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

-need to fix top level definition (see next item), so we can incorporate all plants

Issues:

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

-how to add growth stages for non-angiosperms

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: The succession of changes leading from a zygote or meiospore to a mature plant.

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.

Do we want to keep the term plant life cycle phase?

Proposed def: A plant growth and development phase that begins with either meiosis or fertilization.

Comment: The life cycle of all plants is characterized by the alternation of phases (or generations). The sporophytic phase has twice the chromosome complement of the gametophytic phase.

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

parts of cells

We have several terms in the PO that are parts of cells. Should they stay in PO, sit in GO, or be in both? What will their parent be, if in PO?

These include:

PO:0000029 root hair tip: "Tip portion of an outgrowth of a root epidermal cell." [TAIR:ki]

This is a part of a cell, so technically outside the domain of PO, but since GO does not have it and people are likely to look here for it, it is important for us to include it.

PO:0002001 papillae: "A soft protuberance on an epidermal cell of the stigma." [ISBN:0471245208]

This is a part of a cell, so technically outside the domain of PO, but since GO does not have it and people are likely to look here for it, it is important for us to include it.

PO:0008031 trichome branch: "The branch on a trichome." [GR:cwt]

This could be a cell or part of a cell.

PO:0000028 pollen tube tip: Tip portion of the pollen tube that is rapidly growing.

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.

banana anatomy/morphology web site: http://www.ikisan.com/links/ap_bananaMorphology.shtml

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

1. Musa leaf terms

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

Proposed 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). Can add comment: generally in flattened petioles, but may also occur as extensions of petioles that are rounded or c-shaped in cross section.

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

This is a phenotype. Should annotate to leaf PO:0025034 and request PATO term for rolled. Can add cigar leaf and candle leaf as narrow synonyms of leaf.

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

Add term 'adaxial petiole': A cardinal organ part that is the adaxial portion of petiole. Comment: Adaxial petiole may be concave or form a canal. Narrow synonym: petiole canal.

Should also then add abaxial petiole, with parallel definition.

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

Organ margin (of which petiole margin is a child) is defined as 'The edge of an organ and the area immediately internally adjacent to it.' Do we want to add term organ edge? Seems a little over the top, because where do you define where the edge begins and ends relative to a margin?

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

We have the term leaf abaxial epidermis (PO:0000049). See comments above for cigar leaf.

2. Musa flower terms

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

Do we want to describe different flowers on the infloresence? If so, we could add general term basal flower: a flower at the proximal end of on an inflorescence. Comment: in Musa, the basal flowers are the first to emerge and have the potential to give rise to fruits.

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

Is this part of an inflorescence, part of an inflorescence axis?

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

This is just a phenoypic descriptor of tepal. We could add free tepal as a synonym of tepal. Need to request PATO term free. Free is the default state for tepal or other phyllomes.

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

This is really a phenotypic descriptor of a type of perianth. Use either collective tepal structure (PO:0025021) and fused (PATO:0000642) or tepal (PO:0009033) and fused (PATO:0000642).

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

We have the terms leaf base (PO:0020040) and leaf apex (PO:0020137). Suggest adding general terms phyllome base and phyllome apex, with new terms tepal base and tepal apex as children of these.

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

This is a tepal apex that is part of a fused tepal.

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

New term peduncle epidermis, is_a shoot epidermis (PO:0005679): A portion of shoot epidermis that is part of a peduncle.

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

New term: peduncle trichome: A trichome that is part of a peduncle epidermis.

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

Could be a child of the new term phyllome apex proposed above.

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

Could be a child of the new term phyllome base proposed above.

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

New term: bract abaxial epidermis, sibling to leaf abaxial epidermis, child of new term phyllome abaxial epidermis.

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

New term: bract adaxial epidermis, sibling to leaf adaxial epidermis, child of new term phyllome adaxial epidermis.

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

Do we want to add term hermaphrodite flower? Proposed definition: A flower that at maturity has as parts a a gynoecium and androecium.

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

Do we want to add term female flower? Proposed definition: A flower that at maturity has as part a a gynoecium but no androecium. Comment: Androecium may be completely absent or may be present in early developmental stages then abort.

Can have corresponding definition fro male flower.

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

Proposed definition: An inflorescence bud that develops into a male inflorescence.

If we go this route, we will need to add male, female and hermaphrodite reproductive bud, male, female and hermaphrodite inflorescence bud, male, female and hermaphrodite floral bud, and male, female and hermaphrodite inflorescence, plus the floral terms described above.

3. Musa fruit terms

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

This could be a narrow synonym of infructescence (PO:0006342). Not sure what they mean by rachis in this definition

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

Musa flower is a compound spike. A branch of the spike develops from the axil of a single bract, and when mature produces a 'hand' of fruits. All of the branches of the compound spike together, when mature, are a bunch of bananas. A hand is an inflorescence branch that matures into a branch of an infructescence.

Current definition of infructescence (PO:0006342): The grouping or arrangement in which fruits are borne on a plant, is_a shoot system, develops_from inflorescence.

First we need to properly redefine inflorescence. Current definition of inflorescence: That part of the axial system of plants above the uppermost foliage leaf/pair of foliage leaves that bears flowers, is_a reproductive shoot system.

Proposed definition of inflorescence: a reproductive shoot system that has as parts all of the shoot axes distal to the most distal foliage leaf of a shoot axis and that has as parts two or more flowers.

