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===
 
  
 +
'''Proposed new parent term: root parenchyma''' (PO:0025095): A portion of parenchyma tissue that is part of a root.
  
−
===Trichomes===
 
  
−
[Term]
+
Original data:
 +
 
 +
id: PO:0020123
  
−
id: PO:0000001
+
name: root cap
  
−
name: embryo proper
+
def: "A group of cells that covers the apical meristem of the root." [APWeb:Glossary]
  
−
def: "The body of the developing embryo attached to the maternal tissue in the ovule by filamentous suspensor." [TAIR:ki]
+
subset: reference
  
 +
Suggest: is_a root parenchyma
  
−
[Term]
+
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.
  
−
id: PO:0000029
 
  
−
name: root hair tip
+
Original data:
  
−
def: "Tip portion of an outgrowth of a root epidermal cell." [TAIR:ki]
+
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:0000032
+
synonym: "columella cells" RELATED [] plus columella root cap
  
−
name: tetrad of microspores
+
relationship: part_of PO:0020123 ! root cap
  
−
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]
+
Suggest: is_a root parenchyma
  
−
subset: reference
+
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.
  
  
−
[Term]
 
  
−
id: PO:0000033
+
Original data:
  
−
name: valve
+
id: PO:0020131
  
−
def: "Portion of an organ that is fragmented; in capsule, the portions into which the pericarp splits at maturity." [APWeb:Glossary]
+
name: lateral root cap
  
−
subset: Arabidopsis
+
def: "The part of the root cap that is parallel to the sides of the axis." [ISBN:0122151704]
  
 +
synonym: "peripheral cells" RELATED []
  
−
[Term]
+
relationship: part_of PO:0020123 ! root cap
  
−
id: PO:0000037
+
Suggest: is_a root parenchyma
  
−
name: shoot apex
+
Proposed definition: A portion of parenchyma tissue that is part of a root cap and is parallel to the sides of a root axis.
  
−
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
 
  
 +
Original data:
  
−
[Term]
+
id: PO:0020149
  
−
id: PO:0002000
+
name: quiescent center
  
−
name: stomatal complex
+
def: "Hemispherically shaped aggregation of mitotically and metabolically inactive cells positioned behind the root cap." [ISBN:0122151704]
  
−
def: "An opening pore on the epidermis of leaves and stems bordered by two guard cells and serving in gas exchange." [ISBN:0471245208]
+
Suggest: is_a meristem, part_of root apical meristem
  
−
synonym: "stoma" RELATED []
+
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.
  
−
synonym: "stomata" RELATED []
 
  
 +
Original data:
  
−
[Term]
+
id: PO:0020135
  
−
id: PO:0002001
+
name: differentiation zone
  
−
name: papillae
+
alt_id: PO:0003002
  
−
def: "A soft protuberance on an epidermal cell of the stigma." [ISBN:0471245208]
+
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]
+
Suggest: is_a cardinal organ part, part_of root
  
−
id: PO:0003023
+
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.
  
−
name: root nodule
+
Could add new parent term "shoot axis differentiation zone" to be parent to this term and to stem internode differentiation zone (PO:0008042)
  
−
def: "Enlargement or swelling on the roots of plants, particularly in the Fabaceae, inhabited by nitrogen-fixing bacteria." [ISBN:0471245208]
 
  
 +
Original data:
  
 +
id: PO:0020125
  
−
[Term]
+
name: elongation zone
  
−
id: PO:0004540
+
def: "The portion of the root that includes small, densely cytoplasmic cells that are dividing and expanding in size." [GR:pj]
  
−
name: fruit columella
+
subset: reference
  
−
def: "Central axis of the fruit." [POC:curators]
+
synonym: "region of cell elongation" RELATED []
−
 
 
−
subset: Tomato
 
  
 +
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
  
−
[Term]
+
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.
  
−
id: PO:0004707
+
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.
  
