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."

New terms for Physcomitrella and related taxa (continued)

Plant Tissues

paraphyllium

Tiny filaments, scales or leaf-like structures scattered on the stems of some leafy bryophytes. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

Crum defines them as "Small green outgrowths formed between the leaves on stems and branches of some pleurocarps (mosses that produce archegonia and sporophytes laterally, rather than on the tips of their axes) and a very few leafy liverworts."

Schofield describes paraphyllia as outgrowths of the epidermis, but he also describes leaves that way.

Moss Ontology has paraphyllium listed as a plant organ, but they do not arise from the SAM as phyllomes do.

Proposed definition: A portion of epidermal tissue that is a small outgrowth from the epidermis between the leaves of a gametophore axis.

Comment: Paraphyllia are much smaller than leaves and may be filamentous, scale-like, or leaf-like. Found in pleurocarpous mosses and a few leafy liverworts.

The paraphyllia are the small, dark structures between the leaves.

paraphysis

Moss Ontology definition: Sterile, septate, usually uniseriate hairs intermixed with sex organs. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

From Parihar: sterile, slender filaments accompanying reproductive organs.

From Schofeld: filamentous sterile structures intermixed with the sex organs of most mosses

These are a kind of trichome

Proposed def.: A multicellular trichome that is a slender, usually uniseriate hair-like structure that grows intermixed with the gametangia.

Comment: Found in bryophytes and pteridophytes, especially in mosses.

adjacent_to gametangium, plural: paraphyses; particpates_in gametophytic phase

axillary hair

Moss Ontology definition: A small filament in an axil consisting of one long terminal cell atop a basal stalk (also called club-hair). Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

This is a type of trichome. Axillary trichomes may also be found in angiosperms, so suggest we specify that this for hair son gametophores.

Proposed def., gametophore axillary hair: A multicellular trichome consisting of one long terminal cell atop a basal stalk that grows in the leaf axil of a non-vascular leaf.

Comment: Found in pleurocarpous mosses.

synonym: club-hair; part_of gametophore

rhizoid

Moss Ontology definition: Filamentous tissue protruding from the gametophore stem with a rooting function.

Rhizoids may also grow from thalli. They arise from the epidermis, and so are like trichomes. Like trichomes, they may be uni- or multicellur

Proposed def.: A trichome that grows from the epidermis of a plant in the gametophytic phase.

Comment: Found in bryophytes and pteridopytes growing from a gametophore or thallus. May be muticellular or unicellur. May anchor the plant to the substrate.

tmema

Moss Ontology definition: An abscission cell at the base of a gemma (vegetative propagule). Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

Their definition defines a cell type, but they have tmema as a tissue type. It would be the tissue composed of tmema cells

Proposed def.: A portion of plant tissue composed of tmema cells.

Comment: Found in bryophytes at the base of a gemma or a brachycyte that will act as a gemma. Participates in abscission of the gemma.

archesporium, amphithecium, endothecium, jacket layer

See separate agenda item for parts of sporangium.

sporogenous tissue or archesporium

Conductive tissue

See separate agenda for conductive cells and tissues

Conductive cells and tissues

THIS PART IS STILL UNDER CONSTRUCTTION

conductive cells for bryophytes

axial cell

First 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.

Descendents of axial cell

Terms 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 in the gametophytic phase and in the seta in the sporophytic phase. [source: ISBN:0962073342 (Crum), ISBN:376821110 (Hebant)]

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. [ISBN:0962073342, ISBN:376821110]

Comment: A food conducting cell found in bryophytes in the gametophytic phase and in the seta of in the sporophytic phase. Food conducting cells in bryophytes range from parenchyma cells that are

part_of leptome

sterid (new term): An axial cell with thickened walls.

Comment: An axial cell that functions in support rather than conduction, found in bryophytes. May or may not retain a living protoplast at maturity. ISBN:376821110

add disjoint_from relations among leptoids, hydroids, and sterids

Existing terms

(We can address these definitions now or come back to them after the next release)

sieve tube member (PO:0000289, alt: PO:0000286):

phloem fiber (PO:0004519):

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):

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 located in the center of non-vascular shoot axes such as a gametophore axis or seta, or in the midrib of a non-vascular leaf.

synonyms: conducting strand, central cylinder

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;