New terms and obsolete terms for May2011 release
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:
-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:
-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:
-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:
-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.
- 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_anatomy_gene_arabidopsis_tair.assoc: move 3 from PO:0005016 replum to ovary replum PO:0025272
PO:0006074 procambium:
-replaced_by procambium PO:0025275
po_anatomy_gene_arabidopsis_tair.assoc: move 16 from PO:0006074 to PO:0025275
PO:0006306 shoot procambium:
-replaced_by shoot procambium (PO:0025276);
po_anatomy_gene_arabidopsis_tair.assoc: Move 3 from PO:0006306 to PO:0025276
PO:0009070 pollen sac:
-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:
-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
