New terms and obsolete terms for May2011 release

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List of Terms made Obsolete with associated annotations:

• PO:0004000 apical cell:2 from TAIR

-replaced_by embryonic apical cell (PO:0025284)

• PO:0005008 fruit septum: 1 from TAIR

-consider fruit septum (PO:0025268) or fruit replum (PO:0025267)

-annotations for Arabidopsis should go to fruit replum, because it does not have a septum.

• PO:0005009 carpel septum: 2 from TAIR

-consider ovary septum (PO:0025262) or ovary replum (PO:0025272)

-annotations for Arabidopsis should go to ovary replum, because it does not have a septum.

• PO:0005016 replum:3 from TAIR

-consider ovary replum (PO:0025272) and fruit replum (PO:0025267).

TAIR should check existing annotation to see where they should go (are they from a mature fruit or a gynoecium? See: http://www.ncbi.nlm.nih.gov/pubmed/17592013?dopt=Abstract)

• PO:0006074 procambium:12 from TAIR

-replaced_by procambium (PO:0025275)

• PO:0006306 shoot procambium: 3 from TAIR

-replaced_by shoot procambium (PO:0025276)

• PO:0009070 pollen sac:9 from TAIR

-replaced_by pollen sac (PO:0025277)

• PO:0020092 megagametophyte: 37 from TAIR

-consider megagametophyte (PO:0025279), consider embryo sac (PO:0025074) and consider, archegonium microgametophyte (PO:0025282)

-Annotations for TAIR should probably go to embryo sac. Embryo sac was a synonym of the obsolete term megagametophyte.

• PO:0020091 (w/ alternate id PO:0020007) microgametophyte:13,808- from TAIR and Maize GDB

-Should be consider microgametophyte (PO:0025280), consider pollen (PO:0025281) and consider, antheridium microgametophyte (PO:0025283)

-Annotations for TAIR and MaizeGDB should probably go to pollen. Pollen and pollen grain were synonyms of the obsolete term microgametophyte.

-comment: original terms for megagametophyte and microgametophyte were created with angiosperms in mind, wanted to make broader definition

List from JE's script:

• apical cell PO:0004000 (2)

* fruit septum PO:0005008 (3)

* carpel septum PO:0005009 (1)

• replum PO:0005016 (3)

* procambium PO:0006074 (16)

• shoot procambium PO:0006306 (3)
• pollen sac PO:0009070 (9)

* microgametophyte PO:0020091 (17,864)

* megagametophyte PO:0020092 (40)

Already obsoleted in live version:

• pollen tube PO:0006345 (1)

• seedling PO:0008037 (5)

New terms added by category:

This page is under construction...

Whole plant growth stages:

PO:0028002 sporophyte phase

PO:0028003 gametophyte phase

PO:0030006 protonema phase

Upper-level PAO terms

PO:0025269 collective organ part structure

PO:0030078 rhizoid

Terms for bryophytes and pteridophytes

(Some of these terms are applicable to seed plants as well)

