Difference between revisions of "New terms and obsolete terms for May2011 release"

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Back to [[May_2011_Release_Page]]
 
Back to [[May_2011_Release_Page]]
  
−
==New terms added==
+
=List of Terms made obsolete with associated annotations:=
 +
* Note: Links below go to the annotations on the '''live browser''', will not work after the release
 +
http://wiki.plantontology.org:8080/index.php/Summary_of_changes_to_the_Plant_Ontology_Oct2010
 +
Numbers based on the most recent association files on the SVN (TAIR Version #1129):
 +
Note some of these are different than the ones on the live site as TAIR has updated since the last release (in bold).
  
−
===week of 02/02/2011===
+
* apical cell PO:0004000 (2)
 +
*'''fruit septum PO:0005008 (3)'''
 +
*'''carpel septum PO:0005009 (1)'''
 +
* replum PO:0005016 (3)
 +
*'''procambium PO:0006074 (16)'''
  
−
PO:0000062 stomatal initial (stomatal meristermoid, stomatal initial cell)
+
* shoot procambium PO:0006306 (3)
 +
* pollen sac PO:0009070      (9)
 +
*'''microgametophyte PO:0020091  (17,864)'''
  
−
PO:0025258 procambial cell
+
*'''megagametophyte PO:0020092 (40)'''
  
−
PO:0025259 leaf procambium
+
'''Already obsoleted in live version:'''  Why are these still in the TAIR file?
 +
See [http://wiki.plantontology.org:8080/index.php/Summary_of_changes_to_the_Plant_Ontology_Oct2010 Oct 2010 Release]
 +
* pollen tube PO:0006345      (1)
 +
This term was made obsolete because it is a subcellular component. See GO for the term pollen tube (GO:0090406). Since a pollen tube is part_of a pollen tube cell, annotations for pollen tube may also go to the more general term pollen tube cell (PO:0025195).
  
−
PO:0025260 shoot axis procambium
+
* seedling PO:0008037      (5)
 +
This term was obsoleted in the previous release -
 +
Replaced by whole plant growth stage 'seedling growth stage' (PO:0007131) and whole plant (PO:0000003) in the PAO.
 +
xref: OBO_SF_PO:2972241
  
−
PO:0000063 leaf procambial cell
+
po_anatomy_gene_arabidopsis_tair.assoc: move to whole plant PO:0000003
  
−
PO:0025261 pericycle cell
+
po_temporal_gene_arabidopsis_tair.assoc: Copy to this file and replace with seedling growth stage (PO:0007131)
  
−
PO:0000064 xylem pole pericycle cell
+
===PO:0004000 apical cell:===
 +
[http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0004000&session_id=1483b1305319929&show_associations=list 2 from TAIR]
  
−
PO:0000065 phloem pole pericycle cell
+
-replaced_by embryonic apical cell (PO:0025284),
  
−
===week of 02/09/2011===
+
po_anatomy_gene_arabidopsis_tair.assoc:  Move (3) from PO:0004000 to PO:0025284
  
−
PO:0025262 ovary septum
+
===PO:0005008 fruit septum:===
 +
[http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0005008&session_id=7270b1305319505&show_associations=list 3 from TAIR]
  
−
PO:0025263 locule
+
-consider fruit septum (PO:0025268) or fruit replum (PO:0025267);
  
−
PO:0025265 sporangium locule
+
-annotations for Arabidopsis should go to fruit replum, because it does not have a septum.
  
−
PO:0025264 anther locule
+
po_anatomy_gene_arabidopsis_tair.assoc: move 3 from PO:0005008 to PO:0025267
  
−
PO:0025266 ovary locule
+
===PO:0005009 carpel septum:===
 +
[http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0005009&session_id=1168b1305319408&show_associations=list 1 from TAIR]
  
−
PO:0025267 fruit replum
+
-consider ovary septum (PO:0025262) or ovary replum (PO:0025272)
  
−
PO:0025268 fruit septum
+
-annotations for Arabidopsis should go to ovary replum, because it does not have a septum.
  
