Difference between revisions of "Categorized list of terms without parents"

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Back to [[POC_Meeting_and_Workshop_Nov_4th_to_6th,_NYBG,_Bronx,_NY]]
 
Back to [[POC_Meeting_and_Workshop_Nov_4th_to_6th,_NYBG,_Bronx,_NY]]
  
 +
Priority rankings next to each item by RW on 11/1/2010. May change.
  
−
===Parts of the root tip===
 
  
 +
===(MP) Parts of the root tip===
 +
We discussed most of these at last week's meeting, and folks have commented on SF. Can move through them quickly or save for phone meeting.
  
−
===Pores/stomata===
 
  
−
[Term]
+
'''Proposed new parent term: root parenchyma''' (PO:0025095): A portion of parenchyma tissue that is part of a root.
  
−
id: PO:0002000
 
  
−
name: stomatal complex
+
Original data:
  
−
def: "An opening pore on the epidermis of leaves and stems bordered by two guard cells and serving in gas exchange." [ISBN:0471245208]
+
id: PO:0020123
  
−
synonym: "stoma" RELATED []
+
name: root cap
  
−
synonym: "stomata" RELATED []
+
def: "A group of cells that covers the apical meristem of the root." [APWeb:Glossary]
  
−
[Term]
+
subset: reference
  
−
id: PO:0006334
+
Suggest: is_a root parenchyma
  
−
name: seed micropyle
+
Proposed definition: A portion of root parenchyma tissue that is part of the root tip and covers the root apical meristem. Comment: Often composed of living and dead parenchyma cells. Protects the root apical meristem.
  
−
def: "A pore on the seed coat which is a remnant of the ovular micropyle." [GR:pj]
 
  
−
relationship: develops_from PO:0020025 ! micropyle
+
Original data:
  
 +
id: PO:0020130
  
 +
name: central root cap
  
−
[Term]
+
def: "The central part of a root cap in which the cells are arranged in longitudinal files." [GR:pj]
  
−
id: PO:0008032
+
synonym: "columella cells" RELATED [] plus columella root cap
  
−
name: stomatal pore
+
relationship: part_of PO:0020123 ! root cap
  
−
def: "The space of variable size controlled by stomatal guard cells in response to environmental clues." [GR:cwt]
+
Suggest: is_a root parenchyma
  
−
synonym: "stomatal aperture" RELATED []
+
Proposed definition: A portion of root parenchyma tissue that is the central part of a root cap in which the cells are arranged in longitudinal files.
  
−
relationship: part_of PO:0002000 ! stomatal complex
 
  
  
 +
Original data:
  
−
[Term]
+
id: PO:0020131
  
−
id: PO:0008044
+
name: lateral root cap
  
−
name: floral stomatal complex
+
def: "The part of the root cap that is parallel to the sides of the axis." [ISBN:0122151704]
  
−
def: "An opening pore on the epidermis of floral organs bordered by two guard cells and serving in gas exchange." [GR:cwt]
+
synonym: "peripheral cells" RELATED []
  
 +
relationship: part_of PO:0020123 ! root cap
  
−
Term]
+
Suggest: is_a root parenchyma
  
−
id: PO:0008046
+
Proposed definition: A portion of parenchyma tissue that is part of a root cap and is parallel to the sides of a root axis.
  
−
name: floral stomatal pore
 
  
−
def: "The space of variable size controlled by floral stomatal guard cells in response to environmental clues." [GR:cwt]
+
Original data:
  
−
relationship: part_of PO:0008044 ! floral stomatal complex
+
id: PO:0020149
  
 +
name: quiescent center
  
 +
def: "Hemispherically shaped aggregation of mitotically and metabolically inactive cells positioned behind the root cap." [ISBN:0122151704]
  
−
===Trichomes===
+
Suggest: is_a meristem, part_of root apical meristem
  
−
[Term]
+
Proposed definition: A hemispherically shaped portion of meristem tissue consisting of mitotically and metabolically inactive cells that is part of the root apical meristem and is positioned behind the root cap.
  
−
id: PO:0002001
 
  
−
name: papillae
+
Original data:
  
−
def: "A soft protuberance on an epidermal cell of the stigma." [ISBN:0471245208]
+
id: PO:0020135
  
−
subset: reference
+
name: differentiation zone
  
 +
alt_id: PO:0003002
  
−
[Term]
+
def: "The portion of the root located behind the elongation zone containing cells that are differentiating into their final form and function." [GR:pj]
  
−
id: PO:0000029
+
subset: reference
  
−
name: root hair tip
+
synonym: "maturation zone" RELATED []
  
−
def: "Tip portion of an outgrowth of a root epidermal cell." [TAIR:ki]
+
synonym: "specialization zone" RELATED []
  
 +
Suggest: is_a cardinal organ part, part_of root
  
−
[Term]
+
Proposed new name: root differentiation zone; Proposed definition: A cardinal organ part that is the part of a root and is located behind the elongation zone and contains cells that are differentiating into their final form and function.
 +
Comment: Most of the primary tissues of a root mature in the differentiation zone. This zone is where root hairs are produced.
  
