POC Conf. Call 4-5-11
POC meeting, Webex Conference Call; Date: Tuesday Apr 5th, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_3-29-11?
Issues arising from last week's meeting:
Collective plant structures:
vascular and non-vascular shoot systems
The Moss Ontology did not request these terms, but suggest adding them in order to classify shoot systems.
non-vascular shoot system: A shoot system that does not have as part a vascular system (or vascular tissue?).
comment: Does not have any xylem of phloem, but may have other conducting cells, such hydroids or leptoids. Can occur in both the gametophytic and sporophytic phases of non-vascular plants.
subsets for bryophytes and pteridophytes
Could we use the relation "lacks_part"? Then we could define this class using intersection_of relations, which would be better. CL has used this (lack_plasma_membrane_part). Works better in OWL; translates into something like has_part exactly 0 (some ?Y) [need to check this].
Children of non-vascular shoot system will be gametophore (see below) and thallus. If we used the lacks_part relation and intersection_of relations, we could make gameotophore a child of shoot system, and the reasoner would infer it was a non-vascular shoot system.
Can't use participates_in gametophyric phase, because the sporophyte of a bryphyte is also a non-vascular shoot system (since it doesn't have roots or vascular tissue).
vascular shoot system: A shoot system that has as part a vascular system (or vascular tissue?).
comment: Has xylem and/or phloem. Occurs only in the sporophytic phase of vascular plants.
participates_in sporophytic phase, has_part vascular system
If we accept these terms, suggest changing definitions of leaf and non-vascular leaf to "A leaf that is part of a non-vascular/vascular shoot system. This would be better than the current definitions which reference their taxonomy (part of a vascular or non-vascular plant) and would help with reasoning.
root-bourne shoot system (PO:0004544) should be is_a vascular shoot system
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 non-vascular 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 the gametophyte of mosses and leafy liverworts, excluding the protonema. In mosses, gametophores develop from buds that form on the caulonema. Antheridia and archegonia arise on the gametophore.
This will work as long as we can call the shoot system in leafy liverworts a gametophore as well.
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 into a gametophore.
Comment: Occurs in mosses (and leaf liverworts?). Develops from a caulonema cell in mosses.
participates_in gametophytic phase, has_part shoot axis apical cell
Thallus
From Parihar: A simple vegetative plant body not differentiated into root, stem and leaf, and lacking vascular tissues.
From Schofeld: A flattened gametophore in which no leaf-like organs dominate the structure.
Saying a thallus is a gametophore implies that it is a shoot system and therefore a collective plant structure (CPS). As a CPS, it must have more that one organ. This is not always true for a thallus (sometime they branch, so you could say they have multiple axes, but it is a stretch. Maybe better to classify it as a whole plant.
alternative proposed definitions:
1) A flat gametophore with no distinct organs.
Comment: A thallus is a whole plant in the gametophytic phase in liverworts and pteridophytes and develops from a short-lived protonema. Roughly two dimensional growth results from division of a single apical cell. Although there are no distinct organs, there may be tissue differentiation and dichotomous branching.
or
2) A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.
Comment: A thallus is a gametophyte of liverworts and pteridophytes and develops from a short-lived protonema. Roughly two dimensional growth results from division of a single apical cell. Although there are no distinct organs, there may be tissue differentiation and dichotomous branching.
Add prothallium (for ferns) as a synonym?
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. They also requested shoot apical cell and phyllid apical cell.
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. a 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, leaf apex, root apex, or gametophore 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). An apical cell is established upon the first cell division of an embryo or germination of a spore.
-note: the last sentence of the comment allows us to classify an embryonic apical cell as an apical cell.
Suggested ontology structure for the children of apical cell:
The dotted lines represent relations inferred by the reasoner.
Includes two ways of classifying: by structure and by gametophyte/sporophyte. Structural relations are asserted as is_a relations. The relations to gametophyte or sporophyte are inferred by the intersection_of terms.
New terms and definitions for apical cells
gametophytic apical cell: An apical cell that is part of a whole plant in the gametophytic phase.
Comment: Occurs in mosses and other bryophytes.
intersection_of: is_a apical cell, intersection_of: participates_in gametophytic phase
sporophytic apical cell: An apical cell that is part of a whole plant in the sporophytic phase.