−
PO:0025269 collective organ part structure
+
po_anatomy_gene_arabidopsis_tair.assoc: Move 1 from PO:0005009 to ovary replum PO:0025272
  
−
===week of 02/16/2011===
+
===PO:0005016 replum:===
 +
[http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0005016&session_id=3879b1305319571&show_associations=list 3 from TAIR]
  
−
PO:0025270 fruit locule
+
-'''consider: ovary replum (PO:0025272):''' A portion of ovary placenta tissue that divides an ovary into two or more chambers and develops from contact of the placental tissue from opposite sides of the ovary early in gynoecium development
 +
 +
-'''consider: fruit replum (PO:0025267):''' A portion of fruit placenta tissue that divides a fruit into two or more chambers and develops from a replum. [source: POC:rw]
  
−
PO:0025271 spore capsule locule
+
Comment: A fruit replum develops from the ovary replum and has no suture line in its center, while a fruit septum (PO:0025262) develops from an ovary septum via the fusion of two adjacent ovary walls. Common in Brassicaceae.
  
−
PO:0025272 ovary replum
+
Annotations for Arabidopsis fruit should go here, and not under fruit septum.
  
−
PO:0025273 stem procambium
+
* 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:0025274 branch procambium
 
  
−
===week of 02/23/2011===
+
po_anatomy_gene_arabidopsis_tair.assoc: move 3 from PO:0005016 replum to  ovary replum PO:0025272
  
−
PO:0025275 procambium
+
===PO:0006074 procambium:===
 +
[http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0006074&session_id=5380b1305319690&show_associations=list 16 from TAIR]
 +
 +
-replaced_by procambium PO:0025275
  
−
PO:0025276 shoot procambium
+
po_anatomy_gene_arabidopsis_tair.assoc: move 16 from PO:0006074 to PO:0025275
  
−
PO:0025277 pollen sac
+
===PO:0006306 shoot procambium:===
 +
[http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0006306&session_id=5380b1305319690&show_associations=list 3 from TAIR]
 +
 +
-replaced_by shoot procambium (PO:0025276);
  
−
PO:0025278 rhizome scale leaf
+
po_anatomy_gene_arabidopsis_tair.assoc: Move 3 from PO:0006306 to PO:0025276
  
−
===week of 3/8/11===
+
===PO:0009070 pollen sac:===
 +
[http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0009070&session_id=2023b1305319861&show_associations=list 9 from TAIR]
  
−
PO:0030001 chloronema cell
+
-replaced_by pollen sac (PO:0025277);
  
−
PO:0030002 caulonema cell
+
po_anatomy_gene_arabidopsis_tair.assoc: Move 9 from PO:0009070 to PO:0025277
  
−
PO:0030003 protonema
+
===PO:0020092 megagametophyte:===
 +
[http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0020092&session_id=7024b1305319991&show_associations=list 29 from TAIR, 8+2 from MaizeGDB, 1 from Gramene]
  
−
PO:0030004 chloronema
+
-'''consider megagametophyte (PO:0025279):''' A whole plant in the gametophytic phase that produces only egg cells. exact synonym: female gametophyte
  
−
PO:0030005 caulonema
+
Comment: Megagametophytes in bryophytes only produce egg cells, but do not develop from megaspores, because there is no heterospory in bryophytes. In some pteridophytes, megagametophytes develop from megaspores. In angiosperms, Gnetum, and Weltwischia, the megagametophyte is greatly reduced. The megagametophyte in angiosperms is an embryo sac.
 +
 +
-'''consider embryo sac (PO:0025074):''' A megagametophyte that is located in an ovule in an ovary.  Comment: Produces an embryo sac egg cell.
  
−
PO:0030006 protonema phase
+
-'''consider archegonium microgametophyte (PO:0025282):'''A megagametophyte that has as parts one or more archegonia.
  
−
===week of 3/22/11===
+
Comment: Megagametophytes in bryophytes only produce egg cells, but do not develop from megaspores, because there is no heterospory in bryophytes. In some pteridophytes, megagametophytes develop from megaspores.
  