−
id: PO:0008031
+
Could add new parent term "shoot axis differentiation zone" to be parent to this term and to stem internode differentiation zone (PO:0008042)
  
−
name: trichome branch
 
  
−
def: "The branch on a trichome." [GR:cwt]
+
Original data:
  
 +
id: PO:0020125
  
 +
name: elongation zone
  
 +
def: "The portion of the root that includes small, densely cytoplasmic cells that are dividing and expanding in size." [GR:pj]
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3007368&group_id=76834&atid=835555 axil]===
+
subset: reference
  
−
(also an open tracker item)
+
synonym: "region of cell elongation" RELATED []
  
−
We need to discuss whether or not to have a generic term 'axil' and, if so, how it should be defined. See also older tracker item [https://sourceforge.net/tracker/index.php?func=detail&aid=1681621&group_id=76834&atid=835555 leaf base vs. axil?]
+
synonym: "region of radial enlargement" RELATED []
  
−
===[https://sourceforge.net/tracker/?group_id=76834&atid=835555 Primordium]===
+
Suggest: obsoleting this term, because the definition is wrong, and making a new term, root elongation zone; is_a cardinal organ part, part_of root tip
  
−
(also an open tracker item)
+
Proposed definition: A cardinal organ part that is part of a root that is located directly behind a root apical meristem, in which the cells are undergoing longitudinal expansion.
  
−
Need a class primordium, and need to make one definition for it. Also need to organize primordium terms
+
Comment: The elongation zone is only a few millimeters in length and is the only portion of the root in which cell elongation generally occurs. Root hairs are not yet produced in this region. Primary root tissue begin to differentiate in the root elongation zone.
  
  
−
[Term]
+
Could add new parent term "shoot axis elongation zone" to be parent to this term and to stem internode elongation zone (PO:0008041)
−
 
 
−
id: PO:0004725
 
−
 
 
−
name: abaxial side of leaf primordium
 
−
 
 
−
def: "The abaxial/outer side of the leaf primordium that becomes the abaxial/lower leaf blade." [TAIR:ki]
 
  
 +
===(HP) Pores/stomata (done)===
  
 
[Term]
 
[Term]
  
−
id: PO:0004726
+
id: PO:0002000
  
−
name: adaxial side of leaf primordium
+
name: stomatal complex
  
−
def: "The adaxial/inner side of the leaf primordium that becomes adaxial/upper leaf blade." [TAIR:ki]
+
def: "An opening pore on the epidermis of leaves and stems bordered by two guard cells and serving in gas exchange." [ISBN:0471245208]
  
 +
synonym: "stoma" RELATED []
  
 +
synonym: "stomata" RELATED []
  
 +
[Term]
  
 +
id: PO:0006334
  
−
===easy ones (ha!)===
+
name: seed micropyle
−
[Term]
 
  
−
id: PO:0000033
+
def: "A pore on the seed coat which is a remnant of the ovular micropyle." [GR:pj]
  
−
name: valve
+
relationship: develops_from PO:0020025 ! micropyle
−
 
 
−
def: "Portion of an organ that is fragmented; in capsule, the portions into which the pericarp splits at maturity." [APWeb:Glossary]
 
  
−
subset: Arabidopsis
 
  
  
 
[Term]
 
[Term]
  
−
id: PO:0000037
+
id: PO:0008032
  
−
name: shoot apex
+
name: stomatal pore
  
−
def: "The topmost part of the shoot, situated at the distal extremity of the shoot axis, consists of apical meristem and the youngest leaf primordia." [TAIR:ki]
+
def: "The space of variable size controlled by stomatal guard cells in response to environmental clues." [GR:cwt]
−
subset: reference
 
  
 +
synonym: "stomatal aperture" RELATED []
  
 +
relationship: part_of PO:0002000 ! stomatal complex
  
−
[Term]
 
  
−
id: PO:0003023
 
  
−
name: root nodule
+
[Term]
  
−
def: "Enlargement or swelling on the roots of plants, particularly in the Fabaceae, inhabited by nitrogen-fixing bacteria." [ISBN:0471245208]
+
id: PO:0008044
  
 +
name: floral stomatal complex
  
 +
def: "An opening pore on the epidermis of floral organs bordered by two guard cells and serving in gas exchange." [GR:cwt]
  
  
−
===miscellaneous===
+
Term]
  
 +
id: PO:0008046
  
−
[Term]
+
name: floral stomatal pore
  
−
id: PO:0000001
+
def: "The space of variable size controlled by floral stomatal guard cells in response to environmental clues." [GR:cwt]
  
−
name: embryo proper
+
relationship: part_of PO:0008044 ! floral stomatal complex
  
−
def: "The body of the developing embryo attached to the maternal tissue in the ovule by filamentous suspensor." [TAIR:ki]
 
  
  
 +
[Term]
  