−
name: fruit dehiscence zone
 
  
−
def: "A narrow band of cells that extends along the dehiscent fruit's dehiscence region which upon fruit maturation by drying, undergoes cell separation. This allows the valves to detach
+
Could add new parent term "shoot axis elongation zone" to be parent to this term and to stem internode elongation zone (PO:0008041)
−
from the replum and for the seeds to be dispersed." [GR:pj, TAIR:ki]
 
−
 
 
−
comment: Found in dehiscent fruit.
 
−
 
 
−
subset: Arabidopsis
 
  
 +
===(HP) Pores/stomata (done)===
  
 
[Term]
 
[Term]
  
−
id: PO:0004719
+
id: PO:0002000
  
−
name: hilum groove
+
name: stomatal complex
  
−
def: "Longitudinal groove in the testa through the prominent hilum of the seed." [POC:curators]
+
def: "An opening pore on the epidermis of leaves and stems bordered by two guard cells and serving in gas exchange." [ISBN:0471245208]
  
−
synonym: "faboid split" RELATED []
+
synonym: "stoma" RELATED []
  
 +
synonym: "stomata" RELATED []
  
 
[Term]
 
[Term]
  
−
id: PO:0004724
+
id: PO:0006334
 +
 
 +
name: seed micropyle
  
−
name: hypocotyl-root junction
+
def: "A pore on the seed coat which is a remnant of the ovular micropyle." [GR:pj]
  
−
def: "Junction point of the embryonic root and hypocotyl." [TAIR:ki]
+
relationship: develops_from PO:0020025 ! micropyle
  
−
subset: reference
 
  
  
 
[Term]
 
[Term]
  
−
id: PO:0004725
+
id: PO:0008032
  
−
name: abaxial side of leaf primordium
+
name: stomatal pore
  
−
def: "The abaxial/outer side of the leaf primordium that becomes the abaxial/lower leaf blade." [TAIR:ki]
+
def: "The space of variable size controlled by stomatal guard cells in response to environmental clues." [GR:cwt]
  
 +
synonym: "stomatal aperture" RELATED []
  
−
[Term]
+
relationship: part_of PO:0002000 ! stomatal complex
−
 
 
−
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]
 
  
  
Line 164: Line 163:
 
[Term]
 
[Term]
  
−
id: PO:0005011
+
id: PO:0008044
  
−
name: anther dehiscence zone
+
name: floral stomatal complex
  
−
def: "A narrow band of cells that extends along the entire length of the anther. This site is observed as an indentation between the locules of each theca. Upon anther maturation, cell
+
def: "An opening pore on the epidermis of floral organs bordered by two guard cells and serving in gas exchange." [GR:cwt]
−
separation within the dehiscence zone allows the anther wall to break and for pollen to be released." [PMID:15319479]
 
  
  
−
[Term]
+
Term]
  
−
id: PO:0006000
+
id: PO:0008046
  
−
name: hull (sensu Poaceae)
+
name: floral stomatal pore
  
−
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
+
def: "The space of variable size controlled by floral stomatal guard cells in response to environmental clues." [GR:cwt]
−
(PO:0006318)." [GR:pj]
 
  
−
subset: Maize
+
relationship: part_of PO:0008044 ! floral stomatal complex
−
 
 
−
subset: Poaceae
 
−
 
 
−
subset: Rice
 
  
  
Line 191: Line 184:
 
[Term]
 
[Term]
  
−
id: PO:0006212
+
id: PO:0020025
  
−
name: protective layer
+
name: micropyle
  
−
def: "The layer of cells in the abscission zone that have lignin and suberin depositions and are found on the axial side of the break or exposed surface of abscission."  
+
def: "A small canal or opening through the integument(s) at the apex of an ovule." [APWeb:Glossary]
−
[ISBN:0122151704]
 
  
 +
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:0006331
 
−
 
 
−
name: seed raphe
 
−
 
 
−
def: "The ridge along the body of the seed formed from the part of funiculus that was adnate to the ovule." [ISBN:047124529]
 
−
 
 
  
  
 
[Term]
 
[Term]
  
−
id: PO:0006332
+
id: PO:0020101
  
 +
name: stomium
  
−
name: seed funicle
+
def: "A fissure or pore in the anther lobe through which the pollen is released." [GR:pj]
  
