New terms and obsolete terms for Jan2011 release

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List of Obsoleted Terms

• pollen tube (PO:0006345) 97 pages of annotations: from Arabidopsis, maize and rice

Consider pollen tube cell (PO:0025195). New term pollen tube has been requested in GO; waiting for GO ID.

• pollen tube tip (PO:0000028) 9 annotations from Arabidopsis

Consider pollen tube cell (PO:0025195). New term pollen tube tip has been requested in GO; waiting for GO ID.

• root hair (PO:0000256) ~100 annotations from various sources

This term was not made obsolete. Instead the name was changed to root hair cell. This is because the definition of the term was for a cell, not just for the hair. Annotations that belong only to the cell extension should be moved to root hair (GO:0035618).

• root hair tip (PO:0000029) 1 annotation from Arabidopsis

Condiser root hair cell (PO:0000256), or root hair tip (GO:0035619).

• floral epidermis (PO:0008043) 1 annotation from Arabidopsis

Consider carpel epidermis (PO:0025096), petal epidermis (PO:0006041), sepal epidermis (PO:0006040), stamen epidermis (PO:0025097), or tepal epidermis (PO:0025184)

• floral stomatal complex (PO:0008044) No Annotations

• elongation zone (PO:0020125) (replaced by root elongation zone (PO:0025181) ~40 annotations, all from Arabidopsis

Replaced by root elongation zone (PO:0025181).

• papillae (PO:0002001) 6 annotations from Arabidopsis

Consider: PO:0025166 papilla cell, PO:0025167 leaf papilla cell, PO:0025168 stigma papilla cell, or GO:0090395 plant cell papilla, GO:0090396 leaf papilla, GO:0090397 stigma papilla

• trichome branch (PO:0008031) (replaced by 'multicellular trichome branch cell' in PO plus unicellular trichome branch in GO):No Annotations

• differentiation zone (PO:0020135)-(replaced by root differentiation zone; PO:0020135)

• basal endosperm transfer layer (PO:0009019) (created new term with same name, but new def'n and id) No annotations

• primary root elongation zone (PO:0003003) ~40 annotations from Arabidopsis, 1 from Oryza

Replaced by new term primary root elongation zone (PO:0025257).

• lateral root elongation zone (PO:0003014) 4 annotations from Arabidopsis

Replaced by new term lateral root elongation zone (PO:0025256).

Others??

floral guard cell (PO:0008045): no annotations

floral stomatal pore (PO:0008046): no annotations

List of New Terms-general:

• plant anatomical entity (PO:0025131): An anatomical entity (CARO:0000000) that is or was part of a plant.
• plant anatomical space (PO:0025117): An anatomical space (CARO:0000005) that is part of a plant.

• axil (child of plant anatomical space)
• leaf axil (PO:0009023) not a new term
• branch axil (PO#)
• bract axil (PO#) (children of axil).

• reproductive shoot system (PO:0025082): A shoot system in the sporophytic phase that has as part at least one sporangium.
• gynoecium ridge (PO:0025088): A gynoecium in the early stages of development, characterized as a ridge on the abaxial surface of the floral meristem that develops from a gynoecium primordium.
• dehiscence zone (PO:0025092): A portion of plant tissue that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure.

• primordium (PO:0025127)
• phyllome primordium
• root parenchyma (PO:0025095): A portion of parenchyma tissue that is part of a root system.

• stele
• shoot axis stele
• branch stele
• stem stele

• sporangium (already there, but didn’t have definition),
• microsporangium
• megasporangium

• pericarp vascular bundle

• shoot system vascular system. Made different vascular systems of above ground parts child of this.

• phyllome vascular system
• sepal vascular system
• flower vascular system
• tepal vascular system new

New terms- cells

• pollen tube cell (PO:0025195): A plant cell that develops from a vegetative cell and forms a tubular extension of the pollen grain. [source: POC:rw] Comment: Carries the male gametes to into or near the ovule. May be branched in gymnosperms. See GO for pollen tube and pollen tube tip. (need to add GO term ids)
• papilla cell (PO:0025166): An epidermal pavement cell with a short protuberance. [source: POC:curators] Comment: See GO for the subcellular component papilla.(need to add GO term ids)

• stigma papilla cell (PO:0025168):
• leaf papilla cell (PO:0025167):
• archegonium egg cell
• embryo sac egg cell
• antheridium sperm cell
• pollen sperm cell

List of new terms: trichome

• trichome (PO:0000282) not new?
• multicellular trichome
• trichome cell
• multicellular trichome branch
• multicellular trichome branch cell (replaces trichome branch)
• bract trichome
• carpel trichome
• stem trichome
• branch trichome
• phyllome trichome (PO:0025186) (parent to leaf trichome; existing?)
• sepal trichome (PO:0025182)
• petal trichome (PO:0025187)
• tepal trichome (PO:0025188)

• phyllome epidermis
• stem epidermis
• branch epidermis

.

• thorn

• prickle (PO:0025169)
• leaf prickle (PO:0025175)
• root prickle (PO:0025170)
• shoot axis prickle (PO:0025171)

• spine

new terms- elongation and differentiation zones:

• plant axis differentiation zone (PO:0025119)
• plant axis differentiation zone (PO:0025119)
• root differentiation zone (PO:0020135); renamed (obsoleted?) old term differentiation zone (PO:0020135)

On dev browser 1-4-11: new:

• branch internode differentiation zone (PO:0025103): A shoot internode differentiation zone that is part of a branch internode.
• plant axis differentiation zone (PO:0025119): A cardinal organ part that is part of a plant axis and is located behind the
• shoot internode differentiation zone (PO:0025102): A plant axis differentiation zone that is part of a shoot axis.
• root differentiation zone (PO:0020135): A plant axis differentiation zone that is the part of a root and is located behind a root elongation zone.(renamed)

Old:

• lateral root differentiation zone (PO:0003016): A root differentiation zone that is part of a lateral root elongation zone and contains cells that are differentiating into their final form and function.
• primary root differentiation zone (PO:0003015): A root differentiation zone that is part of a primary root.

• stem internode differentiation zone ; PO:0008042 [show def][view annotations]

• root elongation zone (PO:0025181): (because definition of elongation zone was incorrect and added new term, new id)
• elongation zone
• plant axis elongation zone(PO:0025180)

Questions about:

• differentiation zone not new??? (see PO:0020135)

List of Terms stomatal complex:

• stomatal complex
• phyllome stomatal complex
• leaf stomatal complex
• petiole stomatal complex

• leaf lamina stomatal complex
• leaf lamina abaxial stomatal complex
• leaf lamina adaxial stomatal complex

• petiole abaxial stomatal complex
• petiole adaxial stomatal complex

• root nodule meristem (PO:0025194): A root meristem that gives rise to a root nodule.
• basal endosperm transfer layer (PO:0025196) (replaces PO:0009019, with same name): A portion of plant tissue that is part of an endosperm and is composed of basal endosperm transfer cells. [source:POC:rw]

List of Renamed Terms

• Secretory trichome was renamed glandular trichome
• seed trichome was made the primary name for PO:0004511, (changed seed hair to exact synonym, added pubescence as related synonym)
• root differentiation zone (PO:0020135; renaming of old term differentiation zone)

Changed valve to fruit valve, and updated definition and parent.

Updated name, definition and parent of Poaceae hull.

Renamed old microsporangium pollen sac and made it a child of new microsporangium. May need to obsolete old term and add new one.

changed name of PO:0025138 from compound collective tepal structure to fused collective tepal structure