−
[Term]
+
id: PO:0020025
  
−
id: PO:0000032
+
name: micropyle
  
−
name: tetrad of microspores
+
def: "A small canal or opening through the integument(s) at the apex of an ovule." [APWeb:Glossary]
  
−
def: "A group of four haploid cells that remained joined together shortly after meiosis. Each cell will give rise to the male gametophyte." [TAIR:ki]
+
comment: In a mature seed the micropyle may remain visible as an occluded pore or may be obliterated. The micropyle originates as an opening in the integuments of an ovule through
 +
which the pollen tube usually enters the embryo sac.
  
 
subset: reference
 
subset: reference
−
 
  
  
 
[Term]
 
[Term]
  
−
id: PO:0004540
+
id: PO:0020101
  
−
name: fruit columella
+
name: stomium
  
−
def: "Central axis of the fruit." [POC:curators]
+
def: "A fissure or pore in the anther lobe through which the pollen is released." [GR:pj]
  
−
subset: Tomato
+
subset: reference
  
 +
relationship: part_of PO:0005011 ! anther dehiscence zone
  
 +
===(HP) Trichomes and hairs (done)===
  
 
[Term]
 
[Term]
  
−
id: PO:0004724
+
id: PO:0002001
  
−
name: hypocotyl-root junction
+
name: papillae
  
−
def: "Junction point of the embryonic root and hypocotyl." [TAIR:ki]
+
def: "A soft protuberance on an epidermal cell of the stigma." [ISBN:0471245208]
  
 
subset: reference
 
subset: reference
Line 217: Line 223:
 
[Term]
 
[Term]
  
−
id: PO:0006000
+
id: PO:0000029
  
−
name: hull (sensu Poaceae)
+
name: root hair tip
−
 
 
−
def: "A leaf like structure often found enclosing the grass fruit, caryopsis. It is derived from the dried lemma (PO:0009037) and palea (PO:0009038) floral bracts found in the grass floret
 
−
(PO:0006318)." [GR:pj]
 
−
 
 
−
subset: Maize
 
−
 
 
−
subset: Poaceae
 
−
 
 
−
subset: Rice
 
  
 +
def: "Tip portion of an outgrowth of a root epidermal cell." [TAIR:ki]
  
  
 
[Term]
 
[Term]
  
−
id: PO:0006345
+
id: PO:0008031
  
−
name: pollen tube
+
name: trichome branch
  
−
def: "A tubular cell extension formed by the germinating pollen grain; carries the male gametes into the ovule." [ISBN:0471245208]
+
def: "The branch on a trichome." [GR:cwt]
  
−
subset: reference
 
  
 +
[Term]
  
 +
id: PO:0020061
  
 +
name: coma
  
−
stopped here
+
def: "A tuft of hairs at one end of a seed." [APWeb:Glossary]
  
 +
synonym: "brush" RELATED []
  
−
[Term]
+
===(LP) [https://sourceforge.net/tracker/?func=detail&aid=3007368&group_id=76834&atid=835555 axil]===
  
−
id: PO:0009019
+
(also an open tracker item)
  
−
name: basal endosperm transfer layer
+
Should the PO have a generic term 'axil' and, if so, how it should be defined? See also older tracker item [https://sourceforge.net/tracker/index.php?func=detail&aid=1681621&group_id=76834&atid=835555 leaf base vs. axil?]
  
−
def: "A cell layer found in basal endosperm transfer cell." [GR:cwt]
 
  
  
−
 
+
Original data:
−
[Term]
 
  
 
id: PO:0009023
 
id: PO:0009023
Line 265: Line 264:
  
 
def: "The angle between the petiole of a leaf and the stem to which it is attached." [GR:cwt]
 
def: "The angle between the petiole of a leaf and the stem to which it is attached." [GR:cwt]
 +
 +
relationship: part_of PO:0020040 ! leaf base
  
 
xref: SF: 3007368
 
xref: SF: 3007368
  
 +
Suggest: is_a axil, part_of shoot system
 +
 +
===(HP) [https://sourceforge.net/tracker/?group_id=76834&atid=835555 Primordium]===
 +
 +
(also an open tracker item)
 +
 +
Need a class primordium, and need to make one definition for it. Also need to organize primordium terms
  
  
 
[Term]
 
[Term]
  
−
id: PO:0009024
+
id: PO:0004725
  
−
name: stylar ridge of lower floret of pedicellate spikelet of ear
+
name: abaxial side of leaf primordium
−
 
 
−
xref: SF:2959654
 
  
 +
def: "The abaxial/outer side of the leaf primordium that becomes the abaxial/lower leaf blade." [TAIR:ki]
  
  
 
[Term]
 
[Term]
  
−
id: PO:0009036
+
id: PO:0004726
  
−
name: lodicule
+
name: adaxial side of leaf primordium
  
−
def: "In a grass floret, one of two or three tiny scales or flaps of tissue outside the stamens, possibly representing reduced perianth segments." [APWeb:Glossary]
+
def: "The adaxial/inner side of the leaf primordium that becomes adaxial/upper leaf blade." [TAIR:ki]
−
 
 
−
subset: reference
 
  
 +
===(LP) easy ones (ha!)===
 +
Can be dealt with at a phone meeting.
  