−
PO:0025279 megagametophyte
 
  
−
PO:0025280 microgametophyte
+
-These annotations should probably go to embryo sac. Embryo sac was a synonym of the obsolete term megagametophyte.
  
−
PO:0030007 apical cell
+
po_anatomy_gene_arabidopsis_tair.assoc: Move 29 from PO:0020092 to embryo sac PO:0025074
  
−
PO:0030008 root apical cell
+
po_anatomy_gene_oryza_gramene.assoc: Move 1
  
−
PO:0030009 shoot apical cell
+
po_anatomy_gene_zea_MaizeGDB.assoc: Move 8
  
−
PO:0030010 shoot axis apical cell
+
po_anatomy_stock_zea_MaizeGDB_Stock.assoc: Move 2
  
−
PO:0030011 leaf apical cell
+
po_anatomy_zea_MaizeGDB_Stock.assoc: Move 2
  
−
PO:0030012 vascular leaf apical cell
+
===PO:0020091 (w/ alternate id PO:0020007) microgametophyte:===
 +
[http://www.plantontology.org/amigo/go.cgi?session_id=3800b1305320136&view=assoc&search_constraint=terms&query=PO:0020091&page=262 17,864]
  
−
PO:0030013 non-vascular leaf apical cell
+
-comment: original terms for megagametophyte and microgametophyte were created with angiosperms in mind, wanted to make broader definition
  
−
PO:0030014 gametophytic apical cell
 
  
−
PO:0030015 sporophytic apical cell
+
-'''Consider microgametophyte (PO:0025280):''' A whole plant in the gametophytic phase that produces only sperm cells. [source: POC:curators]
  
−
PO:0030016 vascular shoot system
+
Comment: Microgametophytes in bryophytes only produce sperm cells, but do not develop from microspores, because there is no heterospory in bryophytes. In seed plants the male gametophyte is reduced to a pollen grain.
  
−
PO:0030017 non-vascular shoot system
+
-'''Consider pollen (PO:0025281):''' A microgametophyte that is located in a pollen sac; Exact Synonym: pollen grain.  Comment: Produces pollen sperm cells.
  
−
PO:0030018 gametophore
+
-'''Consider antheridium microgametophyte (PO:0025283):''' A microgametophyte that has as parts one or more antheridia.  Exact synonyms: antheridial microgametophyte.
 +
 +
Comment: Microgametophytes in bryophytes only produce sperm cells, but do not develop from microspores, because there is no heterospory in bryophytes. In some pteridophytes, microgametophytes develop from microspores.
  
−
PO:0030019 gametophore apical cell
 
  
−
PO:0030020 gametophore axis
+
-Annotations for angiosperms should probably go to pollen. Pollen and pollen grain were synonyms of the obsolete term microgametophyte.
  
−
PO:0030021 gametophore branch
+
po_anatomy_gene_arabidopsis_tair.assoc: Move ~17,371 from PO:0020091 to PO:0025281
  
−
PO:0030022 gametophore stem
+
po_anatomy_gene_zea_MaizeGDB.assoc: 198
  
−
PO:0030023 gametophore axis apical cell
+
po_anatomy_stock_zea_MaizeGDB.assoc: 120
  
−
PO:0030024 vascular shoot axis apical cell
+
po_anatomy_stock_zea_MaizeGDB_Stock.assoc:120
  
−
PO:0030025 thallus apical cell
+
po_anatomy_gene_oryza_gramene.assoc: 9
  
−
===week of 3/29/11===
+
po_anatomy_qtl_oryza_gramene.assoc:44
  
−
PO:0025281 pollen
+
po_anatomy_gene_Nicotiana_sgn.assoc: 1
  
−
PO:0025282 archegonial megagametophyte
+
po_anatomy_gene_S.lycopersicum_sgn.assoc: 1
  
−
PO:0025283 antheridial microgametophyte
+
=New terms added by category:=
  
−
===week of 4/12/11===
+
This page is under construction...
  