−
def: "Remnants of the funicle from the ovary where it attaches the ovule to the placenta." [GR:pj]
+
subset: reference
  
 +
relationship: part_of PO:0005011 ! anther dehiscence zone
  
 +
===(HP) Trichomes and hairs (done)===
  
 
[Term]
 
[Term]
  
−
id: PO:0006334
+
id: PO:0002001
  
−
name: seed micropyle
+
name: papillae
  
−
def: "A pore on the seed coat which is a remnant of the ovular micropyle." [GR:pj]
+
def: "A soft protuberance on an epidermal cell of the stigma." [ISBN:0471245208]
−
 
 
−
relationship: develops_from PO:0020025 ! micropyle
 
  
 +
subset: reference
  
  
 
[Term]
 
[Term]
  
−
id: PO:0006345
+
id: PO:0000029
  
−
name: pollen tube
+
name: root hair tip
−
 
 
−
def: "A tubular cell extension formed by the germinating pollen grain; carries the male gametes into the ovule." [ISBN:0471245208]
 
−
 
 
−
subset: reference
 
  
 +
def: "Tip portion of an outgrowth of a root epidermal cell." [TAIR:ki]
  
  
Line 252: Line 237:
  
 
def: "The branch on a trichome." [GR:cwt]
 
def: "The branch on a trichome." [GR:cwt]
−
 
  
  
 
[Term]
 
[Term]
  
−
id: PO:0008032
+
id: PO:0020061
  
−
name: stomatal pore
+
name: coma
  
−
def: "The space of variable size controlled by stomatal guard cells in response to environmental clues." [GR:cwt]
+
def: "A tuft of hairs at one end of a seed." [APWeb:Glossary]
  
−
synonym: "stomatal aperture" RELATED []
+
synonym: "brush" RELATED []
  
−
relationship: part_of PO:0002000 ! stomatal complex
+
===(LP) [https://sourceforge.net/tracker/?func=detail&aid=3007368&group_id=76834&atid=835555 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 [https://sourceforge.net/tracker/index.php?func=detail&aid=1681621&group_id=76834&atid=835555 leaf base vs. axil?]
  
−
[Term]
 
  
−
id: PO:0008044
 
  
−
name: floral stomatal complex
+
Original data:
  
−
def: "An opening pore on the epidermis of floral organs bordered by two guard cells and serving in gas exchange." [GR:cwt]
+
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]
  
−
[Term]
+
relationship: part_of PO:0020040 ! leaf base
  
−
id: PO:0008046
+
xref: SF: 3007368
  
−
name: floral stomatal pore
+
Suggest: is_a axil, part_of shoot system
  
−
def: "The space of variable size controlled by floral stomatal guard cells in response to environmental clues." [GR:cwt]
+
===(HP) [https://sourceforge.net/tracker/?group_id=76834&atid=835555 Primordium]===
  
−
relationship: part_of PO:0008044 ! floral stomatal complex
+
(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:0009019
+
id: PO:0004725
  
−
name: basal endosperm transfer layer
+
name: abaxial side of leaf primordium
−
 
 
−
def: "A cell layer found in basal endosperm transfer cell." [GR:cwt]
 
  
 +
def: "The abaxial/outer side of the leaf primordium that becomes the abaxial/lower leaf blade." [TAIR:ki]
  
  
 
[Term]
 
[Term]
  
−
id: PO:0009023
+
id: PO:0004726
  
−
name: leaf axil
+
name: adaxial side of leaf primordium
  
−
def: "The angle between the petiole of a leaf and the stem to which it is attached." [GR:cwt]
+
def: "The adaxial/inner side of the leaf primordium that becomes adaxial/upper leaf blade." [TAIR:ki]
−
 
 
−
xref: SF: 3007368
 
  
 +
===(LP) easy ones (ha!)===
 +
Can be dealt with at a phone meeting.
  
