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:
based on the most recent TAIR file on the SVN:
- 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
