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Senescence and aging in GO
PO has the following terms: sporophyte senescent stage (PO:0007017), gametophyte senescent stage (PO:0025343), H anther senescence (PO:0001036), and 4 leaf senescence stage (PO:0001054). Rather than writing out the definition senescence in every term, we would like to be able to refer to a GO biological process term.
Go had the general term:
senescence GO:0010149: OBSOLETE. A preprogrammed process associated with the dismantling of an anatomical structure and an overall decline in metabolism. This may include the breakdown of organelles, membranes and other cellular components. An example of this process is found in Arabidopsis thaliana, when older leaves or floral organs are shed.
but, as their comment says: "This term was made obsolete because its name is ambiguous and it is covered by the two more specific terms: 'organ senescence ; GO:0010260' and 'cell aging ; GO:0007569'."
The POC needs a term for whole organism senescence, and we feel that the existing definitions of aging is not appropriate for plants, or even for cell aging (which is a subtype of aging).
Existing GO terms
GO tree view:
aging
>cell aging
>>cellular senescence
>multicellular organismal aging
>organ senescence
>>leaf senescence
See References/notes, below, for source of definitions.
aging (GO:0007568)
current definition: The inherent decline over time, from the optimal fertility and viability of early maturity, that may precede death and may be preceded by other indications, such as sterility.
proposed definition: A developmental process that is a deterioration and loss of function over time.
Comment: Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes processes like cellular senescence, but is more inclusive. May precede death (GO:0016265) and may succeed developmental maturation (GO:0021700). May be preceded by other indications, such as sterility in animals. (RW: Isn't sterility part of aging? GO has a term for aging-dependend sterility, synonym of chromatin silencing at silent mating-type cassette.)
Note: GO:biological process already states that this applies is "pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms", and GO:developmental process states that it is a "progression of an integrated living unit... over time from an initial condition to a later condition".
cell aging (GO:0007569)
current definition: Progression of the cell from its inception to the end of its lifespan. Source: GOC:jh, PMID:12044934
proposed definition: An aging process that has as participant a cell.
Comment: Occurs after a cell has stopped dividing. Precedes cell death (GO:0008219) and may succeed cell maturation (GO:0048469). Aging includes processes like cellular senescence, but is more inclusive.
cellular senescence (GO:0090398)
current definition: A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest. Source: GOC:BHF
proposed definition: A cellular aging process in which a cell loses the ability to divide further (put in GO process here).
Comment: Cellular senescence is accompanied by other cell aging processes, such as wear and tear or the dismantling of cellular components. May be a response to cellular stress or other stimuli, whereby normal cells lose the ability to divide through irreversible cell cycle arrest (post-mitotic senescence) or it may be intrinsic, in cells that have a finite capacity for division (mitotic senescence).
We may want to make two new subtypes, mitotic cellular senescence and post-mitotic cellular senescence.
multicellular organismal aging (GO:0010259):
current definition: The inherent decline of a multicellular organism over time, from the optimal fertility and viability of early maturity, that may precede death and may be preceded by other indications, such as sterility. Source: GOC:dph, GOC:isa_complete, GOC:mtg_sensu, GOC:sm
proposed definition: An aging process that has as participant a whole multicellular organism.
Comment: Multicellular organisms aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700). May be preceded by other indications, such as sterility in animals. (RW: Isn't sterility part of aging? GO has a term for aging-dependend sterility, synonym of chromatin silencing at silent mating-type cassette.)