  
 
[Term]
 
[Term]
  
−
id: PO:0009024
+
id: PO:0000037
  
−
name: stylar ridge of lower floret of pedicellate spikelet of ear
+
name: shoot apex
  
−
xref: SF:2959654
+
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: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
 
  
  
Line 337: Line 315:
 
[Term]
 
[Term]
  
−
id: PO:0009070
+
id: PO:0003023
  
−
name: microsporangium
+
name: root nodule
  
−
def: "A sporangium producing microspores, usually many in number." [APWeb:Glossary]
+
def: "Enlargement or swelling on the roots of plants, particularly in the Fabaceae, inhabited by nitrogen-fixing bacteria." [ISBN:0471245208]
−
 
 
−
subset: reference
 
−
 
 
−
synonym: "anther lobe" RELATED []
 
  
−
synonym: "pollen sac" RELATED []
+
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:0009076
+
id: PO:0000001
  
−
name: stylar ridge of lower floret of sessile 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:0009079
+
id: PO:0020096
  
−
name: stylar ridge of upper floret of pedicellate spikelet of ear
+
name: egg apparatus
  
−
xref: SF:2959654
+
def: "The egg cell and two synergids located at the micropylar end of the embryo sac." [TAIR:lr]
  
 +
subset: reference
  
  
 
[Term]
 
[Term]
  
−
id: PO:0009090
+
id: PO:0020108
  
−
name: aril
+
name: suspensor
  
−
def: "A structure associated with and often partly or wholly covering a seed and developed from the funicle or raphe." [APWeb:Glossary]
+
def: "A nearly always single file of cells at the base of the embryo derived from the basal cell." [GR:pj]
−
 
 
−
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
 
  
 +
comment: It anchors the embryo in the embryo sac and pushes it into the endosperm.
  
  
 
[Term]
 
[Term]
  
−
id: PO:0009092
+
id: PO:0020110
  
−
name: stylar ridge of upper floret of sessile spikelet of ear
+
name: scutellum
−
 
 
−
xref: SF:2959654
 
  
 +
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:0019022
 
−
 
−
name: arilloid
 
−
 
−
def: "An outgrowth from parts of the seed other than from the funiculus or raphe." [ISBN:0080280293]
 
  
  
 +
===(MP) miscellaneous===
  
 
[Term]
 
[Term]
  
−
id: PO:0020005
+
id: PO:0000033
  
−
name: placentoid
+
name: valve
  
−
def: "An inpushing of the anther wall." [APWeb:Glossary]
+
def: "Portion of an organ that is fragmented; in capsule, the portions into which the pericarp splits at maturity." [APWeb:Glossary]
  
−
subset: reference
+
subset: Arabidopsis
  
  
Line 420: Line 387:
 
[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
Line 435: Line 399:
 
[Term]
 
[Term]
  
−
id: PO:0020061
+
id: PO:0004540
  
−
name: coma
+
name: fruit columella
  
−
def: "A tuft of hairs at one end of a seed." [APWeb:Glossary]
+
def: "Central axis of the fruit." [POC:curators]
  
−
synonym: "brush" RELATED []
+
subset: Tomato
  
  
Line 447: Line 411:
 
[Term]
 
[Term]
  
−
id: PO:0020063
+
id: PO:0004724
  
−
name: hilum
+
name: hypocotyl-root junction
  
−
def: "The scar on a seed at the place where it was attached to its funicle." [APWeb:Glossary]
+
def: "Junction point of the embryonic root and hypocotyl." [TAIR:ki]
  
 +
subset: reference
  
  
 
[Term]
 
[Term]
  
−
id: PO:0020096
+
id: PO:0006000
  
−
name: egg apparatus
+
name: hull (sensu Poaceae)
  
−
def: "The egg cell and two synergids located at the micropylar end of the embryo sac." [TAIR:lr]
+
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: reference
+
subset: Maize
  
 +
subset: Poaceae
  
−
 
+
subset: Rice
−
[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
 
  
  
Line 483: 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 []
+
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.
  
−
[Term]
+
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).
−
 
 
−
id: PO:0020123
 
−
 
 
−
name: root cap
 
−
 
 
−
def: "A group of cells that covers the apical meristem of the root." [APWeb:Glossary]
 
−
 
 
−
subset: reference
 
  
  
Line 519: 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 537: 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 553: 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 567: 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 581: 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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