  
 
[Term]
 
[Term]
  
−
id: PO:0009070
+
id: PO:0000037
  
−
name: microsporangium
+
name: shoot apex
  
−
def: "A sporangium producing microspores, usually many in number." [APWeb:Glossary]
+
def: "The topmost part of the shoot, situated at the distal extremity of the shoot axis, consists of apical meristem and the youngest leaf primordia." [TAIR:ki]
  
 
subset: reference
 
subset: reference
  
−
synonym: "anther lobe" RELATED []
+
Proposed definition: A shoot axis that is the most distal part of a shoot and has as parts a shoot apical meristem and the youngest leaf primordia."
−
 
 
−
synonym: "pollen sac" RELATED []
 
  
  
Line 310: Line 315:
 
[Term]
 
[Term]
  
−
id: PO:0009076
+
id: PO:0003023
 +
 
 +
name: root nodule
  
−
name: stylar ridge of lower floret of sessile spikelet of ear
+
def: "Enlargement or swelling on the roots of plants, particularly in the Fabaceae, inhabited by nitrogen-fixing bacteria." [ISBN:0471245208]
  
−
xref: SF:2959654
+
Proposed definition: A cardinal organ part that is an outgrowth of a root and is inhabited by nitrogen-fixing bacteria. Comment: root nodules are a symbiosis between a plant (often, but not exclusively, of the Fabaceae) and bacteria of the genera Rhizobium, Bradyrhizobium, or Azorhizobium. part_of root
  
 +
We may want to add the term root nodule meristem, dbxref: PMID:1809347
  
 +
===parts of embryo===
  
 
[Term]
 
[Term]
  
−
id: PO:0009079
+
id: PO:0000001
  
−
name: stylar ridge of upper floret of pedicellate spikelet of ear
+
name: embryo proper
−
 
 
−
xref: SF:2959654
 
  
 +
def: "The body of the developing embryo attached to the maternal tissue in the ovule by filamentous suspensor." [TAIR:ki]
  
  
 
[Term]
 
[Term]
  
−
id: PO:0009090
+
id: PO:0020096
  
−
name: aril
+
name: egg apparatus
  
−
def: "A structure associated with and often partly or wholly covering a seed and developed from the funicle or raphe." [APWeb:Glossary]
+
def: "The egg cell and two synergids located at the micropylar end of the embryo sac." [TAIR:lr]
−
 
 
−
comment: Also used more generally to refer to a similar structure derived from any part of the ovule - there has been much and sometimes acrimonious debate over the correct
 
−
definition of the term, so when used the origin of the aril should generally be given for clarity.
 
  
 
subset: reference
 
subset: reference
−
 
  
  
 
[Term]
 
[Term]
  
−
id: PO:0009092
+
id: PO:0020108
  
−
name: stylar ridge of upper floret of sessile spikelet of ear
+
name: suspensor
  
−
xref: SF:2959654
+
def: "A nearly always single file of cells at the base of the embryo derived from the basal cell." [GR:pj]
  
 +
comment: It anchors the embryo in the embryo sac and pushes it into the endosperm.
  
  
 
[Term]
 
[Term]
  
−
id: PO:0019022
+
id: PO:0020110
  
−
name: arilloid
+
name: scutellum
  
−
def: "An outgrowth from parts of the seed other than from the funiculus or raphe." [ISBN:0080280293]
+
def: "A more or less shield-shaped and absorptive portion of an embryo of grasses, probably a modified cotyledon." [APWeb:Glossary]
  
 +
synonym: "haustorial cotyledon" RELATED []
  
  
−
[Term]
 
−
 
−
id: PO:0020005
 
−
 
−
name: placentoid
 
−
 
−
def: "An inpushing of the anther wall." [APWeb:Glossary]
 
−
 
−
subset: reference
 
  
  
 +
===(MP) miscellaneous===
  
 
[Term]
 
[Term]
  
−
id: PO:0020025
+
id: PO:0000033
  
−
name: micropyle
+
name: valve
  
−
def: "A small canal or opening through the integument(s) at the apex of an ovule." [APWeb:Glossary]
+
def: "Portion of an organ that is fragmented; in capsule, the portions into which the pericarp splits at maturity." [APWeb:Glossary]
  
−
comment: In a mature seed the micropyle may remain visible as an occluded pore or may be obliterated. The micropyle originates as an opening in the integuments of an ovule through
+
subset: Arabidopsis
−
which the pollen tube usually enters the embryo sac.
 