−
gametophore bud (PO:0030026)
+
===Whole plant growth stages:===
 +
PO:0028002 sporophyte phase
  
−
thallus (PO:0030027)
+
PO:0028003 gametophyte phase
  
−
pergonial bract (PO:0030028)
+
PO:0030006 protonema phase
  
−
sporphyte foot (PO:0030029)
+
===Upper-level PAO terms===
 +
PO:0025269 collective organ part structure
  
−
perichaetal bract (PO:0030030)
+
PO:0030078 rhizoid
  
−
gametophytic perianth (PO:0030031)
+
===Terms for bryophytes and pteridophytes===
 +
(Some of these terms are applicable to seed plants as well)
  
−
seta (PO:0030032)
+
====whole plants====
 +
PO:0025282 archegonium megagametophyte
  
−
antheridiophore (PO:0030033)
+
PO:0025283 antheridium microgametophyte
  
−
archegoniaphore (PO:0030034)
+
PO:0030027 thallus
  
−
antheridium stalk (PO:0030035)
+
====plant organs====
 +
PO:0030020 gametophore axis
  
−
archegonium stalk (PO:0030036)
+
PO:0030021 gametophore branch
  
−
spore capsule calyptra (PO:0030037)
+
PO:0030022 gametophore stem
  
−
venter (PO:0030038)
+
PO:0030028 pergonial bract
  
−
archegonium neck(PO:0030039)
+
PO:0030029 sporphyte foot
  
−
sporangium base (PO:0030040)
+
PO:0030030 perichaetal bract
  
−
sporangium theca (PO:0030041)
+
PO:0030031 gametophytic perianth
  
−
peristome (PO:0030042)
+
PO:0030032 seta
  
−
peristome tooth (PO:0030043)
+
PO:0030033 antheridiophore
  
−
spore capsule operculum (PO:0030044)
+
PO:0030034 archegoniaphore
  
−
===week of 4/12/11===
+
PO:0030055 pseudopodium
  
−
callus parenchyma PO:0025285
+
====plant cells====
 +
PO:0025317 axillary hair terminal cell
  
−
embryonic coleoptile PO:0025286
+
PO:0025319 axillary hair basal cell
  
−
seedling coleoptile PO:0025287
+
PO:0030001 chloronema cell
  
−
==Terms made obsolete==
+
PO:0030002 caulonema cell
  
−
PO:0005009 carpel septum, consider ovary septum (PO:0025262) or replum (PO:0005016)
+
PO:0030007 apical cell
  
−
PO:0005008 obsolete fruit septum, consider fruit septum (PO:0025268) or fruit replum (PO:0025267)
+
PO:0030008 root apical cell
  
−
--the two terms above were made obsolete because their definitions we ambiguous, and they had annotations from Arabidopsis that should have been on replum.
+
PO:0030009 shoot apical cell
  
−
PO:0005016 replum, consider ovary replum (PO:0025272) and fruit replum (PO:0025267). TAIR should check existing annotation to see where they should go.
+
PO:0030010 shoot axis apical cell
  
−
PO:0006074 obsolete procambium, replaced_by procambium (PO:0025275)
+
PO:0030011 leaf apical cell
  
−
PO:0006306 obsolete shoot procambium, replaced_by procambium (PO:0025276)
+
PO:0030012 vascular leaf apical cell
  
−
PO:0009070 obsolete pollen sac, replaced_by pollen sac (PO:0025277)
+
PO:0030013 non-vascular leaf apical cell
  
−
PO:0020092 obsolete megagametophyte, was created with angiosperms in mind, want to make broader definition, replaced_by megagametophyte (PO:0025279)
+
PO:0030014 gametophytic apical cell
  
−
PO:0020091 w/ alternate id PO:0020007 obsolete microgametophyte, was created with angiosperms in mind, want to make broader definition, replaced_by microgametophyte. (PO:0025280)
+
PO:0030015 sporophytic apical cell
  
−
PO:0004000 obsolete apical cell, replaced_by embryonic apical cell (PO:0025284).
+
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
 +
 
 +
PO:0030086 protonema sub-apical initial
 +
 
 +
PO:0030087 non-vascular leaf 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==
 
==Merged terms==
Line 207: Line 552:
 
Merged spore capsule locule (PO:0025271) into sporangium locule (PO:0025265).
 
