POC Conf. Call 3-15-11

POC meeting, Webex Conference Call; Date: Tuesday Mar 15th, 2011 10am (PST)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_3-8-11?

Issues arising from last week's meeting:

Special technical meeting?

Physcomitrella terms

Gametangium, antheridium, archegonium

May want to use the name plant gametangium, to make it clear that we are not including algae.

Proposed definitions:

Plant gametangium: A cardinal organ part (?) that is part of a whole plant in the gametophytic phase and produces gametes.

(need to distinguish this from embryo sac somehow)

Antheridium: A gametangium that produces antheridium sperm cells.

Archegonium: A gametangium that produces archegonium egg cells.

We also have the terms:

archegonium egg cell (PO:0025122): An egg cell that is produced by an archegonium.

embryo sac egg cell (PO:0025123): An egg cell that is produced by a megagametophyte.

These two sets of definitions are circular. Need better defs for antheridium and archegonium.

apical cell

Moss Ontology 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. The moss apical meristem may differ from that of vascular plants, but it is still possible to call it an apical meristem.

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). Meristematic cell is part_of meristem, and a meristem is a portion of tissue and therefore two or more cells. We do not need to add apical cell part of apical meristem, but logically it will be part of a meristem.

Non-seed vascular plants can also have an apical cell, similar to bryophytes. Suggest we add separate terms for sporophytic apical cell and gametophytic apical cell.

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

Comment: Occurs in mosses and other bryophytes. Something about how it divides.

Proposed def. of gametophytic apical cell: A meristematic cell at the apex of a shoot apical meristem that ...something about being distinct from other cells at the apex and/or about being a single cell rather than an undistiguishable group of cells.

Comment: Occurs in lycopods and ferns (what about Psilotum?).

Moss ontology also requested shoot apical cell and phyllid apical cell.

shoot apical cell: A cell at the tip of the shoot that divides to produces leave initial cells and ohter stem tissues. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

phyllid apical cell: A cell at the tip of the phyllid that divides to produce phyllid tissues. C. Jill Harrison et al. (2009): Local Cues and Asymmetric Cell Divisions Underpin Body Plan Transitions in the Moss Physcomitrella patens.

Collective plant structures:

gametophore

Def'n supplied by Moss Ontology: 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 Moss Ontology: 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

Cardinal organ parts

Terms requested by MO:

• calyptra

Moss Ontology definition: A membranous or hairy cap or hood that forms from the wall of the archegonium and protects the embryonic sporophyte. It is formed from the archegonium by mitotic divisions, and hence it is haploid. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered from David Cove.

• base

Moss Ontology definition: The sterile bottom of the sporangium. Also called neck or if swollen apophysis or hypophysis. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

• peristome

Moss Ontology definition: A single or double circle of teeth inside the mouth of a moss sporangium. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

• theca

Moss Ontology definition: The main body (urn) of a sporangium. Altered from Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

We already have the term theca (PO:0009069) to describe paired microsporangia in angiosperms.

• lid

Moss Ontology definition: Either the lid that blocks the capsule mouth or the apical portion of a sporangium that opens during dehiscence. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

• foot

Moss Ontology definition: The base of the sporophytes in mosses

• neck canal

Moss Ontology definition: A stalk of made of gametophytic tissue that holds up a sporangium (different from seta, which is sporophytic)

Other cardinal organ part terms for mosses, not from Moss Ontology

• epiphram

A portion of plant tissue that forms a circular membrane that is attached to the ends of the peristome teeth and covers the mouth.

Comment: Present in some moss species of the family Polytrichaceae.

• spore capsule mouth

• pseudopodium

• venter

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 (Accepted) LC is working with the other organizers to develop the workshop plans and a call for papers.

Full-Day Workshops Schedule:

July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies

July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

July 26 6.30pm-9pm Evening Workshop: Common Logic

July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium

- LC will attend and represent the PO, will submit a short paper/poster for the workshop (deadline April 1st).

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

Plant Biology 2011

Early-bird registration ends May 13.

Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.

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.

TAIR is organizing an Outreach Booth and we are invited to take part.

* 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.

Early bird registration deadline - Extended 1 March 2011 Deadline for registration by presenters 1 March 2011

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