Synonym: multicellular organism senescence
organ senescence (GO:0010260)
under construction
current definition: The process that occurs in an organ near the end of its active life that is associated with the dismantling of cell components and membranes, and an overall decline in metabolism. An example of this process is found in Arabidopsis thaliana. Source: GOC:mtg_sensu, GOC:sm
proposed definition: An aging process that has as participant an organ
leaf senescence (GO:0010150)
under construction
current definition: The process that occurs in a leaf near the end of its active life that is associated with the dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism. Source: ISBN:0387987819
proposed definition:
References/notes
Google definitions:
se·nes·cence, Noun:
1. The condition or process of deterioration with age. 2. Loss of a cell's power of division and growth.
de·gen·er·a·tion, Noun:
1. The state or process of being or becoming degenerate; decline or deterioration. 2. Deterioration and loss of function in the cells of a tissue or organ.
wordnetweb.princeton.edu/perl/webwn:
viability:
(of living things) capable of normal growth and development. (note that this would include senescence, since it is a "normal" developmental process)
Nooden and Leopold, 1988, Senescence and Aging in Plants:
Senescence and aging are both degenerative processes. Aging is passive and senescence is active.
Aging: wear and tear
Senescence: internal dismantling of cells, tissues, and organs
Gan, 2010, in Senescence Processes in Plants (Annual Plant Reviews):
ISBN:9781405139847
When cells lose the ability to divide further (either intrinsically or through stress), they begin to age and degenerate. This process is called "cellular aging", "postmitotic aging", or "postmitotic senescence". In plants, postmitotic senescence occurs in leaves/flowers/fruits and involves active but slow degenerative processes, or may be a hypersensitive response, involving an active and very quick degenerative process.
Two types of senescence (for cells or organs):
mitotic senescence: When cells that could divide a finite number of time stop dividing, e.g., arrest of apical meristem or arrest of cell divisions early in fruit development. Also called proliferative senescence. Similar to replicative senescence in yeast and animals.
post-mitotic senescence: Occurs in (cells in) organs like leaves and petals that, once formed, rarely undergo cell division, although the cells retain the ability to divide. Usually involves predominantly somatic tissue, and is similar to cellular senescence in Drosophila and C. elegans
Organism aging or organism senescence: "At the organismal level, when an organism's ability to respond to stress declines, its homeostasis becomes increasingly imbalnaced, and its risk of disease increase with age, which lead to the ultimate death of the whole organism. Although cellular senescence may contribute to organismal senescence, the latter is much more inclusive."
Monocarpic senescence: senescence associated with a monocarpic life history - a single (sporophytic) reproductive event in the life cycle. Includes three coordinated processes:
1. senescence of organs and tissues such as leaves (post-mitotic senescence)
2. arrest of the SAM (mitotic or proliferative senescence)
3. permanent suppression of axillary buds
PO terms
See initial discussion at Saturday_Sept_10th,_2011#Task_4._Work_existing_upper-_to_mid-level_terms_into_the_hierarchy_determined_in_task_3.
-Even though a plant may die from other causes before the end of normal senescence, the senescent stage of a whole plant ends with death.
proposed definition, senescence: A plant structure development stage that is (1) initiated by an event of cell death within the plant structure, (2) terminated in the death of the plant structure in such a way that (3) the former is connected to the latter by processes of dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism. [source: POC:curators, BS]
sporophyte senescent stage (PO:0007017)
A gametophyte development development stage that has as a participant a gametophyte/occurs during the interval between an event of cell death and the death of the gametophyte, such that the initial cell death is connected to the death of the organism by processes of dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism.
gametophyte senescent stage (PO:0025343)
H anther senescence (PO:0001036)
current def.: Stage during which the senescence of anther and stamen occurs. Shrinkage of cells and anther structure takes place. [source: TAIR:Katica_Ilic] is_a anther development stage
4 leaf senescence stage (PO:0001054)
current def.: The final stage of leaf development when the leaf ceases metabolic activity and senesces. is_a leaf development stage.
User requests open on Source Forge; PDSO
terms for seed trichome development stages
Requests for terms for cotton fiber development, Open since 07-28-2010, from AgBase curators
These items are on the agenda for POC_Conf._Call_11-15-11 and POC_Conf._Call_11-22-11.
from MaizeGDB:
coleoptile emergence
This was discussed at the NYBG Meeting, on Sunday_Sept_11th,_2011
We don't need to deal with all of this before the release, because Mary will use radicle emergence stage instead of coleoptile emergence.
