown under laboratory / open room conditions, with very few controlled parameters. This may involve supplemental treatments in addition to any naturally occurring conditions.
• EO:0007256 ! field study The treatment where the plants were grown under field conditions. This may involve supplemental treatments in addition to any naturally occurring conditions.
• EO:0007269 ! growth chamber study The treatment involving study type in which plants were grown in growth chambers.
• EO:0007280 ! unknown study type The treatment involving study type where nothing is known in the reported literature/study about the kind of growth facilities used.

Problems with study type branch:

• study type: labels should never have 'type' in the label
• 'unknown'
• the classes are defined as if they were treatments, but they are placed as children
• the grouping class 'plant experimental condition' makes no sense

We are somewhat constrained in what we do with these terms as out in the wild, e.g. https://arapheno.1001genomes.org/phenotype/90/

Proposal:

• define 'plant experimental condition' as an awkward union, possibly changing its label if we are allowed
• treat 'study type' as a subclass of http://purl.obolibrary.org/obo/OBI_0000471 'study design execution'
• preferably change label of 'study type' if we are allowed
• for children of 'study type', use a DP of occurs_in some X, where X can come from a mixture of AGRO (greenhouse, field), OBI (laboratory), ENVO etc
• hold our nose and accept the unknown but weakly deprecate with a do_not_annotate subset

from discussion with @marieALaporte and @austinmeier

[cmungall]

We all agreed to obsolete: EO:0007280 ! unknown study type

[austinmeier]

3 options discussed:

1. study becomes material entity
2. study becomes a treatment
3. study becomes OBI study design execution

Settling on option 3. - propose to rename plant study (execution)

propose to remove top level plant experimental condition?

[cmungall]

We will go ahead and define the study branch using OBI 'study design execution' as genus

E.g. 'study design execution' and occurs_in some ENVO:greenhouse

[ddooley]

Action on this? I was struggling to understand what "plant study" was, as it was under "plant experimental condition".

Also what is a "plant exposure"? Is that a process of some duration, or is it a quality of an environment + plant?

I was trying to include "spring season exposure" etc. in FoodOn to describe when a crop was tilled for a USDA-used data point (not part of an experiment though).