New terms and obsolete terms for May2011 release
Back to May_2011_Release_Page
New terms added, 12/2010-5/2011
In numerical order
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 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
By category
Whole plant growth stages:
PO:0028002 sporophyte phase
PO:0028003 gametophyte phase
===Terms for bryophytes and pteridophytes
PO:0025282 archegonium megagametophyte
PO:0025283 antheridium microgametophyte
embryonic 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
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 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
Miscellaneous
PO:0000062 stomatal initial (stomatal meristermoid)
PO:0000063 leaf procambial cell
PO:0000064 xylem pole pericycle cell
PO:0000065 phloem pole pericycle cell
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:0025298 fruit operculum
PO:0025299 perianth calyptra
=Terms that replace obsoleted terms:
Terms made obsolete
PO:0005009 carpel septum, consider ovary septum (PO:0025262) or replum (PO:0005016)
PO:0005008 obsolete fruit septum, consider fruit septum (PO:0025268) or fruit replum (PO:0025267)
--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:0005016 replum, consider ovary replum (PO:0025272) and fruit replum (PO:0025267). TAIR should check existing annotation to see where they should go.
PO:0006074 obsolete procambium, replaced_by procambium (PO:0025275)
PO:0006306 obsolete shoot procambium, replaced_by procambium (PO:0025276)
PO:0009070 obsolete pollen sac, replaced_by pollen sac (PO:0025277)
PO:0020092 obsolete megagametophyte, was created with angiosperms in mind, want to make broader definition, replaced_by megagametophyte (PO:0025279)
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:0004000 obsolete apical cell, replaced_by embryonic apical cell (PO:0025284).
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).
Other
(will move a lot of this to changes page)
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).
Changed primary name of bud scale (PO:0020054) to bud scale leaf.
Added "leaf, vascular" and "scale-like leaf" as synonyms of vascular leaf.
Removed modified aleurone part_of aleurone layer, because it was already is_a aleurone layer.
Added Spanish synonyms for plant cell and plant embryo, but accented characters don't display properly in Amigo.
Added "portion of … tissue" as synonyms to several tissue types of tissue that had single word names (like epidermis, collenchyma).
Changed names of child terms of sporangium/spore capsule:
PO:0025093 Moss capsule annulus>spore capsule annulus
PO:0025231 Moss capsule columella>spore capsule columella
PO:0025229 Moss capsule valve>spore capsule valve
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.
Made theca is_a collective organ part structure, part of anther, has_part pollen sac.
Made microsporocyte part of microsporangium, instead of part of microsporocyte. Made sporocyte part of sporangium.
Added synonyms to vascular leaf (frond, needle-like leaf) and non-vascular leaf (phyllid, gametophyll, gametophytic leaf).
Moved juvenile, transition and adult leaf from vascular leaf to leaf. Also simple leaf and compound leaf.
Moved leaf aerenchyma, leaf mesophyll, leaf lamina, leaf margin, leaf intercalary meristem and leaf sheath from part_of vascular leaf to part_of leaf.
Moved leaf endodermis from part_of leaf to part_of vascular leaf.\
Add subsets for bryophytes, pteridophytes and gymnosperms (in addition to angiosperms)
Add new relation participates_in
Removed has_part relations from all pairs of terms that has reciprocal has_part/part_of relations
Updated definition of radicle. Removed radicle part_of embryo axis, added embryo axis has_part radicle.
Updated definition of hypocotyl and made it is_a stem internode, instead of is_a cardinal organ part.
Updated definition of epicotyl and made it is_a stem internode, instead of is_a embryonic plant structure.
Made hypocotyl-root junction is_a cardinal organ part. Already part of embryo axis.
Made mesocotyl is_a stem internode. Did not change definition, need to wait for discussion.
Made embryonic leaf is_a leaf, part_of embryo.
Made plumule is_a terminal bud, part_of embryo.
Made scutellar node is_a stem node, part_of embryo axis.
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.
Updated definition of embryo sac.
Updated definitions of archegonium egg cell, embryo sac egg cell, antheridium sperm cell, and pollen sperm cell
Added vascular leaf and non-vascular leaf part_of vascular and non-vascular shoot system, respectively.
Changed embryo to plant embryo.
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)
Added prothallium as narrow synonym of whole plant.
Added appropriate subsets for apical cell terms and other terms.
Changed theca (PO:0009069) to anther theca
Made sporangium (PO:0025094) is_a plant organ instead of is_a cardinal organ part.
Made female archesporial cell (PO:0006015) and male archesporial cell (PO:0006014) children of archesporial cell (PO:0030056)
Renamed:
- cultured somatic plant embryo (PO:0000011)
- nucellar plant embryo (formerly adventitious embryo)(PO:0004537)
Renamed parts of the anther wall:
(also added pollen sac… as synonyms for all of these)
-Endothecium (PO:0020002) > anther wall endothecium (needs new definition – not a hypodermis)
-Exothecium (PO:0020004) > anther wall exothecium
-Middle layer (PO:0004700) > anther wall middle layer (definition needs work)
-primary parietal cell layer (PO:0006006) > anther wall primary parietal cell layer (definition needs work)
-secondary parietal cell layer (PO:0006007) > anther wall primary parietal cell layer (definition needs work)
-inner secondary parietal cell layer (PO:0006008) > anther wall inner secondary parietal cell layer (definition needs work)
-outer secondary parietal cell layer (PO:0006009) > anther wall outer secondary parietal cell layer (definition needs work)
-tapetum (PO:0009071) > anther wall tapetum
Made pollen sac part_of microsporophyll, instead of part_of anther, and added anther has_part pollen sac.
Made anther wall is_a microsporangium wall
Made nucellar epidermis (PO:0008006) is_a megasporangium exothecium
Removed anther wall tapetum develops-from anther wall inner secondary parietal cell layer. Made is_a microsporangium tapetum.
Added new relation: adjacent_to: Used when one plant structure (the child) is in permanent contact with another plant structur (the parent).
Added stamen epidermis intersection_of is_a epidermis, intersection_of part_of stamen. Did the same thing for other phyllome epidermises (except the various leaf abaxial and leaf adaxial stomatal epidermises). This allows stomatal complexes and prickles to be inferred is_a children of their respective portions of epidermal tissue, without creating dual parentage.
Added a bunch of adjective/noun synonyms. For example, archegonium egg cell as synonym for archegonial egg cell, antheridial jacket layer as synonym of antheridium jacket layer. At some point, the names should be normalized.