From MS (MaizeGDB): It would be more useful for maize if the definition for coleoptile emergence PO:0007045 were altered to be: Emergence of coleoptile from the seed. (rather than above ground)
This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.
At the POC meeting on Sunday_Sept_11th,_2011, we agreed to keep the existing terms that reference emergence from the soil, but rename them as stages, and add new terms for emergence from seed coat. Need to copy over list of existing synonyms to new emergence terms.
Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. Imbibition (sibling of shoot emergence) also has no is_a parent.
current structure:
Shoot emergence (stage) should be is_a seedling growth (stage). Seedling growth (stage) should be is_a vegetative growth stage.
Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.
current and proposed terms and definitions
All of the terms below originally described a single point in time. We need to figure out when the shoot emergence stage should end.
current: shoot emergence (PO:0007030): Shoot or leaf breaks through the soil surface.
proposed: shoot emergence from growth medium development stage (PO:0007030): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the growth medium and ???.
Comment: This terms is used only for seed plants.
proposed: shoot emergence from seed coat development stage (new number): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the seed coat and ???.
Comment: May occur simultaneously with shoot emergence form the growth medium. This terms is used only for seed plants.
current: coleoptile emergence (PO:0007045): Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]
proposed: coleoptile emergence from growth medium development stage (PO:0007045): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the growth medium and ???
Comment: This terms is used only for seed plants.
proposed: coleoptile emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the seed coat and ???
Comment: May occur simultaneously with coleoptile emergence form the growth medium. This terms is used only for seed plants.
current: cotyledon emergence (PO:0007049): Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]
proposed: cotyledon emergence from growth medium development stage (PO:0007049): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the growth medium and ???
Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.
proposed: cotyledon emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the seed coat and ???
Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination. May occur simultaneously with cotyledon emergence form the growth medium.
current: epicotyl emergence (PO:0007054): Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]
proposed: epicotyl emergence from growth medium development stage (PO:0007054): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the growth medium and ???
Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination.
proposed: epicotyl emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the seed coat and ???
Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination. May occur simultaneously with epicotyl emergence form the growth medium.
current: hypocotyl emergence (PO:0007043): Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]
proposed: hypocotyl emergence from growth medium development stage (PO:0007043): A shoot emergence stage has as a participant a whole plant during the interval between emergence of a hypocotyl from the growth medium and ???
Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.
proposed: hypocotyl emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a hypocotyl from the seed coat and ???
Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination. May occur simultaneously with hypocotyl emergence form the growth medium.
Could also add terms for feeder emergence for some gymnosperms.
For all of the above terms, need to check existing synonyms and move or copy them as needed.
tuber growth and development stages
This item has been open on SF since 6/2009
I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).
Suggested stages:
-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
-tuber initiation
-tuber growth
-tuber maturation
How we work these in will depend on restructuring of PGDSO
l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
User requests open on Source Forge: PAO
notes:
other terms for cacti: glochid and areole
spinule: word for when the spines are stipules – synonym of stipule spine
Luctenbergia
root terms
Submitted by Rich Zobel (Nov 2009).
Still need to work on definitions for these terms.
Conductive cells and tissues for vascular and non-vascular plants
THIS PART IS STILL UNDER CONSTRUCTION
vascular tissue types
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 change definition to include xylem or phloem.
Proposed definition: A portion of plant tissue that has as parts tracheary elements or sieve tube members.
Comment: Functions in conduction and support. In shoot axes, vascular tissue is often found as part of a stele or as scattered vascular bundles. May include other types of tissue, such as fibers.
part_of vascular system (should add vascular system participates_in sporophytic phase)
vascular bundle (PO:0005020) current def.: 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 and phloem. May also contain other types of tissue such as plant fibers, vascular cambium, or portions of ground tissue.
part_of vascular system
add vein as exact synonym -- can be in any organ
phloem
phloem (PO:0005417) current def.: 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 elements.