Merged spore capsule locule (PO:0025271) into sporangium locule (PO:0025265).
  
−
==Other==
+
==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
  
−
(will move a lot of this to changes page)
+
PO:0030050 stereome
  
−
TAIR should move annotations that were on PO:0005009 (carpel septum) to PO:0025272 (ovary replum). Should check if annotation from PO:0005016 (replum) belong with ovary replum (PO:0025272) or fruit replum (PO:0025267).
+
PO:0030051 central strand
  
−
Changed primary name of bud scale (PO:0020054) to bud scale leaf.
+
PO:0030052 antheridium jacket layer cell
  
−
Added "leaf, vascular" and "scale-like leaf" as synonyms of vascular leaf.
+
PO:0030053 antheridium jacket layer
  
−
Removed modified aleurone part_of aleurone layer, because it was already is_a aleurone layer.
+
PO:0030054 epiphragm
  
−
Added Spanish synonyms for plant cell and plant embryo, but accented characters don't display properly in Amigo.
+
PO:0030055 pseudopodium
  
−
Added "portion of … tissue" as synonyms to several tissue types of tissue that had single word names (like epidermis, collenchyma).
+
PO:0030056 archesporial cell
  
−
Changed names of child terms of sporangium/spore capsule:
+
PO:0030057 alar cell
  
−
PO:0025093 Moss capsule annulus>spore capsule annulus
+
PO:0030058 brachycyte
  
−
PO:0025231 Moss capsule columella>spore capsule columella
+
PO:0030059 tmema cell
  
−
PO:0025229 Moss capsule valve>spore capsule valve
+
PO:0030060 gametophore axillary hair
  
−
Added anther lobe as narrow synonym of pollen sac. Was there on the old term, but didn’t get transferred when it was obsoleted and replaced.
+
PO:0030061 tmema
  
−
Made theca is_a collective organ part structure, part of anther, has_part pollen sac.
+
PO:0030062 gametophore axillary hair terminal cell
  
−
Made microsporocyte part of microsporangium, instead of part of microsporocyte. Made sporocyte part of sporangium.
+
PO:0030063 gametophore axillary hair base
  
−
Added synonyms to vascular leaf (frond, needle-like leaf) and non-vascular leaf (phyllid, gametophyll, gametophytic leaf).
+
PO:0030064 gametophore axillary hair basal cell
  
−
Moved juvenile, transition and adult leaf from vascular leaf to leaf. Also simple leaf and compound leaf.
+
PO:0030065 archegonium neck canal cell
  
−
Moved leaf aerenchyma, leaf mesophyll, leaf lamina, leaf margin, leaf intercalary meristem and leaf sheath from part_of vascular leaf to part_of leaf.
+
PO:0030066 archegonium neck canal
  
−
Moved leaf endodermis from part_of leaf to part_of vascular leaf.\
+
PO:0030067 protonema side branch initial
  
−
Add subsets for bryophytes, pteridophytes and gymnosperms (in addition to angiosperms)
+
PO:0030068 epidermal rhizoid initial
  
−
Add new relation participates_in
+
PO:0030069 paraphyllium
  
−
Removed has_part relations from all pairs of terms that has reciprocal has_part/part_of relations
+
PO:0030070 paraphysis
  
−
Updated definition of radicle. Removed radicle part_of embryo axis, added embryo axis has_part radicle.
+
PO:0030071 epidermal rhizoid
  
−
Updated definition of hypocotyl and made it is_a stem internode, instead of is_a cardinal organ part.
+
PO:0030072 costa
  
−
Updated definition of epicotyl and made it is_a stem internode, instead of is_a embryonic plant structure.
+
PO:0030073 exothecium
  
−
Made hypocotyl-root junction is_a cardinal organ part. Already part of embryo axis.
+
PO:0030074 archesporium
  
−
Made mesocotyl is_a stem internode. Did not change definition, need to wait for discussion.
+
PO:0030075 antheridium head
  
