Categorized list of terms without parents

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 []