Friday, November 5th

UNDER CONSTRUCTION

Back to POC_Meeting_and_Workshop_Nov_4th_to_6th,_NYBG,_Bronx,_NY

Pankaj and Barry will both arrive between 9 and 10am

9am-11am-Focus on PGDSO

Revise upper level structure of PGDSO (high priority items from 10-13-10

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

Reorganization of upper level structure of the PGDSO

-so we can incorporate all plants

-need to fix top level definition (see next item)

-figure out where gametophytic phase and sporophytic phase should sit. Should there be a class 'plant life cycle phase'?

gametophytic phase and sporophytic phase

These were moved to be children of whole plant growth stage (PO:0007033) and the term "plant life cycle phase (PO:0028001) was obsoleted for now till we have further discussion on it.

Proposed definitions (based on our definitions of gametophyte and sporophyte):

gametophytic phase:

sporophytic phase:

plant growth and developmental stage(s)

The top class in the PGDSO ontology has a definition that only applies to the sporophytic phase

Current def'n = The succession of changes leading from the zygote to the mature plant.

Proposed definition:

11AM-12PM TraitNet

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

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

plant structure development stage

-Should we add new classed for plant structure developmental stages for non-seed plant (e.g., thallus development, capsule development)?

-Categorize as gametophytic and sporophytic structures?

old Source Forge item: tuber growth and development stages

-This item has been open on SF since 6/2009

SGN requested the following terms:

'have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only http://www.ncbi.nlm.nih.gov/pubmed/16088399)':

-sprout development -tuber initiation -tuber growth -tuber maturation

Suggestion from PJ:

sprout development is a case of either adding synonyms or adding the new term under PO:0007073 : 2 formation of axillary shoot http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0007073

As a suggestion, we can have two siblings of this term.

PO:0007073 : 2 formation of axillary shoot -is_a- formation of axillary shoot from non-dormant shoot (PO:new_A) -is_a- formation of axillary shoot from dormant shoot (PO:new_B)

1. Thus any axillary shoot developments from tuber would be annotated to

PO:new_B

1. All the existing children of PO:0007073 : 2 formation of axillary shoot

would become children of PO: new_A

For the following three we need to come up with new terms may be for 'food storage structure development' under PO:0007021 : plant structure development stages

e.g. PO:0007021 : plant structure development stages -is_a- food storage structure development (PO:new)

---

is_a- tuber development (PO:new)

---

is_a- tuber initiation (PO:new)

---

is_a- tuber growth (PO:new)

---

is_a- tuber maturation (PO:new)

If we do this we need to first define the 'food storage structure' in the 'plant structure' section and add it as a parent term for 'tuber' as well.

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.

Proposed definition from POC meeting on 7-21-10: A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues.

Comment: Adventitious embryos and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010), including haploid embryos, are in vitro plant structures. Embryos occur prior to germination in vascular plants.

is_a whole plant

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.

The new term vegetative shoot system has been suggested, to parallel the ontology structure of bud and to go along with the new term reproductive shoot system (added during last revision).

Proposed definition: A shoot system that does not contain a reproductive shoot system as a part.

Children would be terminal vegetative shoot system and axillary vegetative shoot system.

This term may be redundant with the existing terms root-borne shoot system (PO:0004544) and shoot-born shoot system (PO:0004545).

egg cell and sperm cell

We need to finalize the definitions for these terms, and make sure they work for all plants.

• Musa terms requested by Rosemary Shrestha (July 2010) Most of these are synonyms of existing terms. Should move through them quickly.

is_a completeness

List_of_terms_without_is_a_parents in numerical order

Categorized list of terms without parents

• 1. Primordium

PO:0004725 abaxial side of leaf primordium and PO:0004726 adaxial side of leaf primordium have no is parents.

PO:0004725 abaxial side of leaf primordium def: "The abaxial/outer side of the leaf primordium that becomes the abaxial/lower leaf blade." [TAIR:ki]

PO:0004726 adaxial side of leaf primordium def: "The adaxial/inner side of the leaf primordium that becomes adaxial/upper leaf blade." [TAIR:ki]

Need a class primordium, and need to make one definition for it. Also need to organize primordium terms

We may also want to link primordia to stages in the PGDSO, where appropriate.

For example, ovule primordium (PO:0000018) participates in ovule primordium visible (PO:0007620) or ovule primordium visible (PO:0007620) has_participant ovule primordium (PO:0000018).

• 2. Parentage of pores/stomata

The following terms have no is_a parents:

PO:0002000 stomatal complex

def: "An opening pore on the epidermis of leaves and stems bordered by two guard cells and serving in gas exchange." [ISBN:0471245208]

synonym: "stoma" RELATED []

synonym: "stomata" RELATED []

PO:0006334 seed micropyle

def: "A pore on the seed coat which is a remnant of the ovular micropyle." [GR:pj]

relationship: develops_from PO:0020025 ! micropyle

PO:0008032 stomatal pore

def: "The space of variable size controlled by stomatal guard cells in response to environmental clues." [GR:cwt]

synonym: "stomatal aperture" RELATED []

relationship: part_of PO:0002000 ! stomatal complex

PO:0008044 floral stomatal complex

def: "An opening pore on the epidermis of floral organs bordered by two guard cells and serving in gas exchange." [GR:cwt]

PO:0008046 floral stomatal pore

def: "The space of variable size controlled by floral stomatal guard cells in response to environmental clues." [GR:cwt]

relationship: part_of PO:0008044 ! floral stomatal complex

PO:0020025 micropyle

def: "A small canal or opening through the integument(s) at the apex of an ovule." [APWeb:Glossary]

comment: In a mature seed the micropyle may remain visible as an occluded pore or may be obliterated. The micropyle originates as an opening in the integuments of an ovule through which the pollen tube usually enters the embryo sac.

subset: reference

PO:0020101 stomium

def: "A fissure or pore in the anther lobe through which the pollen is released." [GR:pj]

subset: reference

relationship: part_of PO:0005011 ! anther dehiscence zone

TraitNet has requested the term anther pore, which could be a synonym of stomium.

• 3. Parentage of trichomes and hairs

The following terms have no is_a parents:

PO:0002001 papillae

def: "A soft protuberance on an epidermal cell of the stigma." [ISBN:0471245208]

subset: reference

PO:0000029 root hair tip

def: "Tip portion of an outgrowth of a root epidermal cell." [TAIR:ki]

PO:0008031 trichome branch

def: "The branch on a trichome." [GR:cwt]

PO:0020061 coma

def: "A tuft of hairs at one end of a seed." [APWeb:Glossary]

synonym: "brush" RELATED []

Furthermore, the term PO:0000282 trichome is classified as an epidermal cell, which does not work for multicellular trichomes, especially since it has the part_of child PO:0008030 trichome cell (a cell that is part of a trichome).

Also, we were pollen tube PO:0006345, which may have some similarity to these terms, since it is a cilindrical outgrowth of a cell.

6:30 PM - 8:30PM - Dinner

Dinner at a restaurant on Arthur Ave in the Bronx