POC Meeting and Workshop Nov 4th to 6th, 2010; NYBG, Bronx, NY

From Plant Ontology Wiki
Jump to navigationJump to search

Minutes are available on the detailed agendas for each day.

Thursday, November 4th

Friday, November 5th

Saturday, November 6th

Dates: Thursday Nov 4th (LC and RW, DWS)

All day on Friday, November 5th (all)

Sat Morning, Nov 6th (LC, RW, PJ, DWS, MAG)


Meeting goals and priorities

Priorities for this meeting:

Ontology Goals:

-Revise upper level structure of PGDSO

-terms without is_a parents

-deal with open SF trackers- PSO and PGDSO


-Work on draft of publication/proposal for TIPS

-plan Collaborators Workshop for PAG 2011

-Plan exhibition for NYBG

-meeting with users/collaborators

-Others? Develops from/derives from relation?

Thursday, Nov 4th

Ramona and Lol work on the following items (For more details, see agenda for Thursday, November 4th ):

1. Ontology Goals: Prepare items for Friday meeting so things can be discussed efficiently

-revise upper level structure of PGDSO

Ramona and Lol will prepare suggestions for the goals for the PGDSO (from POC meeting on 10/13/2010) for discussion on Friday. See details on agenda for Friday, November 5th.

-deal with open SF trackers

Ramona and Lol will prioritize items and prepare suggested definitions for meeting on Friday.

See detailed list of open items on agenda for Thursday, November 4th

-terms with out is_a parents Ramona and Lol will prioritize these items and prepare suggested definitions for meeting on Friday.

There are still about 40 classes without parents, so we won't have time to talk about them all. Focus on terms that require new parent terms and group input

2. Publication for TIPS and/or Plant Physiology

Draft proposal to be submitted to TIPS

3. PAG Workshop planning

Friday, November 5th- 9AM - 6PM

Pankaj and Barry will both arrive between 9 and 10am

For more details, see agenda for Friday, November 5th

9am-11am-Focus on PGDSO

-Barbara Ambrose (fern evo-devo) from the New York Botanic Garden will join this part of the meeting.


finalize definition and placement of gametophytic phase and sporophytic phase

Rework definition of 'plant growth and developmental stage(s)' so it is appropriate for all plants

Reorganize the entire upper level structure of the PGDSO, so we can incorporate all plants

11AM-12PM TraitNet

Dan Bunker (New Jersey Institute of Technology) and Farshid Ahrestani (Columbia University) will present a brief overview of TraitNet and how they might interact with the PO.

12PM to1PM Lunch at Garden Cafe

Joined by Dan, Farshid, and Barbara

1PM to 2:30PM - continue work on PGSDO from morning session

-complete unfinished items from the morning

-add new plant structure development stages such as gametophytic and sporophytic structures, categories for non-seed plants (thallus development, capsule development)- time allowing

-deal with old Source Forge item: tuber growth and development stages - time allowing

2:30PM to 3PM Plans for publications

TIPS paper - target for this fall - review proposal

Plant Physiology paper - target for January, after next release

3PM to 6PM-Focus on PSO

Open Source forge tracker items, user requests

-embryo: We have a proposed definition of embryo from 7/2010. We need to finalize this and close the tracker.

-egg cell and sperm cell: we need to finalize the definitions for these terms, and make sure they work for all plants.

-reorganization of shoot system: We started working on this during the last round of revisions (with bud, and terms like reproductive shoot system), but it still needs some tweaking. Need to discuss vegetative shoot system and how it overlaps with shoot-borne shoot system (PO:0004545)

-Musa terms requested by Rosemary Shrestha (July 2010) Most of these are synonyms of existing terms.

-other items, time allowing

is_a completeness

List_of_terms_without_is_a_parents in numerical order and Categorized list of terms without parents

Priorities for this meeting:


-Parentage of pores/stomata

-Parentage of trichomes and hairs

-other items, time allowing

6:30 PM - 8:30PM - Dinner

Dinner at a restaurant on Arthur Ave in the Bronx

Saturday, November 6, 2010

For more details, see agenda for Saturday, November 6th

8AM - 12Noon

  • PlantSystematics.org discussion

-consider writing REU grant proposals to get students to help with imaging

  • Gymnosperm ATOL

-creating PO annotation from gymnosperms data sets

  • technical discussions
  • outreach- Exhibition at NYBG

-Jan Stevenson from NYBG will take part in this discussion

  • Mappings to other ontologies (?)
  • TIPS paper planning continued


Pankaj, Barry and Laurel will stay at the Hampton Inn in Yonkers.