Comment: Functions in the conduction of organic substances in vascular plants.
Note: currently, sieve element is listed as a synonym of sieve tube member, but this does not correctly follow Esau's usage. It was okay when we only had angiosperms in PO, but is no longer valid. Suggest we make a new term for sieve element, rather than have it as synonym. See below under conductive_and_related_cell_types.
metaphloem (PO:0006076) current def.: 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 primary phloem that differentiates after the protophloem.
Comment: Differentiates before the secondary phloem, if any is formed.
protophloem (PO:0006077) current def.: The first-formed elements of the primary phloem.
proposed definition: A portion of primary phloem tissue that has as parts the first-formed sieve elements of the primary phloem.
primary phloem (PO:0006075) current def.: A portion of phloem tissue of the primary plant body.
proposed definition: A portion of phloem tissue that develops from the procambium.
Comment: Primary phloem develops as part of GO:xxxx primary growth. (see below)
develops_from PO:0025275 procambium
secondary phloem (PO:0005043) current def.: A portion of phloem tissue formed by the activity of the vascular cambium.
proposed definition: A portion of phloem tissue that develops from the vascular cambium.
Comment: Secondary phloem develops as part of GO:0080117 secondary growth.
develops_from PO:0005598 vascular cambium
proposed terms for GO
definitions from Esau (ISBN:0471245208 or 9780471245209)
primary growth (new terms):
proposed definition: A type of growth of a plant structure from the time of its initiation by an apical meristem until its expansion is completed.
comment: Has its inception in the apical meristems and continues in their derivative meristems - protoderm and procambium - even in older tissues. Primary and secondary growth can occur simultaneously.
is_a growth (GO:0040007)
secondary growth (GO:0080117):
Current definition: Increase in plant girth due to the activity of lateral meristems (vascular and cork cambium). Source: PMID:19074290
Proposed definition: A type of growth of a stem or root, characterized by an increase in thickness resulting from formation of secondary vascular tissues by the vascular cambium.
Comment: Occurs in vascular plants (including gymnosperms and most dicots). Commonly supplemented by activity of the cork cambium (phellogen) forming a phelloderm. Primary and secondary growth can occur simultaneously. Some monocots have a primary peripheral thickening meristem, located near shoot apical meristem, that gives the appearance of secondary growth.
xylem
xylem (PO:0005352) current def.: A portion of vascular tissue composed of xylem elements.
comment: The principal function is the upward translocation of water and solutes. See also primary xylem and secondary xylem.
proposed definition: A portion of vascular tissue that has as parts tracheary elements.
comment: Functions in the translocation of water and solutes from roots to the shoot system and in support.
primary xylem (PO:0005849) current def.: A portion of xylem tissue of the primary plant body. [source: GR:Pankaj_Jaiswal, ISBN:0122151704, ISBN:0471245194]
Comment: In stem or root it is differentiated behind the apical meristem.
proposed definition: A portion of xylem tissue that differentiates from the procambium.
Comment: Primary xylem develops as part of GO:xxxx primary growth.
develops_from PO:0025275 procambium
protoxylem (PO:0000272) current def.: A portion of xylem tissue composed of any of the first formed elements of the primary xylem. [source: ISBN:047125208]
proposed definition: A portion of primary xylem that has as parts the first formed xylem elements of the primary xylem.
metaxylem (PO:0000372) current def.: A portion of xylem tissue that is part of the primary xylem and differentiates after the protoxylem and before the secondary xylem, if any of the latter is formed. [source: ISBN:047125208]
proposed definition: A portion of primary xylem that differentiates after the protoxylem.
Comment: Differentiates before the secondary xylem, if any is formed.
secondary xylem (PO:0005848) current def.: A portion of xylem tissue that develops from a vascular cambium. [source: ISBN:0471245194, POC:Curators]
Comment: Absent in some dicots and most monocots. The "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas.
