Notes on PGDSO revisions fall 2011

Plan for revising the PGDSO, fall 2011

The current PGDSO is a mixture of processes and phases (although it was intended to be all stages/phases), and was designed with angiosperms in mind.

We need to correct some specific problems with the PGDSO, and to make it applicable to all plants, as we have done withe PAO.

Strategy

RW: In my opinion, the PGDSO should restrict its domain to growth and development stages, plus any landmarks needed to describe transitions between phases (some which are in GO already, e.g., GO:0007126 meiosis, GO:0009845 seed germination).

Growth and development processes (and other biological processes in plants) are already in the domain of GO, and should be left there. There is no reason we can’t suggest new terms to GO, if we feel they are missing. Although some PGDSO terms seem to reflect processes (e.g., imbibition, senescence, anthesis), I think these terms were intended to describe the phase during which the process occurs, not the process itself. Furthermore, terms for phase are what are needed by the genetics and genomics communities to describe the temporal aspect of tissue sampling. Given our limited time and resources, I suggest that we stay focused on our existing domain, and not try to expand it too much at this point.

Goals 1 and 2 could be accomplished fairly easily, without the addition of any new terms, once we agree on policies for creating names and definitions. Most of this can be based on our experience with the PAO. Goals 3 and 4 will require the most work and discussion. These should be the focus of our NYBG meeting, particularly goal 3. Goal 4 will probably require input from CM, and we will need additional meetings with him. Goal 5 is mostly important for future work, and does not require much immediate attention, but we should keep it in mind as we work through the other goals.

Specific tasks

We should try to work on tasks 1-5 at the POC meeting at the NYBG, even if we can't finish them all. Tasks 6 and 7 can be handled over conference calls.

1. Clarify the domain of the PGDSO and define the root-level term accordingly

• if possible, refer to BFO or other upper-level ontology

2. Develop and implement a sound naming policy

• choose between “stage” and “phase”
• decide whether or not to eliminate letters and numbers from term names
• most naming problems can be remedied pretty easily (add stage or phase to the end of the name)

3. Develop the top levels of the PGDSO

• determine what categories we will need to provide ancestors for all existing lower-level terms
• determine what any new categories we want to include (e.g., life cycle boundary/landmark)
• determine tree structure for top-level terms
• write definitions of top-level terms that are general enough to encompass all plants

4. Work existing upper- to mid-level terms into the hierarchy determined in step 3.

• write genus-differentia definitions for these terms, and check for generality

5. Populate any new top-level categories, such as life cycle boundary/transition

• we have notes/suggestions for this from our last meeting
• first focus on major transitions and those that can be clearly defined; more ambiguous sub-divisions can be added as time allows

6. Add new mid-level terms need to describe growth or development stages for non-angiosperm plants

7. Determine which relations are needed to link the PAO and PGDSO

• participates_in and variants
• has_participant and variants
• others

Suggestions/notes for specific tasks

1. Naming policies

a. Stage versus phase

• Barry prefers phase

• Stage is already in the name. If we change to phase, it would become the PGDPO, which might lead to confusion, but I don’t know how many people outside PO internal use PGDSO.

• Could use "phase" for major parts of a life cycle, like gametophyte phase and sporophyte phase, and keep "stage" for time periods, like flower development stage.

• Important question: do we mean the same thing when we say stage or phase? If so, it is not that crucial which one we use. If they are the same thing, we need to be careful that our definitions are consistent with that. We can't have a phase be a subtype of a stage or vice versa unless they are truly interchangable.

b. Numbers and letters in name

• make browsing easier, because terms are in temporal rather than alphabetic order

• names without letters and numbers can be added as exact synonyms

• names with letters and numbers are confusing when terms are viewed in isolation

c. Whole plant growth stage names

Current names for some of these are confusing, even though the definitions and comments in them clarify. For example: PO:0007016 4 flowering. If we rename this “flowering phase”, it will not be clear from the name alone that it represents a whole plant growth phase.

Suggest renaming it something like “whole plant flowering phase”

PO:0007130 "B reproductive growth" would be “whole plant reproductive phase”, etc.

2. top-level of PGDSO

a. root term: plant process

Based on previous discussions, should be a BFO occurent.

BFO definitions:

(note: process is a subtype of occurent)

occurent: Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.

Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor

process: Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.

Examples: the life of an organism, the process of sleeping, the process of cell-division

GO:0008150 (biological process): Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

In our last discussion, we chose plant process as the root term.

proposed def.: a BFO process that (has_participant?) plant NCBITaxon:3193 (Embryophyta).

Alternative is to define is as a GO:biological process in a plant, but this may be too much overlap with GO.

b. Top level structure and terms

RW suggests something similar to our earlier proposal (from December), but omitting the branch for "plant development process", because that belongs in GO. The PGDSO would have two main branches, one for plant structure growth and development phase (domain of current PGDSO) and one for plant life cycle boundaries. Many of the boundaries are already in GO. For any that aren't we should request them in GO. Then this branch could either be removed from PO or populated with GO terms.

Barry suggested that we need a term like "plant life" or "life of whole plant", of which all phases would form parts. Maybe plant life cycle would be a clearer name for plant biologists. Not sure where this term should go -- as a child or a sibling of whole plant growth and development phase or a child of plant process.

plant life cycle boundary: A BFO process boundary that is part of a plant life cycle and marks the transition from one life cycle phase to another.

Comment: May be a bona fide or a fiat boundary. Some of these processes will be in GO already.

plant structure growth and development phase: A plant process (or processual entity?) that describes the temporal interval during which particular aspects of the growth and/or development of a plant structure occur.

Comment: This term is used to describe a period of time during which certain growth or development processes occur, not to describe the growth or development processes themselves. Includes phases in of growth and development of a whole plant or a proper part of a plant. Only plant structures can grow and develop, therefore, temporal intervals during which changes to plant anatomical spaces or plant substances can only be described relative to the structures that surround or produce them.

whole plant growth and development phase: A plant structure growth and development phase that is a (proper) part of a plant life cycle and has as participant a whole plant.

Open SourceForge trackers for the PGDSO

See Items_for_future_meetings#User_requests_still_open_on_Source_Forge.3B_PGDSO for a complete list.

PGDSO terms without is_a parents

imbibition (PO:0007022)

seedling growth (PO:0007131)

shoot emergence (PO:0007130)

'plant life' ('life of whole plant')

Barry suggested that we need a term like "life of whole plant", of which all phases would form parts.

Previous proposal

See POC_Conf._Call_12-15-10#Restructuring_PGDSO_for_Occurents for a description of a proposal that BS, LC and RW worked on in December.

Also see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/branches/PGDSO_2011/plant_ontology_test.obo?view=log for a copy of the test ontology file and changes in new PGDSO version for a summary of changes that were made to the test file.

In that proposal, the root term, plant growth and development stage, would be replaced by 'plant life cycle process' (an "Occurrent"). The top level structure would have three branches, as below:

The proposal described here is simpler than December's (does not include biological processes, which could be in GO), but follow many of the same principals.

New relations linking the PAO and the PGDSO

derives_from

At the POC meeting on 7-19-11, we agreed to create a new relation in the PO called derives_by_manipulation_from (see POC_Conf._Call_7-19-11#derives_from_relations_in_PO:). This would be a special case of the RO relation derives_from.

participates_in and has_participant

See POC_Conf._Call_7-19-11#participates_in_relation

Chris asked: "will you add temporal relations to the stages?"

other

We may want to add temporal relations such as preceded_by, precedes and follows, or perhaps more precisely, immediately_preceded_by, immediately_precedes. This would be comparable to the adjacent_to relation.