POC Conf. Call 3-29-11

POC meeting, Webex Conference Call; Date: Tuesday Mar 29th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_3-22-11?

Physcomitrella and related terms

Collective plant structures:

Discussion of the items below was postponed until next week.

gametophore

Definition 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.: 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. Gametophores develop from buds that form on the caulonema. 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 that develops on a caulonema 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

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.

foot

Moss Ontology definition: The base of the sporophytes in mosses

Proposed name and def.: sporophyte foot: A plant organ (?) that is the base of a whole plant in the sporophytic phase, below the seta, that attaches it to the gametophore. (ref: Schofeld)

Comment: Found in bryophytes. The sprophyte foot serves for both attachment and absorption. The outer portion of the foot is the absorptive haustorium. (From Crum)

participates_in sporophytic phase, has_part transfer cell, only_in_taxon bryophytes (I know this isn't a clade, will have to create a pseudo-clade).

- Should we add a term for sporophyte foot haustorium when we deal with portions of plant tissue or is the whole foot the haustorium?

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 should add them now.

perichaetal bract

Proposed def'n: A bract that subtends an archegonium. part_of gametophore

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 a gametophore axis and surround the calyptra (capsule?).

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

-has_part parachaetal bract, part_of gametophore, disjoint_from perianth (PO:0009058)

Comment: The parachaetal bracts may fuse laterally in the gametophytic perianth. The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.

seta

-The stalk of a moss sporophyte.

Proposed def.: A plant axis that that holds up a spore capsule. participates_in sporophytic phase

Comment: Found in mosses.

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.

We also have a request (from PJ) for calyptra, which is part of the fruit in Eucalyptus. That term should be named fruit calyptra (see below under operculum), and this term should be named spore capsule calyptra, to distinguish them.

Proposed name and def.: spore capsule calyptra: A cardinal organ part that develops from a venter and surrounds a sporangium.

Comment: Found in mosses and pteridophytes. The calyptra ia a membranous or hairy cap composed of gametophytic tissue that protects the embryonic sporophyte within the archegonium. In some species, the calyptra may persist after the sporophyte develops and gets carried upward as the seta elongates.

participates_in gametophytic phase, develops_from venter

• venter

This term was not suggested by Moss Ontology, but perhaps we should add it.

proposed def.: A cardinal organ part that is the enlarged basal part of an archegonium and contains an egg cell.

part_of archegonium

• archegonium neck

This term was not suggested by Moss Ontology, but perhaps we should add it.

proposed def.: A cardinal organ part that is the elongated apica part of an archegonium.

Comment: Early in development, the neck is occluded by a single row of neck canal cells. At maturity, the neck canal cells disintegrate, creating a canal for the sperm to enter the archegonium.

part_of archegonium

(can also add term for neck canal cell when we deal with cells)

• 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

Proposed name and def.: sporangium base: A cardinal organ part that is the basal part of a sporangium.

Comment: Term used in mosses and other bryophytes (what about pteridophytes?). The sporangium base is the sterile part of the sporangium below the theca. If swollen and distinct from the rest of the sporangium, it is called an apophysis or hypophysis.

part_of sporangium; Synonyms: sporangium neck, apophysis, and hypophysis

• 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. Maybe we should call that anther theca and call this term sporangium theca:.

Proposed name and def.: sporangium theca: A cardinal organ part that is the main body of a sporangium that contains the spores.

Comment: Term used in mosses and other bryophytes (what about pteridophytes?)

• 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

proposed definition: A cardinal organ part that is a single or double circle of teeth inside a spore capsule mouth.

Comment: The peristome is located under the operculum, if an operculum is present. Upon maturity of a capsule, the teeth of the peristome open to release the spores.

• peristome tooth

Not requested by Moss Ontology, but should add it.

Proposed def: A cardinal organ part that is a single lobe or tooth of a peristome.

• lid/operculum

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.

We also have a request (from PJ) for operculum, which is part of the fruit in Eucalyptus. That term should be named fruit operculum, and this term should be named spore capsule operculum, to distinguish them.

Proposed name and def.: spore capsule operculum: A cardinal organ part that is the apical part of a spore capsule that separates from the rest of the capsule during dehiscence.

Comment: Found in mosses. May remain partly attached to the rest of the capsule.

Also add:

fruit operculum: A cardinal organ part that is the apical part of a capsular fruit that separates from the rest of the capsule (the fruit calyptra) during dehiscence. part_of fruit

Comment: Found in Eucalyptus.

Is is a cardinal organ part (formed from a single carpel) or collective organ part structure (formed from parts of multiple carpels)?

fruit calyptra: A cardinal organ part that is the basal part of a capsular fruit that separates from the fruit operculum during dehiscence. part_of fruit

Comment: Found in Eucalyptus. The capsule may remain attached to the plant after the fruit operculum dehisces.

Other related terms for mosses, not from Moss Ontology

• spore capsule mouth

Proposed definition: A plant anatomical space that is the opening on the distal end of a spore capsule.

Comment: The mouth is formed when the operculum separates from the capsule. The mouth may be covered by a peristome.

• epiphram

Schofeld says it is a "membranelike expansion of the columella covering most of the mouth of the sporangium in Polytrichidae (hair cap mosses)."

From Crum: "A circular membrane at the tip of the columella to which the peristome teeth of the prolytrichaceae are attached."

Proposed definition: A portion of plant tissue that forms a circular membrane extending from a spore capsule collumella and attached to the ends of the peristome teeth that covers a spore capsule mouth.

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

What kind of tissue is it?

• pseudopodium

From Crum: "An elongation of the gametophytic axis on which the capsule is borne in Sphagnum and Andreaea."

From Schofeld: "An elongated mass of leafless gaemtophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."

Proposed definition: An extension of a gametophore axis on which a spore capsule is borne.

Comment: Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.

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 outgrowth from the epidermis between the leaves of a gametophore axis.

Comment: Paraphyllia are much smaller than leaves and may be filamentous, scale-like, or leaf-like. 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 (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