Proposed definition of infructescence: a reproductive shoot system that has as parts all of the shoot axes distal to the most distal foliage leaf of a shoot axis and has as parts two or more fruits. Develops_from inflorescence.

We already have the term inflorescence branch (PO:0009081: Any branch forming from the primary or the higher order inflorescence axis). Suggest modifying this slightly to: A secondary or higher order branch of an inflorescence. is_a reproductive shoot system, part_of inflorescence.

Based on this, we can add new term infructescence branch, which has the synonym hand.

Proposed definition of infructescence branch:: A secondary or higher order branch of an infructescence. is_a reproductive shoot system, develops_from inflorescence branch, part_of infructescence. Synonym: hand [narrow]

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

Probably should just annotate to whatever part of the flower it is that remains (petal, tepal, etc.)

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

This would probably be a synonym of axillary shoot, but will depend on how we end up organizing shoot system (see above).

Will probably need to be a broad synonym, because (I think) people also use the term sucker to refer to root-borne shoots.

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

Tricky. Could this be a collective phyllome structure?

o Pseudostem underlayers: Abaxial side of the inner sheath which is not visible until the outermost sheath has been removed. part_of CO_125.0000046 ! pseudostem

This is the abaxial portion of a leaf sheath (PO:0020104). We could make a new term leaf sheath abaxial epidermis (sibling of petiole abaxial epidermis, is_a leaf epidermis)

is_a completeness

List_of_terms_without_is_a_parents in numerical order

Categorized list of terms without parents

Primordium

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

Current definitions:

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

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

Suggest that we add new class primordium, as parent to these and other primordia. 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).

Right now, different types of primordia are defined consistently. Currently, there are two different types of definitions:

1. anther primordium (PO:0006089): An organized group of cells that will differentiate into anther.

2. carpel primordium (PO:0004703): The very first appearance of a carpel. It initiates from the carpel anlagen region of the floral meristem.

Currently, each type of primordium is a child of what it is the primordium of. For example, carpel primortium is_a carpel, anther primordium is_a anther. These relationships make sense with definition type 2, but not with defintion type 1.

Proposed definition of primordium: A portion of plant tissue that differentiates and develops from meristem tissue into a new organ. Comment: A visible primordium of an organ is the first distinct stage of the respective organ development. is_a portion of plant tissues (this is the same definition PJ suggested on SF, but with 'organized group of cells' changed to portion of plant tissue.

With this definition, we would have to delete all the is_a relations between types of primordia and the structure they develop into, because those relationships imply that a primordia is an organ or a collective plant structure, depending on the type of primordium (e.g., carpel primordium is_a carpel, which is_a organ, flower primordium is_a flower which is_a collective plant structure, ovule primordium is_a ovule, which is a cardinal organ part).

If we want to keep the is_a relations to the respective structures, we would have to come up with (at least) three different primordium classes: organ primordium, collective phyllom structure primordium, and cardinal organ part primordium. They could have a common parent called plant structure primordium, which would have to be a child of plant structure.

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: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]

This is somewhat different than the other terms, because it includes two guard cell and the space in between them.

>>These first two items are somewhat different than the others, because they contain both immaterial (pores) and material (cells) objects

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: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.

These terms need a new parent pore

Since a pore is an immaterial object, it cannot technically be a child of plant structure, because plant structure defined as a CARO:0000003 anatomical structure: Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.

Instead, pore should reference CARO:0000005 anatomical space: Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.

CARO's top level structure is as follows (including only the relevant terms):

Anatomical entity

>immaterial anatomical entity

>>anatomical space

>material anatomical entity

>>anatomical structure

Alternatively (or in addition) we could add upper level terms based on BFO

Parentage of trichomes and hairs

The following terms have no is_a parents:

PO:0000029 root hair tip

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

This is a part of a cell, so technically outside the domain of PO, but since GO does not have it and people are likely to look here for it, it is important for us to include it.

PO:0002001 papillae

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

subset: reference

This is a part of a cell, so technically outside the domain of PO, but since GO does not have it and people are likely to look here for it, it is important for us to include it.

PO:0008031 trichome branch

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

This could be a cell or part of a cell.

PO:0020061 coma

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

synonym: "brush" RELATED []

This is a collection of hairs, so presumably multiple cells. Maybe portion of plant tissue?

The term PO:0000282 trichome is classified as an epidermal cell, which does not work for multicellular trichomes or part of trichomes. Also, trichome has the part_of child PO:0008030 trichome cell (a cell that is part of a trichome), which does not make sense.

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

The difficulty is that trichomes can be either a cell, a part of a cell, or multiple cells.

Link to TriCHOME: A Comparative Omics Database for Plant Trichome

Pollen tube

(time permitting)

pollen tube (PO:0006345): Current definition: A tubular cell extension formed by the germinating pollen grain; carries the male gametes into the ovule. [ISBN:0471245208, Esau]

Proposed definition: A plant cell that develops from the tube cell and forms a tubular extension of the pollen grain. Comment: carries the male gametes to into or near the ovule.

(MP) Parts of the root tip

(time permitting)

We discussed most of these at last week's meeting, and folks have commented on SF. Can move through them quickly or save for phone meeting.

See suggested definitions at Categorized_list_of_terms_without_parents

6:30 PM - 8:30PM - Dinner

Dinner at a restaurant on Arthur Ave in the Bronx