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.
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:
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)
portion of non-vascular conducting tissue: A portion of axial tissue that has a parts non-vascular conducting cells [=hydroids or leptoids, see more below]
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. Often surrounded by leptome. May function in water conduction and may provide support.
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, often surrounding a central hydrome. May function in the conduction of organic substances, similar to phloem in vascular plants.
central strand:
portion of plant fiber: Currently is a plant cell, but maybe it 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.
sterome:
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 cells for bryophytes
THIS PART IS STILL UNDER CONSTRUCTTION (RW)
axial cell
We need to address the definition of axial cell, as it was written with angiosperms in mind.
axial cell (PO:0000081): A vascular cell derived from the fusiform cambial initial and oriented with its longest diameter parallel with the main axis of stem or root. [source: ISBN:0471245208]
Comment: These cells make up the axial system, also known as vertical or longitudinal system.
Current children are:
hydroid (PO:0025032)
leptoid (PO:0025033)
phloem fiber (PO:0004519)
sieve tube member (PO:0000289, alt: PO:0000286)
xylem element (PO:0000273)
>tracheary element (PO:0000273)
>>tracheid (PO:0000301)
>>vessel member (PO:0002003)
>xylem fiber (PO:0000274)
>>fiber tracheid (PO:0000355)
>>libriform fiber (PO:0004520)
>>septate fiber (PO:0004521)
(some of their definitions need work, but that is not a priority for now)
Currently, axial cells develops_from fusiform initial, which is_a cambium initial, which is part_of vascular cambium, which is part_of vascular system. This won't work for hydroids and leptoids or for xylem and phloem cells in leaves, which do not arise from a vascular cambium (such as in phyllomes). Also, the term vascular cell does not exist in the PO, so it does not work for the definition.
Is it valid to use the term axial cell for all cell types vascular or non-vascular tissue? Would it be better to have a different name for this class of cell types? Do we want to keep the existing definition, and make it a subset of a more general class?
Proposed def. of axial cell: A elongated plant cell that is part of a portion of axial tissue. .
Comment: Axial cells are oriented parallel to other cells in a portion of axial tissue Axial cells are involved in conduction of water, carbohydrates and minerals or are accessory to the conductive cells.
In plant axes, axial cells are oriented with their longest diameter parallel with the axis, but in phyllomes, they may have other orientations.
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