Comment: Occurs in pteridophytes and the sporophyte of bryophytes.
intersection_of: is_a apical cell, intersection_of: participates_in sporophytic phase
root apical cell: A sporophytic apical cell that is part of a root apical meristem.
comment: Only occurs in the sporophytic phase of vascular plants.
part_of root apical meristem
shoot apical cell: An apical cell that is part of a shoot system.
comment: May occur in shoot axes or leaves of bryophytes or ferns.
part_of shoot system
gametophore apical cell: A shoot apical cell that is part of a gametophore.
comment: Occurs in the non-vascular shoot system of the gametophyte of mosses.
intersection_of: is_a shoot apical cell, intersection_of: part_of gametophore
thallus apical cell: A gametophore apical cell that is part of a thallus.
comment: We still need to add the term thallus.
part_of thallus (once we add it)
leaf apical cell: A shoot apical cell that is part of a leaf apex.
comment: Occurs in the non-vascular leaves of bryophytes and the vascular leaves of some mosses. Only in plants where leaf growth is apical.
part_of leaf
non-vascular leaf apical cell: A leaf apical cell that is part of a leaf apex of a non-vascular leaf.
comment: Occurs in the non-vascular leaves of bryophytes, which grow by division of a single, wedge-shaped apical cell with two cutting faces.
part_of non-vasucular leaf; synonym: phyllid apical cell
vascular leaf apical cell: A leaf apical cell that is part of the leaf apex of a vascular leaf.
comment: Occurs in vascular leaves of some ferns in their sporophytic phase.
part_of vascular leaf
shoot axis apical cell: An apical cell at the tip of a shoot apical meristem.
Comment: Divides to produces leaf initial cells and other stem tissues.
part_of shoot apical meristem
gametophore axis apical cell: A shoot axis apical cell at the tip of a gametophore axis.
Comment: Occurs at the tips of the stems and branches of bryophytes.
part_of gametophore axis; synonym: cauloid apical cell, non-vascular shoot axis apical cell
vascular shoot axis apical cell: A shoot axis apical cell at the tip of a shoot apical meristem in a vascular shoot system.
Comment: Occurs in some ferns in their sporophytic phase.
part_of vascular_shoot system; synonym: fern shoot axis apical cell
Also:
embryonic apical cell (PO:0004000): A shoot axis apical cell that is part of an embryo and is the uppermost cell formed after the first division of the zygote.
Comment: For plants that grow via an apical cell in their sporophytic phase, the embryonic apical cell may remain an apical cell throughout the plant's life.
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 shoot axis that is part of a gametophore.
Synonyms: cauloid, gametophyte axis, non-vascular shoot axis (broad, because it can also apply to the seta); participates_in gametophytic phase.
intersection_of: is_a plant axis, intersection_of: part_of gametophore
-Also suggest adding terms for gametophore stem and gametophore branch.
gametophore stem: A stem that is part of a gametophore.
is_a stem, part_of gametophore
gametophore branch: A branch that is part of a gametophore.
is_a branch, part_of gametophore
-If the intersection_of relations are asserted in the end user's version (e.g. Amigo), users will see dual parentage (is_a gametophore axis and is_a stem or 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?
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.
antheridiophore and archeginiophore
These are stalks that hold up the antheridia or archegonia in Marchantiales
Proposed definitions:
antheridiophore: A plant axis that bears antheridia.
participates_in gametophytic phase
Comment: Found in Marchantiales.
archeginiophore: A plant axis that bears archegonia.
participates_in gametophytic phase
Comment: Found in Marchantiales.
Cardinal organ parts
Terms requested by MO:
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 cells of the lower part of an archegonium (should we say venter?) and surrounds a sporangium.
Comment: Found in mosses and pteridophytes (according to Parihar). The calyptra ia a membranous or hairy cap or hood 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 (more specific) or archegonium (more general)?
subsets for bryophytes, pteridophytes
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 has an egg cell located in it.
part_of archegonium
subsets for bryophytes, pteridophytes, gymnosperms
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)
subsets for bryophytes, pteridophytes, gymnosperms
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. (ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition)
part_of sporangium; Synonyms: sporangium neck, apophysis, hypophysis
subsets for bryophytes
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 and has spores located in it.
Comment: Term used in mosses and other bryophytes (what about pteridophytes?)
part_of sporangium
subsets for bryophytes, maybe pteridophytes
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.
part_of sporangium
subsets for bryophytes
- 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.
Comment: Peristome teeth may be simple or compound, and may be attached by their tips to the epiphragm.
part_of peristome
subsets for bryophytes
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.
Synonym: sporangium lid
part_of sporangium
subsets for bryophytes
Also add these terms for angiosperms:
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 calyptra may remain attached to the plant after the fruit operculum dehisces.
Question: is the calyptra actually the base of the fruit, or it is an enlarged hypanthium that surrounds the fruit?
Proposed definition: A plant anatomical space that is the opening on the apical 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.
part_of sporangium
subsets for bryophytes
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 parenchyma 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.
Synonym: tympanum
subsets for bryophytes
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 gametophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."
Proposed definition: A plant axis that is a leafless 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.
participates_in gametophytic phase
subsets for bryophytes
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