Existing definition is okay.
New comment: Secondary xylem develops as part of GO:0080117 secondary growth. Found in gymnosperms and most dicots. The "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas. Some monocots have a primary peripheral thickening meristem, located near shoot apical meristem, that gives the appearance of secondary growth and may produce lignified tissue that appears woody, but is not composed o secondary xylem.
develops_from PO:0005598 vascular cambium
Note: exarch, endarch, mesarch are descriptors for different types of xylem development.
tracheid bar (PO:0019026) current def.: 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]
proposed definition: A portion of xylem tissue that is a distinct ring-like structure, composed of tracheid cells, which surrounds the hilum and forms a groove in the surface of the pericarp immediately adjacent to the hilum.
Comment: Found some taxa such as Phaseolus. [ISBN:0080280293]
part_of seed; adjacent_to hilum
leaf vein, midrib, costa
- leaf vein (PO:0020138), current def: A strand of vascular tissue in the leaf blade.
is_a portion of vascular tissue; part_of leaf vascular system
proposed definition, leaf vein (PO:0020138): A vascular bundle that is part of a leaf lamina in a vascular leaf.
part_of leaf vascular system, part_of leaf lamina
synonym: leaf vascular bundle
Suggest new term primary leaf vein: A leaf vein that originates from the base of a leaf lamina where it attaches to the petiole or to the shoot axis if no petiole is present.
Comment: A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139).
- midvein (PO:0020139): The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary]
Since midvein is_a leaf vein, it should say just "leaf" instead of "leaf or leaf-like organ.
proposed definition: A primary leaf vein that is the central vein of a vascular leaf.
Comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf.
broad synonyms: mid rib, midrib, mid-rib, vascular leaf midvein
related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128
We already have terms for secondary, tertiary, quaternary, and higher order veins.
plant fibers - new tissue types
Currently fibers are plant cell types, but they should also be a tissue type.
Proposed definition, portion of plant fiber: A portion plant tissue that has as parts fiber cells.
Comment: Contains elongated, lignified fiber cells that are dead at maturity. May function in strengthening and support the plant.
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.
under costruction
Current parent: axial cell
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.
Existing descendents of axial cell:
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)
The term axial cell, and the current definition, describe a particular type of vascular cells found in wood. This is not appropriate as the parent for xylem and phloem cells. Also, the term axial cell is not widely used. "Axial system" is widely used to describe the vascular tissue in wood (in contrast to the radial system).
Suggest that we obsolete this term, possibly replace with new terms for axial system and radial system.
New proposed hierarchy (children of plant cell):
plant cell
>sieve element (new term)
>>sieve tube member (syn.: sieve tube element)
>>sieve cell (new term)
>tracheary element
>>tracheid
>>vessel member
>ground tissue cell (PO:0025030)
>>sclerenchyma cell (PO:0000077)
>>>sclerid (new term)
>>>fiber cell (new term)
>>>>phloem fiber cell
>>>>xylem fiber cell
>>>>other kinds of fiber cells?
New definitions
sieve element (new term)
proposed def.:
sieve tube member (PO:0000289)
current def.:
proposed def.:
syn.: sieve tube member
sieve cell (new term)
proposed def.:
tracheary element ()
current def.:
proposed def.:
tracheid ()
current def.:
proposed def.:
vessel member ()
current def.:
proposed def.:
sclerenchyma cell (PO:0000077)
current def.:
proposed def.:
sclerid (new term)
proposed def.:
fiber cell (new term)
proposed def.:
phloem fiber cell ()
current def.:
proposed def.:
xylem fiber cell ()
current def.:
proposed def.:
other kinds of fiber cells?
other wood terms
Wood is a synonym for secondary xylem (PO:0005848) -- see definition above.
axial wood parenchyma ; PO:0004533: Parenchyma tissue in the axial system of secondary xylem.
