Changes in new PGDSO version

Revision# 987 Changes made during meeting (LC, RW, BS):

Changed top level term from plant life cycle process to plant process. This way it encompasses all process. Ultimately, many of these may end up in GO.

Made new parent term plant life cycle boundary/landmark (final name to be decided). This is a parent of plant life cycle phase transition and plant life cycle fiat boundary. -The ultimate goal may be to get rid of all of these landmarks as terms, and instead incorporate them into the definitions of phases (see working definitions of gametophytic phase and sporophytic phase as examples).

If we keep boundaries/landmarks, may want to change their names. As an example, change seed germination to “phase transition between embryo and juvenile”, which is defined by germination, then germination goes under plant structure development process.

Other notes: Landmarks as a super class of phase transition, mark specific points in life cycle, but don’t necessarily mark a phase transition

Rename some of the growth stages/phases: remove growth and add whole plant where needed. For example: vegetative growth phase would become whole plant vegetative phase

May want to get rid of the word structure in plant structure development phase.

Revision 986 by Ramona Walls

Left merged terms as they are, but probably need to unmerge them if we go ahead.

Created new term plant structure developmental phase as parent term. Changed plant life cycle phase (PO:0025106) to whole plant life cycle phase, and made it a child of plant structure developmental phase.

Moved all of the different plant structure developmental stages to be children of plant structure developmental phase.

Moved the whole plant developmental stages to be children of whole plant life cycle phase and added (phase) to their names for clarity.

Moved (seed) germination, imbibition, and seedling growth to plant structure development branch, part_of sporophyte development. -Made new terms for seed phase and seedling phase, made them part_of sporophytic phase. -This makes seed germination both a plant life cycle process and a plant life cycle phase transition. Probably need to distinguish between the two or get rid of one of them.

Seedling growth should not part of germination; removed part_of relation.

Left radicle emergence and shoot emergence as they were, as an example of why current PGDSO is inconsistent (a mixture of developmental processes and developmental phases).

Can development (such as seedling development or shoot emergence) be part_of a life cycle phase (seedling phase)?

Put in GO definition of developmental process (GO: 0032502) under plant structure development. Changed to developmental process (makes it more clear that this is a not a phase).

Details of changes made in version #984: -Created working file 'plant_ontology_test.obo' -destroyed duplicate terms: gametophytic phase and sporophytic phase created at NYBG meeting as a test. -moved the existing PO terms: gametophytic phase and sporophytic phase to is a children of 'plant life cycle phase' -created new namespace 'plant_life_cycle_process' and movd the new upper level parent terms from 'plant_ontology' to it. -moved gametophytic phase and sporophytic phase to 'plant_life_cycle_process' namespace -moved all the children of 'plant life cycle phase transition' to 'plant_life_cycle_process' namespace

-moved all the children of plant structure development stage (PO:0007021) to the new term plant structure development (PO:0025101), except for leaf development stages, which were moved to 'plant organ development (PO:0025103)'

-merged Whole plant growth stages (PO:0007033) into whole plant development (PO:0025102)

-merged plant structure development stage (PO:0007021) into plant structure development (PO:0025101)