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 that is angiosperm-centric
• existing leaf terms mostly for angiosperms
• is_a and part_of relations have not been used consistently for subtypes

Possible Goals for revision of PGDSO

1. Compliance with OBO Foundry guidelines and best practices

• provide is-a parents for all terms {only a few left: imbibition (PO:0007022), seedling growth (PO:0007131), and shoot emergence (PO:0007130)}
• provide accurate names for terms
• provide accurate text definitions for all terms in genus-differentia form

2. Alignment with BFO

• define root node in relation to a BFO or other upper-level ontology term
• 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

3. 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

4. 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)

5. Develop PGDSO terms needed to describe plant phenotypes/traits

Work on goals and tasks for revision (10:00 AM - 12:30 AM)

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.

Lunch (12:30 PM - 1:30 PM)

Walk to Garden Cafe for lunch.

Dinner (6:30 PM)

At a local restaurant, to be determined.