−
 
 
−
subset: reference
 
  
  
Line 392: Line 387:
 
[Term]
 
[Term]
  
−
id: PO:0020061
+
id: PO:0000032
  
−
name: coma
+
name: tetrad of microspores
  
−
def: "A tuft of hairs at one end of a seed." [APWeb:Glossary]
+
def: "A group of four haploid cells that remained joined together shortly after meiosis. Each cell will give rise to the male gametophyte." [TAIR:ki]
  
−
synonym: "brush" RELATED []
+
subset: reference
  
  
Line 404: Line 399:
 
[Term]
 
[Term]
  
−
id: PO:0020063
+
id: PO:0004540
 +
 
 +
name: fruit columella
  
−
name: hilum
+
def: "Central axis of the fruit." [POC:curators]
  
−
def: "The scar on a seed at the place where it was attached to its funicle." [APWeb:Glossary]
+
subset: Tomato
  
  
Line 414: Line 411:
 
[Term]
 
[Term]
  
−
id: PO:0020096
+
id: PO:0004724
  
−
name: egg apparatus
+
name: hypocotyl-root junction
  
−
def: "The egg cell and two synergids located at the micropylar end of the embryo sac." [TAIR:lr]
+
def: "Junction point of the embryonic root and hypocotyl." [TAIR:ki]
  
 
subset: reference
 
subset: reference
  
  
 +
[Term]
  
−
[Term]
+
id: PO:0006000
  
−
id: PO:0020101
+
name: hull (sensu Poaceae)
  
−
name: stomium
+
def: "A leaf like structure often found enclosing the grass fruit, caryopsis. It is derived from the dried lemma (PO:0009037) and palea (PO:0009038) floral bracts found in the grass floret
 +
(PO:0006318)." [GR:pj]
  
−
def: "A fissure or pore in the anther lobe through which the pollen is released." [GR:pj]
+
subset: Maize
  
−
subset: reference
+
subset: Poaceae
  
−
relationship: part_of PO:0005011 ! anther dehiscence zone
+
subset: Rice
  
  
Line 440: Line 439:
 
[Term]
 
[Term]
  
−
id: PO:0020108
+
id: PO:0006345
  
−
name: suspensor
+
name: pollen tube
  
−
def: "A nearly always single file of cells at the base of the embryo derived from the basal cell." [GR:pj]
+
def: "A tubular cell extension formed by the germinating pollen grain; carries the male gametes into the ovule." [ISBN:0471245208]
  
−
comment: It anchors the embryo in the embryo sac and pushes it into the endosperm.
+
subset: reference
  
 +
Also pollen tube tip (PO:0000028): Tip portion of the pollen tube that is rapidly growing. [source: TAIR:ki] (this may be problematic, because it is a part of a cell)
  
  
 
[Term]
 
[Term]
  
−
id: PO:0020110
+
id: PO:0009019
  
−
name: scutellum
+
name: basal endosperm transfer layer
  
−
def: "A more or less shield-shaped and absorptive portion of an embryo of grasses, probably a modified cotyledon." [APWeb:Glossary]
+
def: "A cell layer found in basal endosperm transfer cell." [GR:cwt]
−
 
 
−
synonym: "haustorial cotyledon" RELATED []
 
−
 
 
−
 
 
−
 
 
−
[Term]
 
  
−
id: PO:0020123
+
part_of basal endosperm transfer cell
  
−
name: root cap
+
This definition and relationship is wrong. The basal endosperm transfer layer is a layer of cells (composed of basal endosperm transfer cells) which is part of the endosperm.
  
−
def: "A group of cells that covers the apical meristem of the root." [APWeb:Glossary]
+
Proposed definition for basal endosperm transfer layer: A portion of plant tissue that is part of the endosperm and is composed of basal endosperm transfer cells.
  
−
subset: reference
+
Proposed definition for basal endosperms transfer cell: A plant cell that is part of a basal endosperm transfer layer and is characterized by ingrowths of the cell wall (need to work on details of definition).
  
  
Line 476: Line 470:
 
[Term]
 
[Term]
  
−
id: PO:0020124
+
id: PO:0009036
  
−
name: root stele
+
name: lodicule
  
−
alt_id: PO:0003012
+
def: "In a grass floret, one of two or three tiny scales or flaps of tissue outside the stamens, possibly representing reduced perianth segments." [APWeb:Glossary]
−
 
 
−
def: "The central column of primary vascular tissue in the root and any tissue that it surrounds." [APWeb:Glossary]
 
−
 
 
−
comment: Includes the pericycle as the outermost layer of the stele.
 
