Difference between revisions of "POC Conf. Call 4-28-11"

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==Conductive cells and tissues==
 
==Conductive cells and tissues==
−
===conductive cells for bryophytes===
 
  
−
====axial cell====
+
===conductive tissue for bryophytes and vascular plants===
  
−
We need to address the definition of axial cell, as it was written with angiosperms in mind.
+
For vascular plants, we have the class:
  
−
'''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]  
+
'''vascular tissue (PO:0009015):''' A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]
  
−
Comment: These cells make up the axial system, also known as vertical or longitudinal system.
+
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)
  
−
Currently has 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. Also, the term vascular cell does not exist in the PO, so it does not work for the definition.
+
children: hydothode (PO:0005660) [''should be cardinal organ part''], leaf vein (PO:0005417), metaphloem (PO:0006076), phloem (PO:0005417), protophloem (), tracheid bar (PO:0019026), xylem (PO:0005352)
  
−
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 definition:''' A portion of axial tissue that has as part xylem or phloem.
  
 +
Comment: Usually contains both xylem and phloem. May also contain other types of tissue such as fibers. Functions in conduction and support. In a stem it is often found as a stele, surrounded by the cortex and surrounding the pith.
  
−
'''Proposed def.:''' A elongated plant cell that is oriented parallel to other cells in the axial tissue.
 
  
−
Comment: 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.
+
For non-vascular plants, we could add the class: '''portion of non-vascular axial tissue'''
−
 
 
−
===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]
+
'''Proposed definition:''' A portion of axial tissue that has as parts hydroids or leptoids.
  
−
Comment: Occurs in the gametophytic phase of a plant life cycle.
+
Comment: non-vascular axial tissue may function in conduction and support, similar to vascular tissue, but does not contain any lignified cells.
  
−
'''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.
+
part_of non-vascular shoot system
  
−
Comment: Water conducting cells found in bryophytes, mainly in the gametophytic phase, but also sometimes in the sporophytic phase.
+
Children:  
−
 
 
−
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.
+
'''hydrome:''' A portion of non-vascular axial tissue that has as parts hyrdoids.
  
−
'''Proposed def.:''' An axial cell that resembles the sieve elements of some seedless vascular plants.
+
Comment: Found in bryophytes, primarily in a gametophore, but may sometimes occur in a seta. Thought to function in water conduction.
  
−
Comment: A food conducting cell found mainly in the gametophytic phase, but also sometimes in the sporophytic phase, of bryopytes.
 
  
−
part_of leptome
+
'''leptome:''' A portion of non-vascular axial tissue that has as parts leptoids.
  
−
===conductive tissue for bryophytes===
+
Comment:
  
−
For vascular plants, we have the class:
 
  
−
'''vascular tissue (PO:0009015):''' A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]
+
Suggest we add a new parent for both: '''axial tissue'''
  
−
Comment: Functions in conduction and support. In the stem it is often found as a stele, surrounded by the cortex and surrounding the pith.
+
'''Proposed definition:'''
  
−
For non-vascular plants, we could add the class: '''portion of non-vascular axial tissue'''
 
  
−
proposed definition: A portion of plant tissue that has non-vascular axial cells as parts and is part of a non-vascular shoot system.
+
disjoint_from cortex
  
−
Comment: non-vascular axial tissue may function in conduction and support, similar to vascular tissue, but does not contain any lignified cells.
+
How to compare phloem and leptome? Make phloem a direct child of axial cell?
  
 
====midrib/costa====
 
====midrib/costa====
Line 90: Line 80:
 
These terms were not proposed by the Physco group, but should be in the PO.
 
These terms were not proposed by the Physco group, but should be in the PO.
  
−
*'''hydrome'''
 
  
−
 
−
*'''leptome'''
 
  
 
===Grouping conductive tissue in vascular and non-vascular plants===
 
===Grouping conductive tissue in vascular and non-vascular plants===
Line 100: Line 87:
  
 
Could keep vascular tissue as is, then 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.
 
Could keep vascular tissue as is, then 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.
 +
 +
===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==
 
==Sporangium parts==

Revision as of 15:31, 15 April 2011

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 last week's meeting:

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 cardinal organ part], leaf vein (PO:0005417), metaphloem (PO:0006076), phloem (PO:0005417), protophloem (), tracheid bar (PO:0019026), xylem (PO:0005352)


Proposed definition: A portion of axial tissue that has as part xylem or phloem.

Comment: Usually contains both xylem and phloem. May also contain other types of tissue such as fibers. Functions in conduction and support. In a stem it is often found as a stele, surrounded by the cortex and surrounding the pith.


For non-vascular plants, we could add the class: portion of non-vascular axial tissue

Proposed definition: A portion of axial tissue that has as parts hydroids or leptoids.

Comment: non-vascular axial tissue may function in conduction and support, similar to vascular tissue, but does not contain any lignified cells.

part_of non-vascular shoot system

Children:

hydrome: A portion of non-vascular axial tissue that has as parts hyrdoids.

Comment: Found in bryophytes, primarily in a gametophore, but may sometimes occur in a seta. Thought to function in water conduction.


leptome: A portion of non-vascular axial tissue that has as parts leptoids.

Comment:


Suggest we add a new parent for both: axial tissue

Proposed definition:


disjoint_from cortex

How to compare phloem and leptome? Make phloem a direct child of axial cell?

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.


Grouping conductive tissue in vascular and non-vascular plants

Could keep vascular tissue as is, then 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.

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

Next meeting scheduled for Tuesday, May 3rd, 2011 at 10am PDT/1pm EDT

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