−
Made embryonic leaf is_a leaf, part_of embryo.
+
PO:0030076 achegonium head
  
−
Made plumule is_a terminal bud, part_of embryo.
+
PO:0030077 protonemal side branch rhizoid initial
  
−
Made scutellar node  is_a stem node, part_of embryo axis.
+
PO:0030078 rhizoid
  
−
Added formal relations for: sporophyte replaced_by saprophytic phase and gametophyte replaced by gametophytic phase. Couldn't do this for the previous release because of separate files. Did not add replaced by relation for seedling, b/c there is not seedling phase yet.
+
PO:0030079 protonemal rhizoid
  
−
Updated definition of embryo sac.
+
PO:0030080 rhizoid meristematic apical cell
  
−
Updated definitions of archegonium egg cell, embryo sac egg cell, antheridium sperm cell, and pollen sperm cell
+
PO:0030081 caulonema meristematic apical cell  
  
−
Added vascular leaf and non-vascular leaf part_of vascular and non-vascular shoot system, respectively.
+
PO:0030082 chloronema meristematic apical cell
  
−
Changed embryo to plant embryo.
+
PO:0030083 gametophore bud initial
  
−
Removed embryonic axis has_part radicle, has_part hypocotyl, has_part epicotyl, hypocotyl-root junction, has_part root meristem (b/c not true in all plants)
+
PO:0030084 amphithecium
  
−
Added prothallium as narrow synonym of whole plant.
+
PO:0030085 protosporangium endothecium
  
−
Added appropriate subsets for apical cell terms and other terms.
+
PO:0030086 protonema sub-apical initial
  
−
Changed theca (PO:0009069) to anther theca
+
PO:0030087 non-vascular leaf initial

Latest revision as of 17:30, 25 May 2011

Back to May_2011_Release_Page

List of Terms made obsolete with associated annotations:

  • Note: Links below go to the annotations on the live browser, will not work after the release

http://wiki.plantontology.org:8080/index.php/Summary_of_changes_to_the_Plant_Ontology_Oct2010 Numbers based on the most recent association files on the SVN (TAIR Version #1129): Note some of these are different than the ones on the live site as TAIR has updated since the last release (in bold).

  • 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: Why are these still in the TAIR file? See Oct 2010 Release

  • pollen tube PO:0006345 (1)

This term was made obsolete because it is a subcellular component. See GO for the term pollen tube (GO:0090406). Since a pollen tube is part_of a pollen tube cell, annotations for pollen tube may also go to the more general term pollen tube cell (PO:0025195).

  • seedling PO:0008037 (5)

This term was obsoleted in the previous release - Replaced by whole plant growth stage 'seedling growth stage' (PO:0007131) and whole plant (PO:0000003) in the PAO. xref: OBO_SF_PO:2972241

po_anatomy_gene_arabidopsis_tair.assoc: move to whole plant PO:0000003

po_temporal_gene_arabidopsis_tair.assoc: Copy to this file and replace with seedling growth stage (PO:0007131)

PO:0004000 apical cell:

2 from TAIR

-replaced_by embryonic apical cell (PO:0025284),

po_anatomy_gene_arabidopsis_tair.assoc: Move (3) from PO:0004000 to PO:0025284

PO:0005008 fruit septum:

3 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_anatomy_gene_arabidopsis_tair.assoc: move 3 from PO:0005008 to PO:0025267

PO:0005009 carpel septum:

1 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_anatomy_gene_arabidopsis_tair.assoc: Move 1 from PO:0005009 to ovary replum PO:0025272

PO:0005016 replum:

3 from TAIR

-consider: ovary replum (PO:0025272): A portion of ovary placenta tissue that divides an ovary into two or more chambers and develops from contact of the placental tissue from opposite sides of the ovary early in gynoecium development

-consider: fruit replum (PO:0025267): A portion of fruit placenta tissue that divides a fruit into two or more chambers and develops from a replum. [source: POC:rw]

Comment: A fruit replum develops from the ovary replum and has no suture line in its center, while a fruit septum (PO:0025262) develops from an ovary septum via the fusion of two adjacent ovary walls. Common in Brassicaceae.