whole plants

PO:0025282 archegonium megagametophyte

PO:0025283 antheridium microgametophyte

PO:0030027 thallus

plant organs

PO:0030020 gametophore axis

PO:0030021 gametophore branch

PO:0030022 gametophore stem

PO:0030028 pergonial bract

PO:0030029 sporphyte foot

PO:0030030 perichaetal bract

PO:0030031 gametophytic perianth

PO:0030032 seta

PO:0030033 antheridiophore

PO:0030034 archegoniaphore

PO:0030055 pseudopodium

plant cells

PO:0025317 axillary hair terminal cell

PO:0025319 axillary hair basal cell

PO:0030001 chloronema cell

PO:0030002 caulonema cell

PO:0030007 apical cell

PO:0030008 root apical cell

PO:0030009 shoot apical cell

PO:0030010 shoot axis apical cell

PO:0030011 leaf apical cell

PO:0030012 vascular leaf apical cell

PO:0030013 non-vascular leaf apical cell

PO:0030014 gametophytic apical cell

PO:0030015 sporophytic apical cell

PO:0030016 seta apical cell

PO:0030019 gametophore apical cell

PO:0030023 gametophore axis apical cell

PO:0030024 vascular shoot axis apical cell

PO:0030025 thallus apical cell

PO:0030045 stereid

PO:0030046 protonema meristematic apical cell

PO:0030052 antheridium jacket layer cell

PO:0030056 archesporial cell

PO:0030057 alar cell

PO:0030058 brachycyte

PO:0030059 tmema cell

PO:0030062 gametophore axillary hair terminal cell

PO:0030064 gametophore axillary hair basal cell

PO:0030065 archegonium neck canal cell

PO:0030067 protonema side branch initial

PO:0030068 epidermal rhizoid initial

PO:0030077 protonemal side branch rhizoid initial

PO:0030080 rhizoid meristematic apical cell

PO:0030081 caulonema meristematic apical cell

PO:0030082 chloronema meristematic apical cell

PO:0030083 gametophore bud initial

portions of plant tissue

PO:0025309 microsporangium endothecium

PO:0025310 megasporangium endothecium

PO:0025311 microsporangium exothecium

PO:0025312 megasporangium exothecium

PO:0025313 tapetum

PO:0025314 microsporangium tapetum

PO:0025315 megasporangium tapetum

PO:0025316 axillary hair

PO:0025318 axillary hair base

PO:0030003 protonema

PO:0030004 chloronema

PO:0030005 caulonema

PO:0030047 hydrome

PO:0030048 leptome

PO:0030049 sporangium wall endothecium

PO:0030050 stereome

PO:0030051 central strand

PO:0030053 antheridium jacket layer

PO:0030054 epiphragm

PO:0030060 gametophore axillary hair

PO:0030061 tmema

PO:0030063 gametophore axillary hair base

PO:0030069 paraphyllium

PO:0030070 paraphysis

PO:0030072 costa

PO:0030073 exothecium

PO:0030074 archesporium

PO:0030084 amphithecium

PO:0030085 protosporangium endothecium

cardinal organ parts

PO:0025306 sporangium wall

PO:0025307 microsporangium wall

PO:0025308 megasporangium wall

PO:0030035 antheridium stalk

PO:0030036 archegonium stalk

PO:0030037 spore capsule calyptra

PO:0030038 venter

PO:0030039 archegonium neck

PO:0030040 sporangium base

PO:0030041 sporangium theca

PO:0030042 peristome

PO:0030043 peristome tooth

PO:0030044 spore capsule operculum

PO:0030066 archegonium neck canal

PO:0030075 antheridium head

PO:0030076 achegonium head

collective plant structures

PO:0030018 gametophore

PO:0030026 gametophore bud

Plant anatomical spaces

PO:0030017 spore capsule mouth

PO:0025322 hydathode pore

rhizoids

PO:0030071 epidermal rhizoid

PO:0030079 protonemal rhizoid

embryo and seedling plant structures

PO:0025284 embryo apical cell

PO:0025285 callus parenchyma cell

PO:0025286 embryo coleoptile

PO:0025287 seedling coleoptile

PO:0025288 embryo coleorhiza

PO:0025289 seedling coleorhiza

PO:0025290 embryo hypocotyl

PO:0025291 seedling hypocotyl

PO:0025292 embryo epicotyl

PO:0025293 seedling epicotyl

PO:0025294 embryo mesocotyl

PO:0025295 seedling mesocotyl

PO:0025296 embryo radicle

PO:0025297 seedling radicle

PO:0025300 embryo hypocotyl-root junction

PO:0025301 seedling hypocotyl-root junction

PO:0025302 somatic plant embryo

PO:0025303 zygotic plant embryo

PO:0025304 cultured zygote-derived plant embryo

PO:0025305 microspore-derived cultured plant embryo

Stomatal terms

PO:0000062 stomatal initial (stomatal meristermoid)

