POC Conf. Call 3-22-11
POC meeting, Webex Conference Call; Date: Tuesday Mar 22nd, 2011 10am (PST)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_3-15-11?
Issues arising from last week's meeting:
Conference call
Physcomitrella terms
May want to use the name plant gametangium, to make it clear that we are not including algae.
Current definitions:
plant gametangium (PO:0025124): A cardinal organ part that is part of a whole plant in the gametophytic phase and produces gametes.
antheridium (PO:0025125): A gametangium that produces antheridium sperm cells.
archegonium (PO:0025126): A gametangium that produces archegonium egg cells.
megagametophyte (PO:0020092): A gametophyte that produces female gametes.
microgametophyte (PO:0020091): A gametophyte that produces pollen sperm cells.
Problems with these defintions:
Definitions of mega/microgametophyte don't work, because we no longer have the term gametophyte to use as a genus.
Need definitions that distinguishes gametangia from megagametophyte (embryo sac) and microgametophyte (pollen). Could use only in taxon/never in taxon relations here.
The definitions are circular (see definitions below of egg cell and sperm cells):
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.
antheridium sperm cell (PO:0025120): A sperm cell that is produced by an antheridium.
pollen sperm cell (PO:0025121): A sperm cell that is produced by a microgametophyte.
Finally, having both sets of egg and sperms cells seems redundant. They were put in to satisfy the part_of relations. We could get around this by using has_part relations, but maybe we dont' want to?
Here is an image of the current PO, showing only female parts:
Here is how it would look using has_part relations:
In this image, archegonium egg cell and embryo sac egg cell have been merged with egg cell.
On the other hand, keeping the separate types of egg cells in this case would not cause too much term inflation, because they don't have any part_of children.
May want to merge embryo sac with female gametophyte. It is the only child of female gametophyte, suggesting they are redundant. This would be analogous to our current situation of having pollen grain as a synonym of microgametophyte.
OR, maybe we need the terms mega- and microgametophyte for bryophytes (and ferns?) that produce separate male and female plants in the gametophytic stage. Should there be classes for that, or is it better to post-compose whole plant in gametophytic phase with male or female from PATO (like for flowers)?
Proposed new definitions:
plant gametangium (PO:0025124): A plant organ that produces gametes. (how to distinguish this from a carpel?)
Comment:
disjoint_from megagametophyte; only_in_taxon bryophytes plus pteridophytes plus gymnosperms
antheridium
From Schofeld: The multicellular male sex organ of bryphytes that consist of a stalked sac containing many sperms enclosed by a unistratose sterile jacket of cells.
From Parihar: The male sex organ of the cryptograms
proposed definition: A gametangium
only_in_taxon bryophytes plus pteridophytes or never_in taxon seed plants?
archegonium
From Schofeld: The flask-shaped multicellular sex organ that conatins a single egg
From Parihar: The female sex organ of bryophytes, pteridophytes and gymnosperms.
proposed definition:
only_in_taxon bryophytes plus pteridophytes plus gymnosperms or never_in taxon angiosperms?
megagametophyte/embryo sac (PO:0020092): A whole plant in the gametophytic phase that is contained in an ovary and produces an egg cell.
microgametophyte/pollen grain (PO:0020091): A whole plant in the gametophytic phase that develops from a microspore within a pollen sac and produces pollen cells.
apical cell
Moss Ontology has requested the term apical cell. Apical growth in byrophytes is via division of a single cell at the tip of the shoot apical meristem.
Non-seed vascular plants can also have an apical cell, that is a single dividing cell at the apex of a root or shoot.
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." The embryonic apical cell can also be found in non-angiosperms. Suggest renaming PO:0004000 embryonic apical cell for clarity and using the name apical cellfor the term described below. May want to obsolete PO:0004000 and replace with the two new terms, to avoid confusion in the names.
Definition of apical cell from Esau: The single initial cell in an apical meristem of root or shoot. Characteristic of many lower vascular plants.
Definition of apical cell from Crum: A single cell at the tip of a stem, leaf, leaf or other structure that divides repeatedly to form new cells; also known as an apical intial.
Is apical cell more consistent with meristematic cell (A cell synthesizing protoplasm and producing new cells by division and with only a primary cell wall) or with initial cell (A meristematic cell that by division gives rise to two cells, one of which remains meristematic, while the other is added to the plant body)? Probably meristematic cell, because the apical cell can give rise to more than two cells (because it can have three or four cutting faces).
Proposed def. of apical cell:A single meristematic cell at the tip of a shoot apex or root apex
Comment: Occurs in bryophytes and some pteridophytes, where apical growth results from division of a single meristematic cell located at the tip of the apical meristem, rather than from a population of meristematic cells located at the tip of the apical meristem. May be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge shaped with two cutting faces (in non-vascular leaves).
Do we need separate terms for sporophytic apical cell and gametophytic apical cell?
gametophytic apical cell: A meristematic cell at the apex of a gametophore or non-vascular leaf.
Comment: Occurs in mosses and other bryophytes. participates_in gametophytic phase
sporophytic apical cell: An apical cell that is part of a shoot apical meristem of a plant in the sporophytic phase.
Comment: Occurs in Pteridophytes (and in the sporophyte of bryophytes?). participates_in sporophytic phase
Moss ontology also requested shoot apical cell and phyllid apical cell.
Proposed names and definitions:
gametophore apical cell: A gametophytic apical cell at the tip of a gametophore.
Comment: Divides to produces leaf initial cells and other stem tissues.
OR shoot apical cell: An apical cell at the tip of a shoot apical meristem.
phyllid apical cell: A gametophytic apical cell at the tip of a non-vascular leaf.
Comment: Divides to produce non-vascular leaf tissues.
(ref: 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. 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.
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 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 that surround the calyptra.
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.
Suggested def'n: 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 the basal part of an archegonium wall (the venter) and surrounds the 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 be carried upward as the seta elongates.
(Definition suggests that we should add a term for archegonium wall, is_a gametangium wall)
- 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
Need to look up if we should add separate terms for , or add as synonyms.
Proposed name and def.: sporangium base: The basal part of a sporangium.
Comment: 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. Term used in mosses and other bryophytes (what about pteridophytes?)
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.
Proposed name and def.: sporangium theca: The main body of the sporangium that contains the spores.
Comment: Term used in mosses and other bryophytes (what about pteridophytes?)
- foot
Moss Ontology definition: The base of the sporophytes in mosses
Proposed name and def.: sporophyte foot: The base of a sporophyte, below the seta, that attaches it to the gametophore. (From Schofeld)
Comment: Found in mosses (and other bryophytes?). The sprophyte foot serves for both attachment and absorption. The outer portion of the foot is the absorptive haustorium. (From Crum)
- Can add term for sporophyte foot haustorium when we deal with portions of plant tissue. Contains transfer cells.
- 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.
- 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 partially 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.
- venter part of an archegonium
- neck (can also add neck canal cell when we deal with cells)
Upcoming meetings 2011:
* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York
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)
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. Invite other plant people?
-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
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.
* 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
