POC Conf. Call 4-28-11
POC meeting, Webex Conference Call; Date: Thursday April 28th, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_4-26-11?
Items arising from previous meetings:
Plant cell and sperm cell
Most sperm cells do not have a plasma membrane (as per definition of cell by GO).
We should add a comment to sperm cell (PO:0000084) and plant cell (PO:0009002): "Motile sperm cells do not have a plasma membrane."
Conductive cells and tissues
conductive tissue for bryophytes and vascular plants
vascular tissue
For vascular plants, we have the class:
vascular tissue (PO:0009015): A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]
Comment: Functions in conduction and support. In the stem it is often found as a stele, surrounded by the cortex and surrounding the pith.
part_of vascular bundle (which is part_of vascular system)
This is okay, but suggest that we make it a child of the new class portion of axial tissue (see below), and also change definition to say xylem or phloem.
Proposed definition: A portion of axial tissue that has as part vascular axial cells [=xylem elements or sieve tube elements, see more below].
Comment: Functions in conduction and support. In a shoot axis, vascular tissue is often found as part of a stele. May include other types of tissue, such as fibers.
currently part_of vascular bundle (Is this appropriate for all plants?)
children of vascular tissue:
hydothode (PO:0005660) - A structural modification of vascular and non-vascular tissues, usually in a leaf, that permits the release of water through a pore in the epidermis. [GR:pj, ISBN:0080374913]
should be is_a cardinal organ part
proposed definition: A cardinal organ part that is a modification of vascular and non-vascular tissues, usually in a leaf, that permits the release of water through a pore in the epidermis.
leaf vein (PO:0005417) - see more below details below
phloem (PO:0005417): A portion of vascular tissue whose principal function is conducting organic substances. [GR:pj]
proposed definition: A portion of vascular tissue that has as parts sieve tube elements.
Comment: Functions in the conduction of organic substances in vascular plants.
metaphloem (PO:0006076): Part of the primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.
should be is_a phloem
protophloem (PO:0006077): The first-formed elements of the primary phloem.
should be is_a phloem
proposed definition: A portion of phloem tissue that has as parts the first-formed elements of the primary phloem.
tracheid bar (PO:0019026): A distinct ring-like structure, composed of tracheid cells, which surrounds the hilum of some taxa e.g., Phaseolus, and forms a groove in the surface of the pericarp (immediately adjacent to the hilum). [ISBN:0080280293]
-should be is_a xylem
xylem (PO:0005352): A portion of vascular tissue composed of (that has as parts) xylem elements.
vascular bundle (PO:0005020): A unit strand of the vascular system containing the vascular tissues, xylem and phloem. In addition vascular cambium is often present. [GR:pj]
This currently is_a portion of plant tissue. Should be is_a portion of vascular tissue.
proposed definition: A portion of vascular tissue that is a unit strand of the vascular system and has as part xylem or phloem.
Comment: Usually contains both xylem or phloem. May also contain other types of tissue such as plant fibers or vascular cambium.
part_of vascular system
portion of axial tissue
Suggest we add a new parent for vascular tissue, fibers, and non-vascular conducting tissue: portion of axial tissue
Proposed definition: A portion of plant tissue that has as parts axial cells.
Comment: Axial tissue occurs in elongated strands. In plant axes, the axial tissue runs parallel to the axis, but may have other orientations in organs such as phyllomes.
disjoint_from cortex, disjoint_from pith
Children of axial tissue: portion of vascular tissue, portion of non-vascular conducting tissue, portion of plant fiber and sterome. Should add disjoint_from relations between vascular tissue and non-vascular conducting tissue. (RW: insert image)
New children of axial plant tissue:
portion of non-vascular conducting tissue: A portion of axial tissue that has a parts non-vascular conducting cells [=hydroids or leptoids, see more above]
hydrome: A portion of axial tissue that has as parts hyrdoids.
Comment: Found in bryophytes, in the center of a non-vascular shoot axis such as a gametophore or seta, or in the midrib of a non-vascular leaf. Often surrounded by leptome. May function in water conduction and support similar to xylem in vascular plants.