PO:0025217 carpel stomatal complex

PO:0025218 petal stomatal complex

PO:0025219 sepal stomatal complex

PO:0025220 stamen stomatal complex

PO:0025221 tepal stomatal complex

in vitro plant structures

PO:0025304 cultured zygote-derived plant embryo

PO:0025305 microspore-derived cultured plant embryo

Miscellaneous

plant organs

PO:0025277 pollen sac

PO:0025278 rhizome scale leaf

plant cells

PO:0000063 leaf procambial cell

PO:0000064 xylem pole pericycle cell

PO:0000065 phloem pole pericycle cell

PO:0025256 lateral root elongation zone

PO:0025257 primary root elongation zone

PO:0025258 procambial cell

PO:0025261 pericycle cell

PO:0030008 root apical cell

PO:0030012 vascular leaf apical cell

portions of plant tissue

PO:0025259 leaf procambium

PO:0025260 shoot axis procambium

PO:0025273 stem procambium

PO:0025274 branch procambium

PO:0025275 procambium

PO:0025276 shoot procambium

cardinal organ parts

PO:0025298 fruit operculum

PO:0025299 perianth calyptra

PO:0025321 cotyledonary node

other

PO:0025262 ovary septum

PO:0025263 locule

PO:0025264 sporangium locule

PO:0025265 anther locule

PO:0025266 ovary locule

PO:0025267 fruit replum

PO:0025268 fruit septum

PO:0025270 fruit locule

PO:0025271 spore capsule locule

PO:0025272 ovary replum

PO:0025279 megagametophyte

PO:0025280 microgametophyte

PO:0025281 pollen

PO:0025320 cotyledonary node rhizoid

Terms that replace obsoleted terms:

(These are duplicated in the lists above)

ovary septum (PO:0025262) or replum (PO:0005016) replaces PO:0005009 carpel septum,

fruit septum (PO:0025268) or fruit replum (PO:0025267) replaces PO:0005008 obsolete fruit septum

ovary replum (PO:0025272) or fruit replum (PO:0025267) replaces PO:0005016 replum

procambium (PO:0025275) replaces PO:0006074 obsolete procambium

shoot procambium (PO:0025276) replaces PO:0006306 obsolete shoot procambium

pollen sac (PO:0025277) replaces PO:0009070 obsolete pollen sac

megagametophyte (PO:0025279) replaces PO:0020092 obsolete megagametophyte

microgametophyte (PO:0025280) replaces PO:0020091 w/ alternate id PO:0020007 obsolete microgametophyte

embryo apical cell (PO:0025284) replaces PO:0004000 apical cell

Merged terms

meristemoid (PO:0000070) was merged into intial cell (PO:0004011)

fruit aleurone layer (PO:0008004) was merged into aleurone layer (PO:0005360). Removed part_of fruit relation, because it was redundant with part_of endosperm relation.

Merged moss capsule (PO:0025232) into sporangium (PO:0025094). Added spore capsule as exact synonym.

Merged spore capsule locule (PO:0025271) into sporangium locule (PO:0025265).

New Terms in numerical order (12/2010-5/2011 ):

PO:0000062 stomatal initial (stomatal meristermoid)