Annotations for Arabidopsis fruit should go here, and not under fruit septum.


po_anatomy_gene_arabidopsis_tair.assoc: move 3 from PO:0005016 replum to ovary replum PO:0025272

PO:0006074 procambium:

16 from TAIR

-replaced_by procambium PO:0025275

po_anatomy_gene_arabidopsis_tair.assoc: move 16 from PO:0006074 to PO:0025275

PO:0006306 shoot procambium:

3 from TAIR

-replaced_by shoot procambium (PO:0025276);

po_anatomy_gene_arabidopsis_tair.assoc: Move 3 from PO:0006306 to PO:0025276

PO:0009070 pollen sac:

9 from TAIR

-replaced_by pollen sac (PO:0025277);

po_anatomy_gene_arabidopsis_tair.assoc: Move 9 from PO:0009070 to PO:0025277

PO:0020092 megagametophyte:

29 from TAIR, 8+2 from MaizeGDB, 1 from Gramene

-consider megagametophyte (PO:0025279): A whole plant in the gametophytic phase that produces only egg cells. exact synonym: female gametophyte

Comment: Megagametophytes in bryophytes only produce egg cells, but do not develop from megaspores, because there is no heterospory in bryophytes. In some pteridophytes, megagametophytes develop from megaspores. In angiosperms, Gnetum, and Weltwischia, the megagametophyte is greatly reduced. The megagametophyte in angiosperms is an embryo sac.

-consider embryo sac (PO:0025074): A megagametophyte that is located in an ovule in an ovary. Comment: Produces an embryo sac egg cell.

-consider archegonium microgametophyte (PO:0025282):A megagametophyte that has as parts one or more archegonia.

Comment: Megagametophytes in bryophytes only produce egg cells, but do not develop from megaspores, because there is no heterospory in bryophytes. In some pteridophytes, megagametophytes develop from megaspores.


-These annotations should probably go to embryo sac. Embryo sac was a synonym of the obsolete term megagametophyte.

po_anatomy_gene_arabidopsis_tair.assoc: Move 29 from PO:0020092 to embryo sac PO:0025074

po_anatomy_gene_oryza_gramene.assoc: Move 1

po_anatomy_gene_zea_MaizeGDB.assoc: Move 8

po_anatomy_stock_zea_MaizeGDB_Stock.assoc: Move 2

po_anatomy_zea_MaizeGDB_Stock.assoc: Move 2

PO:0020091 (w/ alternate id PO:0020007) microgametophyte:

17,864

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


-Consider microgametophyte (PO:0025280): A whole plant in the gametophytic phase that produces only sperm cells. [source: POC:curators]

Comment: Microgametophytes in bryophytes only produce sperm cells, but do not develop from microspores, because there is no heterospory in bryophytes. In seed plants the male gametophyte is reduced to a pollen grain.

-Consider pollen (PO:0025281): A microgametophyte that is located in a pollen sac; Exact Synonym: pollen grain. Comment: Produces pollen sperm cells.

-Consider antheridium microgametophyte (PO:0025283): A microgametophyte that has as parts one or more antheridia. Exact synonyms: antheridial microgametophyte.

Comment: Microgametophytes in bryophytes only produce sperm cells, but do not develop from microspores, because there is no heterospory in bryophytes. In some pteridophytes, microgametophytes develop from microspores.


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

po_anatomy_gene_arabidopsis_tair.assoc: Move ~17,371 from PO:0020091 to PO:0025281

po_anatomy_gene_zea_MaizeGDB.assoc: 198

po_anatomy_stock_zea_MaizeGDB.assoc: 120

po_anatomy_stock_zea_MaizeGDB_Stock.assoc:120

po_anatomy_gene_oryza_gramene.assoc: 9

po_anatomy_qtl_oryza_gramene.assoc:44

po_anatomy_gene_Nicotiana_sgn.assoc: 1

po_anatomy_gene_S.lycopersicum_sgn.assoc: 1

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

PO:0030086 protonema sub-apical initial

PO:0030087 non-vascular leaf 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

PO:0030086 protonema sub-apical initial

PO:0030087 non-vascular leaf initial

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