Synonyms: hydrom, leptoxylem (Hebant)
leptome: A portion of axial tissue that has as parts leptoids.
Comment: Found in bryophytes, in non-vascular shoot axes such as a gametophore or seta, or in the midrib of a non-vascular leaf. Often surrounding a central hydrome. May function in the conduction of organic substances, similar to phloem in vascular plants.
Synonyms: leptom, leptophloem (Hebant)
central strand: A unit strand of non-vascular conducting tissue that has as part hydrome or leptome.
Comment: Usually contains both hydrome and leptome. Found in bryophytes, in non-vascular shoot axes such as a gametophore or seta, or in the midrib of a non-vascular leaf.
portion of plant fiber: Currently fibers are plant cell types, but they should also be a tissue type.
Proposed definition: A portion axial tissue that has as parts fiber cells.
[Can it have other cell types, or is it exclusively fiber cells?]
Comment: Contains elongated, lignified fiber cells that are dead at maturity.
phloem fiber: A portion of plant fiber that has as parts phloem fiber cells.
xylem fiber: A portion of plant fiber that has as parts xylem fiber cells.
stereome: A portion of axial tissue that has as parts stereids.
Comment: Found in bryophytes.
From Hebant: A typical moss stem comprises, from the outside to the inside, an epidermis with a thin cuticle but no stomata, an outer cortex which frequently consists of supporting ells with thickended walls ("stereids"), an inner cortex of thin-walled conducting cells, and, in a number of species, a central strand of hydroids.
leaf vein, midrib, costa
Moss Ontology has requested the term midrib for bryophytes. It is often called a costa.
We have the term midvein (PO:0020139): The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary]
Perhaps this should refer to phyllome, rather than saying a "leaf or leaf-like organ".
Midvein (PO:0020139) is_a leaf vein (PO:0020138): A strand of vascular tissue in the leaf blade.
is_a portion of vascular tissue; part_of leaf vascular system
This term only applies to vascular leaves, and should be renamed vascular leaf vein. Like vascular bundle, it should be is_a portion of axial tissue, instead of is_a portion of vascular tissue.
Proposed definitions:
phyllome vein (new term): A portion of axial tissue that is part of a phyllome and has a part a vascular bundle or a hydrome or a leptome
vascular leaf vein (PO:0020138): A phyllome vein that is part of a vascular leaf leaf and has as part vascular tissue.
Refs:
Sperry 2003, IJPS; Hebant 1977;
Conductive cell types for bryophytes
hyrdoid (PO:0025032):: An elongate, water conducting cell that is dead at maturity, with tapered ends that are thin and partially hydrolyzed, that lacks specialized wall thickenings or lignin. [source: ISBN:0962073342 (Crum), ISBN:9780717810073]
Comment: Occurs in the gametophytic phase of a plant life cycle.
Proposed def.: An axial cell that is dead at maturity, with tapered ends that are thin and partially hydrolyzed, and lacking specialized wall thickenings or lignin.
Comment: Water conducting cells found in bryophytes, mainly in the gametophytic phase, but also sometimes in the sporophytic phase.
part_of hydrome
leptoid (PO:0025033): A food conducting cell associated with hydroids that resembles the sieve elements of some seedless vascular plants. [source: ISBN:962073342, ISBN:9780717810073]
Comment: Occurs in the gametophytic phase of a plant life cycle.
Proposed def.: An axial cell that resembles the sieve elements of some seedless vascular plants.
Comment: A food conducting cell found mainly in the gametophytic phase, but also sometimes in the sporophytic phase, of bryopytes.
part_of leptome
Sporangium parts
This is continued from our discussion at the POC_Conf._Call_3-8-11
Currently classes like exothecium, endothecium, primary parietal cell layer and tapetum are part of anther wall (PO:0000002). However, these layers and their constituent cell types can be part of any sporangium, not just an anther. Proposed making them part of a general class sporangium wall (as we did for parts of leaf).
See Summary of sporangium development