PO:0000063 leaf procambial cell

PO:0000064 xylem pole pericycle cell

PO:0000065 phloem pole pericycle cell

PO:0028002 sporophyte phase

PO:0028003 gametophyte phase

PO:0025217 carpel stomatal complex

PO:0025218 petal stomatal complex

PO:0025219 sepal stomatal complex

PO:0025220 stamen stomatal complex

PO:0025221 tepal stomatal complex

PO:0025256 lateral root elongation zone

PO:0025257 primary root elongation zone

PO:0025258 procambial cell

PO:0025259 leaf procambium

PO:0025260 shoot axis procambium

PO:0025261 pericycle cell

PO:0025262 ovary septum

PO:0025263 locule

PO:0025264 sporangium locule

PO:0025265 anther locule

PO:0025266 ovary locule

PO:0025267 fruit replum

PO:0025268 fruit septum

PO:0025269 collective organ part structure

PO:0025270 fruit locule

PO:0025271 spore capsule locule

PO:0025272 ovary replum

PO:0025273 stem procambium

PO:0025274 branch procambium

PO:0025275 procambium

PO:0025276 shoot procambium

PO:0025277 pollen sac

PO:0025278 rhizome scale leaf

PO:0025279 megagametophyte

PO:0025280 microgametophyte

PO:0025281 pollen

PO:0025282 archegonium megagametophyte

PO:0025283 antheridium microgametophyte

PO:0025284 embryo apical cell

PO:0025285 callus parenchyma cell

PO:0025286 embryo coleoptile

PO:0025287 seedling coleoptile

PO:0025288 embryo coleorhiza

PO:0025289 seedling coleorhiza

PO:0025290 embryo hypocotyl

PO:0025291 seedling hypocotyl

PO:0025292 embryo epicotyl

PO:0025293 seedling epicotyl

PO:0025294 embryo mesocotyl

PO:0025295 seedling mesocotyl

PO:0025296 embryo radicle

PO:0025297 seedling radicle

PO:0025298 fruit operculum

PO:0025299 perianth calyptra

PO:0025300 embryo hypocotyl-root junction

PO:0025301 seedling hypocotyl-root junction

PO:0025302 somatic plant embryo

PO:0025303 zygotic plant embryo

PO:0025304 cultured zygote-derived plant embryo

PO:0025305 microspore-derived cultured plant embryo

PO:0025306 sporangium wall

PO:0025307 microsporangium wall

PO:0025308 megasporangium wall

PO:0025309 microsporangium endothecium

PO:0025310 megasporangium endothecium

PO:0025311 microsporangium exothecium

PO:0025312 megasporangium exothecium

PO:0025313 tapetum

PO:0025314 microsporangium tapetum

PO:0025315 megasporangium tapetum

PO:0025316 axillary hair

PO:0025317 axillary hair terminal cell

PO:0025318 axillary hair base

PO:0025319 axillary hair basal cell

PO:0025320 cotyledonary node rhizoid

PO:0025321 cotyledonary node

PO:0025322 hydathode pore

PO:0030001 chloronema cell

PO:0030002 caulonema cell

PO:0030003 protonema

PO:0030004 chloronema

PO:0030005 caulonema

PO:0030006 protonema phase

PO:0030007 apical cell

PO:0030008 root apical cell

PO:0030009 shoot apical cell

PO:0030010 shoot axis apical cell

PO:0030011 leaf apical cell

PO:0030012 vascular leaf apical cell

PO:0030013 non-vascular leaf apical cell

PO:0030014 gametophytic apical cell

PO:0030015 sporophytic apical cell

PO:0030016 seta apical cell

PO:0030017 spore capsule mouth

PO:0030018 gametophore

PO:0030019 gametophore apical cell

PO:0030020 gametophore axis

PO:0030021 gametophore branch

PO:0030022 gametophore stem

PO:0030023 gametophore axis apical cell

PO:0030024 vascular shoot axis apical cell

PO:0030025 thallus apical cell

PO:0030026 gametophore bud

PO:0030027 thallus

PO:0030028 pergonial bract

PO:0030029 sporphyte foot

PO:0030030 perichaetal bract

PO:0030031 gametophytic perianth

PO:0030032 seta

PO:0030033 antheridiophore

PO:0030034 archegoniaphore

PO:0030035 antheridium stalk

PO:0030036 archegonium stalk

PO:0030037 spore capsule calyptra

PO:0030038 venter

PO:0030039 archegonium neck

PO:0030040 sporangium base

PO:0030041 sporangium theca

PO:0030042 peristome

PO:0030043 peristome tooth

PO:0030044 spore capsule operculum

PO:0030045 stereid PO:0030045

PO:0030046 protonema meristematic apical cell

PO:0030047 hydrome

PO:0030048 leptome

PO:0030049 endothecium

PO:0030050 stereome

PO:0030051 central strand

PO:0030052 antheridium jacket layer cell

PO:0030053 antheridium jacket layer

PO:0030054 epiphragm

PO:0030055 pseudopodium

PO:0030056 archesporial cell

PO:0030057 alar cell

PO:0030058 brachycyte

PO:0030059 tmema cell

PO:0030060 gametophore axillary hair

PO:0030061 tmema

PO:0030062 gametophore axillary hair terminal cell

PO:0030063 gametophore axillary hair base

PO:0030064 gametophore axillary hair basal cell

PO:0030065 archegonium neck canal cell

PO:0030066 archegonium neck canal

PO:0030067 protonema side branch initial

PO:0030068 epidermal rhizoid initial

PO:0030069 paraphyllium

PO:0030070 paraphysis

PO:0030071 epidermal rhizoid

PO:0030072 costa

PO:0030073 exothecium

PO:0030074 archesporium

PO:0030075 antheridium head

PO:0030076 achegonium head

PO:0030077 protonemal side branch rhizoid initial

PO:0030078 rhizoid

PO:0030079 protonemal rhizoid

PO:0030080 rhizoid meristematic apical cell

PO:0030081 caulonema meristematic apical cell

PO:0030082 chloronema meristematic apical cell

PO:0030083 gametophore bud initial

PO:0030084 amphithecium

PO:0030085 protosporangium endothecium