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.

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

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)

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

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 on work on goals or tasks from the 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 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.

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 will keep the numbers in the names, but try putting them in parentheses. Can't use square brackets because obo interprets those differently.

Task 3. Develop the top levels of the PGDSO

Top level (root) term will be plant development stage'.

• 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

Task 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

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

Tasks 5 and 7: Did not work much on these.

Dinner (6:30 PM)

At a local restaurant, to be determined.