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:

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

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.

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.

After the meeting, we tested it and it worked fine germination

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.

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).

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
• 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

We 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

Specific tasks for achieving the goals outlined above

Notes in this section cover our work on the goals or tasks from the both morning and afternoon.

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 development 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.

from the Google doc:

New Top level term: Plant Structure Development Stage: proposed def'n: A stage in the life of a plant structure during which the plant structure undergoes GO:developmental processes.(POC curators)

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.

We will not have a term plant life cycle as a child of plant structure development stage, because there is not single plant structure that participates in an entire life cycle.

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.

proposed definition, gametophyte development stage: A whole plant development stage that has as a participant a whole plant during the interval between meiosis or apospory and its death or fertilization.

proposed definition, sporophyte development stage: A whole plant development stage that has as a participant a whole plant during the interval between fertilization or apogamy and its death.

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.

proposed definition, senescence: A plant structure development stage that is (1) initiated by an event of cell death within the plant structure, (2) terminated in the death of the plant structure in such a way that (3) the former is connected to the latter by processes of dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism. [source: POC:curators, BS]

This definitions can be modified for specific structures (like sporophyte, gametophyte, leaf, etc.).

proposed definition, gametophyte reproductive development stage: A gametophyte development stage that is initiated with the development of a gamete producing structure and terminated with fertilization.

Comment: Some gametophytes may dies before fertilization.

proposed definition, gametophyte vegetative development stage: A gametophyte development stage that succeeds spore germination and ends with the formation of gametangia.

Worked on new children of gametophyte reproductive development stage and gametophyte vegetative development stage. Whole plant development stages that are named after a plant structure that is not a whole plant will need to have the words "whole plant" in their name, to distinguish them from other structure development stages. For example, gametophore reproductive whole plant development stage is a whole plant development stage, while gametophore development stage is a stage in the development of an individual gametophore.

proposed definition, gametophore reproductive whole plant development stage (needs work): A gametophyte reproductive development stage in which gametophores and gametangia are being produced.

proposed definition, gametophore vegetative whole plant development stage (needs work): A gametophyte vegetative whole plant development stage during which a gametophore is being produced but no gametangia are being produced. Succeeds a protonema stage.

proposed definition, protonema whole plant development stage (PO:0030006): A gametophyte development stage during which a gametophyte undergoes filamentous growth. This succeeds spore germination and precedes a thalloid development stage (planar growth) or gametophore development stage.

Can also add new terms for thalloid reproductive whole plant development stage and thalloid vegetative whole plant development stage.

Task 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

Did not work much on this. We can do more on this as we move forward

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.

Terms like gametangium development stage (their gametangia development stages), gametophore development stage, protonema developmental stage, or spore development stage will be subtypes of "plant structure development stage".

Their term "gametophore growth" appears to be referring to what we have called the "gametophore whole plant vegetative development stage".

Task 7: Determine which relations are needed to link the PAO and PDSO

• participates_in and variants
• has_participant and variants
• others

Is there a way we can implement color coding the Anatomy and Development terms differently so that when they display under the other aspect it is clearer where they came from? This was a suggestion raised by PJ during the discussion of the cross-ontology relations.

This has been added to the POC_Technical_Issues_Page for consideration

OBO Foundry application

BS said that the OBO foundry is working on a form to send to applicants. We can fill that in once it is available.

We also need a PO web/wiki page that shows the annotations by source database and links to those pages where the PO is featured.

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).

Comment from BS: In order to improve the chances of getting this accepted by Plant Physiology, it would be good to reduce the focus in the beginning section on the "update" and offer it as a new work.

-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

Dinner

Dinner at DWS's house.