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?

New terms for Physcomitrella and related taxa (continued)

Conductive cells and tissues

conductive tissue for bryophytes and vascular plants

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)

children: hydothode (PO:0005660) [should be is_a cardinal organ part, not is_a vascular tissue], leaf vein (PO:0005417), metaphloem (PO:0006076), phloem (PO:0005417), protophloem (PO:0006077), tracheid bar (PO:0019026), xylem (PO:0005352). [Some of these definitions need work, but we can address that later.]

Proposed definition: A portion of axial tissue that has as part vascular axial cells [=xylem or phloem, see above].

Comment: Functions in conduction and support. In a shoot axis, vascular tissue is often found as part of a stele. May be associated with other types of tissue, such as fibers.

part_of vascular bundle (Is this appropriate for all plants?);

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 is not a portion of tissue, because it usually consists of multiple tissue types. Not really a cardinal organ part either, because it may be part of one organ or extend throughout the plant. Probably should be is_a plant structure.

proposed definition: A xxxx? that is a unit strand of the vascular system that has as part a portion of vascular tissue.

Comment: May contain xylem or phloem, or, usually, both. May contain other types of tissue such as fibers.

disjoint_from cortex, disjoint_from pith

portion of axial tissue

Suggest we add a new parent for vascular tissue, fibers, and non-vascular conducting tissue: 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.

Children of axial tissue: vascular tissue, , hydrome, leptome

Children of axial tissue:

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.

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.

Grouping conductive tissue in vascular and non-vascular plants

To compare vascular and non-vascular tissue, users can look at annotation for axial tissue. If we ant. we could add a new class: portion of conductive tissue. Like portion of secretory tissue (PO:0005656), this is a functional classification, and should serve only as a secondary classification, specified by intersection_of terms.

portion of conducting tissue: A portion of axial tissue that is participates in conduction of water, minerals, or organic substances.

is_a portion of axial tissue, intersection_of: is_a vascular tissue, intersection_of: is_a hydrome, intersection_of: is_a leptome

Using this set up, any portion of xylem, phloem, hydrome, or leptome would be is_a conductive tissue.

portion of water conducting tissue: A portion of conducting tissue that is participates in conduction of water and dissolved minerals.

is_a portion of conducting tissue, intersection_of: is_a xylem, intersection_of: is_a hydrome

portion of organic substance conducting tissue: A portion of conducting tissue that is participates in conduction of organic substances.

is_a portion of conducting tissue, intersection_of: is_a phloem, intersection_of: is_a leptome

midrib/costa

Moss Ontology definition: The nerve of a phyllid. Altered from Bill and Nancy Malcolm (2006)

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] (which, by the way, should just say phyllome, instead of leaf or leaf-like organ). However, midvein is_a leaf vein, which is a portion of vascular tissue, so it cannot apply to mosses.

We should have a term that groups conductive tissue together for both vascular and non-vascular plants, kind of like we have axial cell for vascular and non-vascular conductive cells.

New child of portion of plant tissue: portion of axial tissue:

(also, we need to redefine phloem to be more like definition of xylem, and not based on function) (need to redefine axial cell so it doesn't say vascular cell)

These terms were not proposed by the Physco group, but should be in the PO.

Refs:

Sperry 2003, IJPS; Hebant 1977;

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.

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