POC Conf. Call 3-8-11

POC meeting, Webex Conference Call; Date: Tuesday Mar 8th, 2011 10am (PST)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_3-1-11?

Physcomitrella terms, continued

Shoot apical meristem/apical cell/phyllome

MO has requested the term apical cell.

We already have the term apical cell (PO:0004000), which is an embryonic cell: "An embryonic plant cell that is the uppermost cell formed after the first division of the zygote." Suggest renaming PO:0004000 "embryonic apical cell" for clarity. The embryonic apical cell can also be found in non-angiosperms.

Growth in mosses (and other bryophytes?) results from divisions of a single apical cell. Branches or leaves form from division and differentiation of sub-apical cells. Mosses do not have an apical meristem in the same sense as vascular plants.

If we define apical cell as is_a meristematic cell, we will have a problem. Even though apical cell is consistent with the definition of meristematic cell (synthesizing protoplasm and producing new cells by division and with only a primary cell wall), it is not consistent with the relation meristematic cell part_of meristem. A meristem is a portion of tissue and therefore two or more cells. We could solve this problem by changing meristematic cell part_of meristem to meristem has_part meristematic cell.

Proposed def. of apical cell: A meristematic cell at the apex of a gametophore or non-vascular leaf (phyllid).

Comment: Occurs in mosses and other bryophytes.

Apical cells also cause an issue with or definition of phyllome (PO:0006001): "A lateral plant organ produced by a shoot apical meristem." This definition is not strictly applicable to non-vascular leaves, which are phyllomes. Suggest we tweak the definition of phyllome to allow for this.

Proposed def. of phyllome: A plant organ produced by the lateral portion of a shoot apex.

Comment: In vascular plants, phyllomes arise from the shoot apical meristem. In non-vascular plants, phyllomes arise from division of a sub-apical cell (sometimes referred to as a leaf initial).

Collective plant structures:

gametophore

Def'n supplied by MO: The leafy moss plant. The gametophore is the adult form of the moss gametophyte and bearer of the sex organs (gametangia).

Ref: Reski (1998): Development, genetics and molecular biology of mosses. Botanica Acta 111, 1-15.

Suggest is_a shoot system.

Proposed def'n.: A shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase. participates_in gametophytic phase

Comment: A gametophore is the leafy part of a moss gametophyte, without the protonema. Antheridia and archegonia arise on the gametophore.

gametophore bud

The term "bud" has been requested: Def'n supplied by MO: A structure produced by a caulonema and able to develop into a gametophore or a stem that includes an apical cell able to develop into a gametophore. The earliest recognizable stage of gametophore development.

Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered by David Cove

Suggest a new term gametophore bud. This could be a child of bud (PO:0000055: An undeveloped shoot system).

Proposed def'n: A bud on a protonema that develops into a gametophore. participates_in gametophytic phase

Comment: Occurs in mosses.

Plant organs:

cauloid

- This is the term used for the gametophore stem or axis.

Suggest using gametophore axis as primary name, cauloid as synonym.

Proposed def'n: A plant axis that is part of a gametophore. is_a plant axis, part_of gametophore, participates_in gametophytic phase

Synonyms: cauloid, gametophyte axis

Also suggest adding terms for gametophore stem and gametophore branch (similar to stem and branch).

perigonial bract

- The specialized phyllids surrounding the antheridia.

Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

A bract (PO:0009055) is defined as: A phyllome, usually different in form from the foliage leaves, subtending a reproductive structure. [source: POC:curators] Comment: Often used to refer to what is called here floral bract.

Proposed def'n: A bract that subtends an antheridium. part_of gametophore, participates in gametophytic phase

Comment: When an antheridium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually perigonial bracts. If an antheridium occurs on a main axis of the gametophore, usually only the terminal phyllomes are perigonial bracts.

Additional moss terms:

These were not requested by the Physcomitrella group, but they are related to the terms above and are commonly used to describe mosses, so we may as well add them now.

perichaetal bract

Proposed def'n: A bract that subtends and archegonium. part_of gametophore, participates_in gametophytic phase.

Comment: When an archegonium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually parichaetal bracts. If an archegonium occurs on a main axis of the gametophore, only the terminal phyllomes are usually parichaetal bracts. The two or three terminal-most perichaetal bracts may fuse to form a gametophytic perianth.

gametophytic perianth

Proposed def'n: A collective phyllome structure that consists of two or more of the most distal parachaetal bracts on an axis that are fused laterally and surround the calyptra.

Should it be surrounds the capsule, in case no calyptra is present?

-has_part parachaetal bract, part_of gametophore, participates_in gametophytic phase, disjoint from perianth (PO:0009058)

Comment: The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.

seta

-The stalk of a moss sporophyte.

Suggested def'n: A plant axis that that holds up a spore capsule. participates_in sporophytic phase

Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

Cardinal organ parts

Terms requested by MO:

calyptra

base

peristome

theca

lid

foot

neck canal

Other terms, not from MO

epiphram

spore capsule mouth

pseudopodium

venter

Plant Tissues

paraphyllium - Tiny filaments, scales or leaf-like structures scattered on the stems of some leafy bryophytes. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

Crum defines them as "Small green outgrowths formed between the leaves on stems and branches of some pleurocarps (mosses that produce archegonia and sporophytes laterally, rather than on the tips of their axes) and a very few leafy liverworts."

Schofield describes paraphyllia as outgrowths of the epidermis, but he also describes leaves that way.

MO has this listed as a plant organ

Proposed definition: A phyllome/portion of plant tissue that is a small filamentous, scale-like, or leaf-like outgrowth from the epidermis between the leaves of a gametophore axis.

Comment: Paraphyllia are much smaller than leaves. Found in pleurocarpous mosses and a few leafy liverworts.

The paraphyllia are the small, dark structures between the leaves.

midrib

rhizoid

archesporium

amphithecium

endothecium

jacket layer

paraphysis

axilliary hair

tmema

Plant Cells

Terms requested by MO:

archesporial cell

apical cell

shoot apical cell

phyllid apical cell

alar cell

brachycyte

chloronema cell

caulonema cell

tmema cell

jacket layer cell

axillary hair terminal cell

axillary hair base cell

neck canal cell

side branch initial

Other terms, not requested by MO:

hyrdoid

leptoid

rhizoid initial

Upcoming meetings 2011:

* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York

ICBO

LC contributed to the workshop proposal "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" Authors: Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland and Laurel Cooper

Submitted: February 15th, 2011

- LC will attend and represent the PO. Invite other plant people? Will talk with Elizabeth Arnaud at the upcoming meeting.

-BS suggested we might want to submit a short paper which could be published in longer form later- see above

*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Early-bird registration ends May 13.

Abstract deadlines: Your abstract must be submitted by March 11 if you want it to be considered for a minisymposium talk.

For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

See IBC 2011 Bio-Ontologies Symposium wiki page for more details