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
THIS PART IS STILL UNDER CONSTRUCTTION
conductive cells for bryophytes
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.
We cannot define axial cell as a vascular cell, because that doesn't exist, and it includes non-conductive cells such as fibers. Also, not all axial cells that we are trying to include are derived from a fusiform initial. They also occur in leaves, with random orientations.
Is axial cell the best name for this term? The phrase "axial system" is already used to describe the vascular tissue in wood, so "axial cells" might be automatically associated with that system.
Proposed definition: A elongated plant cell that is oriented parallel to other axial cells in the same portion of axial tissue
Comment: In plant axes, axial cells and axial tissue are oriented with their longest axis parallel to the axis, but in phyllomes, they may have other orientations. Axial cells function in support or in the conduction of water, carbohydrates and minerals.
Children of axial cell:
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)
conductive tissue for bryophytes and vascular plants
vascular tissue
For vascular plants, we have the class:
portion of 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 parts tracheary elements or sieve tube members and is part of a vascular system.
Comment: Functions in conduction and support. In shoot axes, vascular tissue is often found as part of a stele or may occur as scattered vascular bundles. May include other types of tissue, such as fibers.
currently part_of vascular bundle. Removed this relation, because it is not true for all plants, and a vascular bundle is now a portion of vascular tissue.
part_of vascular system
children of vascular tissue:
hydathode (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. Do hydathodes ever occur on stems or branches, or are they always part of phyllomes?
proposed definition: A cardinal organ part that releases water through a pore.
Comment: Usually found on leaves. Hydathodes may have one or more pores that appear to be incompletely developed stomata that lack the ability to open and close. Generally, hydathodes are located at the end of a minor vein. In many plants, hydathodes includes a portion of thin-walled parenchyma between the tracheary elements and the pore, known as an epithem. In some plants, hydathodes are associated with secretory tissue.
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 members.
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.
proposed definition: A portion of phloem tissue that is the part of a primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.
protophloem (PO:0006077): The first-formed elements of the primary 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. May also contain portions of ground tissue.
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;
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
