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'?

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:

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: A plant life cycle phase that arises through meiosis. [source: POC:rw] Comment: During the gametophytic phase, a plant may produce gametes by mitosis.

sporophytic phase: A plant life cycle phase that is the product of fertilization. [source: POC:rw] Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis.

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.

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 made the following request: '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 on SF: 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)

Thus any axillary shoot developments from tuber would be annotated to PO:new_B and 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.

RW: It may be better to classify tuber development as a child of a new class 'shoot axis development'. This would match the existing structure of the PSO.

Suggestion from RW on SF: May want to add a class vegetative structure development stage, with children leaf development stage (PO:0001050), root development stage (PO:0007520) and shoot axis development stage (new)

Sprout development could be considered a later stage of tuber development, in the sense that it occurs after the tuber matures and (usually) has been dormant for a while. We can link it to the term tuber axillary vegetative bu (PO:0025040)

We should make sure the definitions of these terms can apply to other tubers, and not just potatoes.

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 w=could be terminal vegetative shoot system and axillary vegetative shoot system, to match buds.

We also have the existing terms root-borne shoot system (PO:0004544) and shoot-born shoot system (PO:0004545).

Root-borne shoot system has no annotations or children, but shoot-born shoot system has the children epicomic shoot and axillary shoot.

Axilary shoot (should be shoot system) has several hundred annotations, and these could be to either vegetative or reproductive shoots.

If we have vegetative and reproductive shoot systems, then for correctness, vegetative and reproductive bud should also be children of these terms.

egg cell and sperm cell

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

Both are is_a gamete (PO:0025006)

Suggested definitions:

Egg cell: A gamete produced by an archegonium or an embryo sac.

Comment: The egg (megagamete) sually larger than the sperm (microgamete). Syn: macrogamete [exact]

Sperm cell: A gamete produced by an antheridium or a male gametophyte.

Comment: The sperm (microgamete) is usually larger than the egg (megagamete). In angiosperms, sperm cells are usually two in number; during double fertilization, one fuses with the egg cell to produce a zygote while another fuses with the two polar nuclei of the central cell to give rise to endosperm. Syn: microgamete [exact], sperm nucleus [related]

Musa terms

Requested by Rosemary Shrestha (July 2010). Most of these are synonyms of existing terms. Also see spread sheet attached to SF tracker item.

Below is a list of the requested terms, with suggested definitions and is a or part of relations (from Rosemary), followed by proposed definitions for PO format.

1. Musa leaf terms

o Petiole wing: Thin extension to the petiole margin. part_of CO_125.0000057 ! Petiole

Suggested def: A petiole margin that extends from a petiole that is otherwise rounded in cross-section. is_a petiole margin

An alternative would be to use petiole margin (PO:0025010) that is enlarged (PATO:0000586) lateral to (PATO:0001193) the petiole (PO:0020038)

o Petiole margin: In section, the narrowing margins of the petiole canal. part_of CO_125.0000057 ! petiole

We already have the term petiole margin (PO:0025010)

o Cigar leaf: Youngest visible leaf, still rolled as a cylinder. CO_125.0000002 ! leaf. syn: "candle leaf" EXACT

o Petiole canal: The upper (adaxial) canal along the petiole. part_of CO_125.0000057 ! petiole

o Petiole margin edge: Line running along the edge of the petiole margins." [ISBN:92-9043-307-8 "IPGRI-INIBAP/CIRAD. 1996. Descriptors for Banana (Musa spp.)"]. is_a: CO_125.0000006 ! petiole margins

o Cigar leaf dorsal surface: External (abaxial) face of the leaf (partly visible). part_of CO_125.0000008 ! cigar leaf

2. Musa flower terms

o Bunch: The descriptive term for all the fruits along the rachis. part_of CO_125.0000048 ! inflorescence. Syn: "infructescence" BROAD

o Basal flower: First flowers emerging on the inflorescence with the potential to give rise to fruits. part_of CO_125.0000136 ! basal bud

o Free tepal: The inner tepal which is free. is_a: CO_125.0000129 ! tepals

o Compound tepal: The outer perianth sheath of 5 fused tepals which has 3 major lobes and 2 minor ones. is_a: CO_125.0000129 ! tepals

o Crown: The raised ridge of tissue to which the pedicels are attached.

o Free tepal apex: Distal end of the free tepal that is often wrinkled. part_of CO_125.0000020 ! free tepal

o Hermaphrodite flower: Flower that contains both functional male and female parts. is_a: CO_125.0000019 ! basal flower

o Compound tepal lobe: One of the 5 free apical portions of the compound tepal. part_of CO_125.0000021 ! compound tepal

o Peduncle surface: Outer covering of the peduncle. part_of CO_125.0000039 ! peduncle

o Male bud: The usually persistent bud when it is only composed of bracts with male flowers. is_a: CO_125.0000146 ! bud; is_a: CO_125.0000146 ! bud

o Female flower: Flower containing functional female parts and non-functional male parts. is_a: CO_125.0000019 ! basal flower

o Peduncle hairs: Hairs growing on the peduncle surface. part_of CO_125.0000036 ! peduncle surface

o Bract apex: Distal end of the bract. part_of CO_125.0000052 ! male bract

o Bract external face: External (abaxial) face of the bract. part_of CO_125.0000052 ! male bract

o Bract internal face: Internal (adaxial) face of the bract. part_of CO_125.0000052 ! male bract

o Bract base: Proximal end of the bract. part_of CO_125.0000052 ! male bract

3. Musa fruit terms

o Hand of fruits: All the fruits that develop in the axil of a single bract. part_of CO_125.0000014 ! bunch

o Flower relicts: Remains of a female flower when it persists on the fruit. part_of CO_125.0000033 ! fruit

4. Musa shoot terms

o Sucker: Lateral shoot that develops from the corm and usually emerges close to the parent plant. is_a: CO_125.0000001 ! plant part

o Pseudostem: 'False stem' of cylinders formed by the concentric leaf sheaths through which the peduncle later grows. is_a: CO_125.0000001 ! plant part

o Pseudostem underlayers

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