  
 
subset: reference
 
subset: reference
−
 
−
synonym: "root vascular cylinder" RELATED []
 
  
  
Line 494: Line 482:
 
[Term]
 
[Term]
  
−
id: PO:0020125
+
id: PO:0009070
  
−
name: elongation zone
+
name: microsporangium
  
−
def: "The portion of the root that includes small, densely cytoplasmic cells that are dividing and expanding in size." [GR:pj]
+
def: "A sporangium producing microspores, usually many in number." [APWeb:Glossary]
  
 
subset: reference
 
subset: reference
  
−
synonym: "region of cell elongation" RELATED []
+
synonym: "anther lobe" RELATED []
  
−
synonym: "region of radial enlargement" RELATED []
+
synonym: "pollen sac" RELATED []
  
  
Line 510: Line 498:
 
[Term]
 
[Term]
  
−
id: PO:0020130
+
id: PO:0009090
  
−
name: central root cap
+
name: aril
  
−
def: "The central part of a root cap in which the cells are arranged in longitudinal files." [GR:pj]
+
def: "A structure associated with and often partly or wholly covering a seed and developed from the funicle or raphe." [APWeb:Glossary]
  
−
synonym: "columella cells" RELATED []
+
comment: Also used more generally to refer to a similar structure derived from any part of the ovule - there has been much and sometimes acrimonious debate over the correct
 +
definition of the term, so when used the origin of the aril should generally be given for clarity.
  
−
relationship: part_of PO:0020123 ! root cap
+
subset: reference
  
  
Line 524: Line 513:
 
[Term]
 
[Term]
  
−
id: PO:0020131
+
id: PO:0019022
  
−
name: lateral root cap
+
name: arilloid
  
−
def: "The part of the root cap that is parallel to the sides of the axis." [ISBN:0122151704]
+
def: "An outgrowth from parts of the seed other than from the funiculus or raphe." [ISBN:0080280293]
−
 
 
−
synonym: "peripheral cells" RELATED []
 
−
 
 
−
relationship: part_of PO:0020123 ! root cap
 
  
  
Line 538: Line 523:
 
[Term]
 
[Term]
  
−
id: PO:0020135
+
id: PO:0020005
  
−
name: differentiation zone
+
name: placentoid
  
−
alt_id: PO:0003002
+
def: "An inpushing of the anther wall." [APWeb:Glossary]
−
 
 
−
def: "The portion of the root located behind the elongation zone containing cells that are differentiating into their final form and function." [GR:pj]
 
  
 
subset: reference
 
subset: reference
  
−
synonym: "maturation zone" RELATED []
 
  
−
synonym: "specialization zone" RELATED []
+
[Term]
  
 +
id: PO:0020124
  
 +
name: root stele
  
−
[Term]
+
alt_id: PO:0003012
  
−
id: PO:0020149
+
def: "The central column of primary vascular tissue in the root and any tissue that it surrounds." [APWeb:Glossary]
  
−
name: quiescent center
+
comment: Includes the pericycle as the outermost layer of the stele.
  
−
def: "Hemispherically shaped aggregation of mitotically and metabolically inactive cells positioned behind the root cap." [ISBN:0122151704]
+
subset: reference
  
−
 
+
synonym: "root vascular cylinder" RELATED []
−
Back to [[POC_Conf._Call_10-6-10]]
 

Latest revision as of 15:10, 1 December 2010

Back to POC_Meeting_and_Workshop_Nov_4th_to_6th,_NYBG,_Bronx,_NY

Priority rankings next to each item by RW on 11/1/2010. May change.


(MP) Parts of the root tip

We discussed most of these at last week's meeting, and folks have commented on SF. Can move through them quickly or save for phone meeting.


Proposed new parent term: root parenchyma (PO:0025095): A portion of parenchyma tissue that is part of a root.


Original data:

id: PO:0020123

name: root cap

def: "A group of cells that covers the apical meristem of the root." [APWeb:Glossary]

subset: reference

Suggest: is_a root parenchyma

Proposed definition: A portion of root parenchyma tissue that is part of the root tip and covers the root apical meristem. Comment: Often composed of living and dead parenchyma cells. Protects the root apical meristem.


Original data:

id: PO:0020130

name: central root cap

def: "The central part of a root cap in which the cells are arranged in longitudinal files." [GR:pj]

synonym: "columella cells" RELATED [] plus columella root cap

relationship: part_of PO:0020123 ! root cap

Suggest: is_a root parenchyma

Proposed definition: A portion of root parenchyma tissue that is the central part of a root cap in which the cells are arranged in longitudinal files.


Original data:

id: PO:0020131

name: lateral root cap

def: "The part of the root cap that is parallel to the sides of the axis." [ISBN:0122151704]

synonym: "peripheral cells" RELATED []

relationship: part_of PO:0020123 ! root cap

Suggest: is_a root parenchyma

Proposed definition: A portion of parenchyma tissue that is part of a root cap and is parallel to the sides of a root axis.


Original data:

id: PO:0020149

name: quiescent center

def: "Hemispherically shaped aggregation of mitotically and metabolically inactive cells positioned behind the root cap." [ISBN:0122151704]

Suggest: is_a meristem, part_of root apical meristem

Proposed definition: A hemispherically shaped portion of meristem tissue consisting of mitotically and metabolically inactive cells that is part of the root apical meristem and is positioned behind the root cap.


Original data:

id: PO:0020135

name: differentiation zone

alt_id: PO:0003002

def: "The portion of the root located behind the elongation zone containing cells that are differentiating into their final form and function." [GR:pj]

subset: reference

synonym: "maturation zone" RELATED []

synonym: "specialization zone" RELATED []

Suggest: is_a cardinal organ part, part_of root

Proposed new name: root differentiation zone; Proposed definition: A cardinal organ part that is the part of a root and is located behind the elongation zone and contains cells that are differentiating into their final form and function. Comment: Most of the primary tissues of a root mature in the differentiation zone. This zone is where root hairs are produced.