axial wood parenchyma cell ; PO:0004526 Parenchyma cell in the axial system of secondary xylem. plant anatomy early wood ; PO:0004515 The wood formed in first part of a growth ring and characterized by a lower density and larger cells than the late wood.
heartwood ; PO:0004512 The inner layers of secondary xylem that have largely ceased to function in storage and conduction and in which reserve materials have been removed or converted into heartwood substances; generally darker colored than the functioning sapwood.
late wood ; PO:0004516 The secondary xylem formed in the later part of a growth ring; denser and composed of smaller cells than the early wood.
procumbent wood ray parenchyma cell ; PO:0004529 Ray cell within secondary xylem having its longest axis in radial direction.
ray wood parenchyma ; PO:0004534 Radially oriented parenchyma tissue in secondary xylem.
ray wood parenchyma cell ; PO:0004527 Parenchyma cell of a ray in secondary xylem.
sapwood ; PO:0004513 Outer part of the wood of stem or root containing living cells and reserves and in which conduction of water takes place. Generally lighter colored than the heartwood.
upright wood ray parenchyma cell ; PO:0004528 Ray cell in secondary xylem oriented axially (vertically in the axis) with its longest dimension.
wood parenchyma ; PO:0004532 Parenchymatous tissue occurring in the wood.
wood parenchyma cell ; PO:0004525 Parenchyma cell occurring within secondary xylem.
wood parenchyma is_a secondary xylem. Should be is_a parenchyma.
wood parenchyma (PO:0000272) current def.: Parenchymatous tissue occurring in the wood. [source: POC:Curators]
proposed definition:
Legume terms
All trackers are now closed. Leaving notes about bristle here for when we are ready to describe phenotypes.
bristle
(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
Meeting of RW, MAG and DWS on 8/29/11: we felt this would be better left as a phenotypic descriptor. Should add terms needed to PATO.
At the POC meeting on 9-27-11, it was decided that bristled stipules should best be handled as a phenotype term. Leaving these notes here for when we start to add phenotypic descriptors.
We have the term stipule spine. Could also add the term stipule bristle: A stipule that has a brush-like appearance.
A bristle is a single thing, like a stiff hair, but many things can be bristled. Better to add bristled as an adjective in PATO (like ovate or acute).
There are two meanings for bristled:
!. Stiff and sharp (e.g., a bristled trichome)
2. Bearing bristles (e.g, a bristled leaf bears many bristle-like hairs)
Suggest two new phenotype descriptors (for PO phenotype branch or for PATO):
1. bristle-like:
This is a combination of two PATO descriptors:
Something describing the shape:
PATO:0001954 (subulate, awl-shaped, needle-shaped): A shape quality inhering in a bearer by virtue of the bearer's being linear, very narrow, tapering to a very fine point from a narrow base.
or
PATO:0001873 (cylindrical): A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
and/or PATO:0001154 (elongated): A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
and something describing a quality of a substance:
PATO has:
PATO:0001544 (flexible): A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. (bendy)
PATO:0001545 (inflexibile): A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. (stiff)
A bristle is stiff but also bendy! I think in addition to flexible/inflexible, PATO needs terms for stiff or rigid/flacid, and that stiff should be a related synonym of inflexible, rather than exact.
PATO:
quality of a substance (existing)
>flexibility (existing)
>>flexible (existing)
>>inflexible (existing)
>rigidity (new)
>>rigid (new)
>>flacid (new)
2. bristle-bearing: A pilosity quality inhering in a bearer by virtue of the bearer's having structures that are bristle-like.
is_a pilosity (PATO:0000066: A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles.)
Synonym: bristly (Beentje 2010: bearing stiff strong hairs or bristles).
To describe legume stipules, we may also need a term brush-like: A shape quality inhering in a bearer by virtue of the bearer's having a shape that is a cluster of bristle-like structures.
Then if we want to, we could add terms like brush-like stipule (is_a stipule) or bristle-like stipule (is_a stipule) or bristle-bearing stipule, or users could post-compose these terms on their own.
