Saturday Sept 10th, 2011
Detailed agenda for Saturday Sept 10th, 2011
Back to main agenda for POC_Meeting_at_NYBG;_Sept_10th-11th,_2011
Restructuring PGDSO:
9:00 AM - 12:30 PM
See Notes on PGDSO revisions fall 2011
The current PGDSO is a mixture of processes and phases (although it was intended to be all phases/stages), 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.
Overview
9:00 AM - 10:00 AM
We will review the problems with the existing PDGSO, followed by discussion of our goals for this revision, then presentation of a proposal for going forward.
Suggested Strategy:
1. Define the domain of the PGDSO to growth and development stages, plus any landmarks needed to describe transitions between phases (many of which are in GO already, e.g. GO:0007126 meiosis, GO:0009845 seed germination).
2. Leave the growth and development processes (and other biological processes in plants) in the domain of GO.
3. Redefine (and or rename) the PGDSO terms that reflect processes (e.g. imbibition, senescence, anthesis).
Issues with current PGDSO:
1. Names:
- many are process names, rather than phase names (e.g., senescence, rather than senescence phase)
- numbers in names (e.g., BO.02 mid boot stage)
- plural names (e.g., root development stages)
We will keep the numbers in the names, but try putting them in parentheses. Can't use square brackets because obo interprets those differently.
We will change any names that suggest that they are not stages, and get rid of plural names.
Will use stage instead of phase throughout. See more notes below.
2. Definitions:
- most (maybe all) have textual definitions, but these are not in the genus differentia form
- many definitions, as with names, describe a process, rather than a phase (e.g,. 6 ripening: Maturation of the fruit.)
- top level terms need better definitions
Will add g-d definitions as we go through the PGDSO, and define all terms as stages. See notes below on upper level definitions.
3. Ontology structure
- limited upper level hierarchy, angiosperm-centric
- existing leaf terms mostly for angiosperms
- is_a and part_of relations have not been used consistently for subtypes
Most stages will be defined as occurring between some landmarks (beginning and end points). In this way, stages that are sub-parts of a larger stage will have is_a relations to the larger stage, rather than part_of. For example, protonema stage is_a gametophyte stage.
Goals for revision of PGDSO:
The primary objective needs to be to clarify the domain of the PGDSO- are we going to just describe the stages and leave the processes to GO?
We also need to decide on whether to use phase or stage or both and how to define them.
General agreement on goals. Goals 1, 3 and 4 were the main goals for this meeting.
1. Provide growth and development stages that allow for annotation of all plant species
- enhance top level of hierarchy, as was done for PAO (more terms, more general definitions)
- populate mid levels with general growth and development phases/stages that can be used for any plant
- use a and b to provide a framework for taxon specific leaf terms: incorporate existing low-level terms into that framework and add new terms (see for example growth stages requested by Cossmoss)
- develop a set of landmarks that can be used to describe phase transitions, making phases comparable across taxa - some of these may need to be in GO -will not have separate terms for landmarks but will use them to describe beginnings and ending of stages
2. Develop a strategy for linking PAO and PGDSO terms
- determine the most appropriate relations and how to implement them (may need to create our own compound relations) -this wasn't discussed much at this meeting
3. Compliance with OBO Foundry guidelines and best practices
- provide is-a parents for all terms (only a few left)
- provide accurate names for terms
- provide accurate text definitions for all terms in genus-differentia form
4. Alignment with BFO
- define root node in relation to a BFO or other upper-level ontology term (is this possible? need to investigate)
- all subtypes in PGDSO should be occurents (already are, but of the wrong type)
- all subtypes in PGDSO should be growth and development stages, and have names and definitions that reflect that
5. Develop PGDSO terms needed to describe plant phenotypes/traits -this was not discussed at this meeting
Work on goals and tasks for revision (10:00 AM - 12:30 PM)
We will discuss the goals for revising the PGDSO and come up with a plan of action for the revision. If we agree on the goals, we can begin to work on some of the specific tasks.
Specific tasks for achieving the goals outlined above
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
Top level: PGDS
2. Develop and implement a sound naming policy
- choose between “stage” and “phase” or a combination of the two: they will be all stages
- 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 for dealing with specific tasks
Some suggestions for ontology structure and definitions of top level terms are on Notes_on_PGDSO_revisions_fall_2011#Suggestions.2Fnotes_for_specific_tasks.
Lunch (12:30 PM - 1:30 PM)
Walk to Garden Cafe for lunch.
