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

Overview

9:00 AM - 10:00 AM LC and RW 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)

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

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

Goals for revision of PGDSO:

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

2. Develop and implement a sound naming policy

• choose between “stage” and “phase” or a combination of the two
• 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

-target journal

-target submission date

• 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.

• 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)

Continue working on goals or tasks from the morning.

Dinner (6:30 PM)

At a local restaurant, to be determined.