Could add new parent term "shoot axis differentiation zone" to be parent to this term and to stem internode differentiation zone (PO:0008042)


Original data:

id: PO:0020125

name: elongation zone

def: "The portion of the root that includes small, densely cytoplasmic cells that are dividing and expanding in size." [GR:pj]

subset: reference

synonym: "region of cell elongation" RELATED []

synonym: "region of radial enlargement" RELATED []

Suggest: obsoleting this term, because the definition is wrong, and making a new term, root elongation zone; is_a cardinal organ part, part_of root tip

Proposed definition: A cardinal organ part that is part of a root that is located directly behind a root apical meristem, in which the cells are undergoing longitudinal expansion.

Comment: The elongation zone is only a few millimeters in length and is the only portion of the root in which cell elongation generally occurs. Root hairs are not yet produced in this region. Primary root tissue begin to differentiate in the root elongation zone.


Could add new parent term "shoot axis elongation zone" to be parent to this term and to stem internode elongation zone (PO:0008041)

(HP) Pores/stomata (done)

[Term]

id: PO:0002000

name: stomatal complex

def: "An opening pore on the epidermis of leaves and stems bordered by two guard cells and serving in gas exchange." [ISBN:0471245208]

synonym: "stoma" RELATED []

synonym: "stomata" RELATED []

[Term]

id: PO:0006334

name: seed micropyle

def: "A pore on the seed coat which is a remnant of the ovular micropyle." [GR:pj]

relationship: develops_from PO:0020025 ! micropyle


[Term]

id: PO:0008032

name: stomatal pore

def: "The space of variable size controlled by stomatal guard cells in response to environmental clues." [GR:cwt]

synonym: "stomatal aperture" RELATED []

relationship: part_of PO:0002000 ! stomatal complex


[Term]

id: PO:0008044

name: floral stomatal complex

def: "An opening pore on the epidermis of floral organs bordered by two guard cells and serving in gas exchange." [GR:cwt]


Term]

id: PO:0008046

name: floral stomatal pore

def: "The space of variable size controlled by floral stomatal guard cells in response to environmental clues." [GR:cwt]

relationship: part_of PO:0008044 ! floral stomatal complex


[Term]

id: PO:0020025

name: micropyle

def: "A small canal or opening through the integument(s) at the apex of an ovule." [APWeb:Glossary]

comment: In a mature seed the micropyle may remain visible as an occluded pore or may be obliterated. The micropyle originates as an opening in the integuments of an ovule through which the pollen tube usually enters the embryo sac.

subset: reference


[Term]

id: PO:0020101

name: stomium

def: "A fissure or pore in the anther lobe through which the pollen is released." [GR:pj]

subset: reference

relationship: part_of PO:0005011 ! anther dehiscence zone

(HP) Trichomes and hairs (done)

[Term]

id: PO:0002001

name: papillae

def: "A soft protuberance on an epidermal cell of the stigma." [ISBN:0471245208]

subset: reference


[Term]

id: PO:0000029

name: root hair tip

def: "Tip portion of an outgrowth of a root epidermal cell." [TAIR:ki]


[Term]

id: PO:0008031

name: trichome branch

def: "The branch on a trichome." [GR:cwt]


[Term]

id: PO:0020061

name: coma

def: "A tuft of hairs at one end of a seed." [APWeb:Glossary]

synonym: "brush" RELATED []

(LP) axil

(also an open tracker item)

Should the PO have a generic term 'axil' and, if so, how it should be defined? See also older tracker item leaf base vs. axil?


Original data:

id: PO:0009023

name: leaf axil

def: "The angle between the petiole of a leaf and the stem to which it is attached." [GR:cwt]

relationship: part_of PO:0020040 ! leaf base

xref: SF: 3007368

Suggest: is_a axil, part_of shoot system

(HP) Primordium

(also an open tracker item)

Need a class primordium, and need to make one definition for it. Also need to organize primordium terms


[Term]

id: PO:0004725

name: abaxial side of leaf primordium

def: "The abaxial/outer side of the leaf primordium that becomes the abaxial/lower leaf blade." [TAIR:ki]


[Term]

id: PO:0004726

name: adaxial side of leaf primordium

def: "The adaxial/inner side of the leaf primordium that becomes adaxial/upper leaf blade." [TAIR:ki]

(LP) easy ones (ha!)

Can be dealt with at a phone meeting.


[Term]

id: PO:0000037

name: shoot apex

def: "The topmost part of the shoot, situated at the distal extremity of the shoot axis, consists of apical meristem and the youngest leaf primordia." [TAIR:ki]

subset: reference

Proposed definition: A shoot axis that is the most distal part of a shoot and has as parts a shoot apical meristem and the youngest leaf primordia."