PO publications (1:30 PM - 2:30 PM)
- Update on manuscript in preparation about changes to the PAO
-tasks remaining to be done: Get annotations for maize, Physcomitrella, grape, and strawberry. Use these annotations to do a comparison of gene expression between vascular and non-vascular leaves and among vascular leaves (or some other structure) in different vascular plants (corn, rice, strawberry, grape, and potato).
-target journal: Plant Physiology
-target submission date: mid-October
- Invited paper for American Journal of Botany
-Topic/theme
"The Plant Ontology as a tool to unify the plant science community"
Review of PO and other ontologies for plant science.
Potential of ontologies for plant science - beyond genomics - systematic applications - homology studies. Include examples from other taxa (like fish) that could be applied to plants.
-Need clarification of what is going to be in the other manuscript, so we can move forward with this one without interfering with the other.
This should be a short paper on what the PO is and why plant biologists (particularly outside genetics and genomics) should care about it. Don't go too much into phenotypes at this stage.
Provide one or two examples of systematic data described using PO terms (structures only, not characters or states). Maybe can use one of MAG's matrices for fossil Eucalypts.
-target submission date: end of October
- Possible future publications:
-report on changes in PGDSO
-plant phenotype terms (with phenotype RCN)
-collaborations with FNA and Morphobank
Restructuring PGDSO (2:30 PM - 6:00 PM)
Notes in this section cover our work on the goals or tasks from the both morning and afternoon.
in progress
Task 1. Clarify the domain of the PGDSO and define the root-level term accordingly
- if possible, refer to BFO or other upper-level ontology
We decided that the PGDSO should encompass only growth stages. We will use landmarks to define stages, but not include landmarks in the PO. Any developmental processes that we use as landmarks that are not already in GO can be requested.
See additional notes below under task 3.
Task 2. Develop and implement a sound naming policy
- choose between “stage” and “phase” or a combination of the two: they will be all stages
- 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)
All terms will use "stage" in their primary name. Can have phase as a synonym for gametophyte and sporophyte stage.
We agreed that we mean the same thing by stage and phase (a part of a plant life cycle), but will keep stage because it is already so widely used in the ontology. See below for definitions.
We will keep the numbers in the names, but try putting them in parentheses. Can't use square brackets because obo interprets those differently. Need to test out parentheses on dev browser.
Task 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
Whole plant development stage (PO:0007033) should be a child of plant structure development stage, because a whole plant is a plant structure. Will add new sibling terms like "collective plant structure development stage" and "plant organ development stage" so PGDSO mirrors PAO.
Now that whole plant development stage is sub-type of plant structure development stage, there is only one sub-type of plant growth and development stage, so we will merge plant structure development stage into plant growth and development stage and rename the root term "plant structure development stage".
proposed def. of plant structure development stage: A stage in the life of a plant structure during which the plant structure undergoes GO:developmental processes.
After reviewing the definition of developmental process on GO, we felt that growth should be a subtype of development, so there was no need to have both words in the names.
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.
proposed def. of whole plant development stage: A plant structure development stage that has as participant a whole plant.
Added a new term, child of whole plant development stage: life of whole plant: A maximal whole plant development stage.
Comment: There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage.
In order for the definition of life of whole plant to work (and for other reasons), we decided that seed (PO:0009010) should no longer be a subtype of whole plant. It will be is_a plant structure.
Task 4. Work existing upper- to mid-level terms into the hierarchy determined in task 3.
- write genus-differentia definitions for these terms, and check for generality
Gametophyte development stage and sporophyte development stage (formerly gametophyte phase and sporophyte phase) are direct children of whole plant development stage. These are defined as any interval between their beginning and end, so other whole plant growth stages are subtypes of gametophyte and sporophyte stages.
Existing terms for vegetative, reproductive, senescent and dormant stages are actually referring only to the sporophyte stage, so they will be made subtypes of sporophyte development stage, and renamed sporophyte vegetative development stage, etc. Corresponding stages will be created as subtypes of gametophyte stage.
We had an extensive discussion of what senescence is, and how to define the landmarks for the beginning and end of the senescent development stage. Some key points:
-Need differnt definitions for a senescent stage in a whole plant and a senescent stage in a part of a plant (like a leaf).
-Even though a plant may die from other causes before the end of normal senescence, the senescent stage of a whole plant ends with death.
Task 6. Add new mid-level terms need to describe growth or development stages for non-angiosperm plants
We looked at the list of growth and development stages requested by the Moss Ontology, and started to work on the placement and definitions for some of them.
Tasks 5 and 7:
Did not work much on these.
Dinner (6:30 PM)
Dinner at DWS's house.