[Term]

id: PO:0003023

name: root nodule

def: "Enlargement or swelling on the roots of plants, particularly in the Fabaceae, inhabited by nitrogen-fixing bacteria." [ISBN:0471245208]

Proposed definition: A cardinal organ part that is an outgrowth of a root and is inhabited by nitrogen-fixing bacteria. Comment: root nodules are a symbiosis between a plant (often, but not exclusively, of the Fabaceae) and bacteria of the genera Rhizobium, Bradyrhizobium, or Azorhizobium. part_of root

We may want to add the term root nodule meristem, dbxref: PMID:1809347

parts of embryo

[Term]

id: PO:0000001

name: embryo proper

def: "The body of the developing embryo attached to the maternal tissue in the ovule by filamentous suspensor." [TAIR:ki]


[Term]

id: PO:0020096

name: egg apparatus

def: "The egg cell and two synergids located at the micropylar end of the embryo sac." [TAIR:lr]

subset: reference


[Term]

id: PO:0020108

name: suspensor

def: "A nearly always single file of cells at the base of the embryo derived from the basal cell." [GR:pj]

comment: It anchors the embryo in the embryo sac and pushes it into the endosperm.


[Term]

id: PO:0020110

name: scutellum

def: "A more or less shield-shaped and absorptive portion of an embryo of grasses, probably a modified cotyledon." [APWeb:Glossary]

synonym: "haustorial cotyledon" RELATED []



(MP) miscellaneous

[Term]

id: PO:0000033

name: valve

def: "Portion of an organ that is fragmented; in capsule, the portions into which the pericarp splits at maturity." [APWeb:Glossary]

subset: Arabidopsis


[Term]

id: PO:0000032

name: tetrad of microspores

def: "A group of four haploid cells that remained joined together shortly after meiosis. Each cell will give rise to the male gametophyte." [TAIR:ki]

subset: reference


[Term]

id: PO:0004540

name: fruit columella

def: "Central axis of the fruit." [POC:curators]

subset: Tomato


[Term]

id: PO:0004724

name: hypocotyl-root junction

def: "Junction point of the embryonic root and hypocotyl." [TAIR:ki]

subset: reference


[Term]

id: PO:0006000

name: hull (sensu Poaceae)

def: "A leaf like structure often found enclosing the grass fruit, caryopsis. It is derived from the dried lemma (PO:0009037) and palea (PO:0009038) floral bracts found in the grass floret (PO:0006318)." [GR:pj]

subset: Maize

subset: Poaceae

subset: Rice


[Term]

id: PO:0006345

name: pollen tube

def: "A tubular cell extension formed by the germinating pollen grain; carries the male gametes into the ovule." [ISBN:0471245208]

subset: reference

Also pollen tube tip (PO:0000028): Tip portion of the pollen tube that is rapidly growing. [source: TAIR:ki] (this may be problematic, because it is a part of a cell)


[Term]

id: PO:0009019

name: basal endosperm transfer layer

def: "A cell layer found in basal endosperm transfer cell." [GR:cwt]

part_of basal endosperm transfer cell

This definition and relationship is wrong. The basal endosperm transfer layer is a layer of cells (composed of basal endosperm transfer cells) which is part of the endosperm.

Proposed definition for basal endosperm transfer layer: A portion of plant tissue that is part of the endosperm and is composed of basal endosperm transfer cells.

Proposed definition for basal endosperms transfer cell: A plant cell that is part of a basal endosperm transfer layer and is characterized by ingrowths of the cell wall (need to work on details of definition).


[Term]

id: PO:0009036

name: lodicule

def: "In a grass floret, one of two or three tiny scales or flaps of tissue outside the stamens, possibly representing reduced perianth segments." [APWeb:Glossary]

subset: reference


[Term]

id: PO:0009070

name: microsporangium

def: "A sporangium producing microspores, usually many in number." [APWeb:Glossary]

subset: reference

synonym: "anther lobe" RELATED []

synonym: "pollen sac" RELATED []


[Term]

id: PO:0009090

name: aril

def: "A structure associated with and often partly or wholly covering a seed and developed from the funicle or raphe." [APWeb:Glossary]

comment: Also used more generally to refer to a similar structure derived from any part of the ovule - there has been much and sometimes acrimonious debate over the correct definition of the term, so when used the origin of the aril should generally be given for clarity.

subset: reference


[Term]

id: PO:0019022

name: arilloid

def: "An outgrowth from parts of the seed other than from the funiculus or raphe." [ISBN:0080280293]


[Term]

id: PO:0020005

name: placentoid

def: "An inpushing of the anther wall." [APWeb:Glossary]

subset: reference


[Term]

id: PO:0020124

name: root stele

alt_id: PO:0003012

def: "The central column of primary vascular tissue in the root and any tissue that it surrounds." [APWeb:Glossary]

comment: Includes the pericycle as the outermost layer of the stele.

subset: reference

synonym: "root vascular cylinder" RELATED []

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