Difference between revisions of "New terms and obsolete terms for Jan2011 release"

From Plant Ontology Wiki
Jump to navigationJump to search
 
(62 intermediate revisions by 2 users not shown)
Line 4: Line 4:
  
 
==List of Obsoleted Terms==
 
==List of Obsoleted Terms==
−
* pollen tube (PO:0006345) [http://www.plantontology.org/amigo/go.cgi?session_id=5689b1294171797&view=assoc&search_constraint=terms&query=PO:0006345&page=94 97 pages of annotations: from ''Arabidopsis'', maize and rice]
+
* pollen tube (PO:0006345) [http://www.plantontology.org/amigo/go.cgi?session_id=5689b1294171797&view=assoc&search_constraint=terms&query=PO:0006345&page=94 97 pages of annotations: 4864 ''Arabidopsis'' and 1 each from S.tuberosum and rice].  Consider pollen tube cell (PO:0025195). New term pollen tube was requested in GO; GO ID (GO:0090406) has been added to the obsoleted term.
  
−
Consider pollen tube cell (PO:0025195). New term pollen tube has been requested in GO; waiting for GO ID.
+
* pollen tube tip (PO:0000028) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=8476b1294171984&view=assoc&query=PO%3A0000028&search_constraint=terms 9 annotations from ''Arabidopsis''].  Consider pollen tube cell (PO:0025195). New term pollen tube tip was requested in GO; GO ID (GO:0090404) has been added to the obsoleted term.
  
−
* pollen tube tip (PO:0000028) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=8476b1294171984&view=assoc&query=PO%3A0000028&search_constraint=terms 9 annotations from ''Arabidopsis'']
+
* root hair tip (PO:0000029) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=4940b1294172538&view=assoc&query=PO%3A0000029&search_constraint=terms 1 annotation from ''Arabidopsis''].  Consider root hair cell (PO:0000256), or root hair tip (GO:0035619).
  
−
Consider pollen tube cell (PO:0025195). New term pollen tube tip has been requested in GO; waiting for GO ID.
+
* floral epidermis (PO:0008043) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=158b1294173248&view=assoc&query=PO%3A0008043&search_constraint=terms 1 annotation from ''Arabidopsis''].  Consider carpel epidermis (PO:0025096), petal epidermis (PO:0006041), sepal epidermis (PO:0006040), stamen epidermis (PO:0025097), or tepal epidermis (PO:0025184)
  
−
* root hair (PO:0000256) [http://www.plantontology.org/amigo/go.cgi?session_id=9177b1294172354&view=assoc&search_constraint=terms&query=PO:0000256&page_size=all ~100 annotations from various sources]
+
* papillae (PO:0002001) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=1797b1294180398&view=assoc&query=PO%3A0002001&search_constraint=terms 6 annotations from ''Arabidopsis''].  Consider: papilla cell (PO:0025166), leaf papilla cell (PO:0025167), stigma papilla cell ( PO:0025168) or plant cell papilla (GO:0090395), leaf papilla (GO:0090396) or stigma papilla
  
−
'''This term was not made obsolete.''' Instead the name was changed to root hair cell. This is because the definition of the term was for a cell, not just for the hair. Annotations that belong only to the cell extension should be moved to root hair (GO:0035618).
+
* primary root elongation zone (PO:0003003) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=4638b1294180703&view=assoc&query=PO%3A0003003&search_constraint=terms 49 annotations from ''Arabidopsis'', 1 from ''Oryza'']. Replaced by new term primary root elongation zone (PO:0025257).
  
−
* root hair tip (PO:0000029) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=4940b1294172538&view=assoc&query=PO%3A0000029&search_constraint=terms 1 annotation from ''Arabidopsis'']
+
* lateral root elongation zone (PO:0003014) [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0003014&session_id=5563b1294180915&show_associations=list 4 annotations from ''Arabidopsis''].  Replaced by new term lateral root elongation zone (PO:0025256).
  
−
Consider root hair cell (PO:0000256), or root hair tip (GO:0035619).
+
'''Others: No Annotations associated with them:'''
  
−
* floral epidermis (PO:0008043) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=158b1294173248&view=assoc&query=PO%3A0008043&search_constraint=terms 1 annotation from ''Arabidopsis'']
+
* basal endosperm transfer layer (PO:0009019) (created new term with same name, but new def'n and id). No annotations
 +
* trichome branch (PO:0008031). replaced by 'multicellular trichome branch cell (PO:0025163)' in PO,  plus unicellular trichome branch in GO- waiting for ID#): No Annotations
 +
* floral stomatal complex (PO:0008044): no annotations
 +
* floral guard cell (PO:0008045): no annotations
 +
* floral stomatal pore (PO:0008046): no annotations
 +
 
 +
==List of Renamed Terms==
 +
* root hair (PO:0000256) [http://www.plantontology.org/amigo/go.cgi?session_id=9177b1294172354&view=assoc&search_constraint=terms&query=PO:0000256&page_size=all ~100 annotations from ''Arabidopsis'', maize, rice and S.lycopersicum]. The name was changed to 'root hair cel'l (PO:0000256), because the definition of the term was for a cell, not just for the hair. Annotations that belong only to the cell extension should be moved to root hair (GO:0035618) or root hair tip (GO:0035619).
 +
 
 +
* differentiation zone (PO:0020135)- Renamed 'root differentiation zone', (PO:0020135), [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=1144b1294356759&view=assoc&query=PO%3A0020135&search_constraint=terms 6 annotations from ''Arabidopsis''].  These should not need to be moved.
 +
 
 +
* elongation zone (PO:0020125) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=1646b1294179675&view=assoc&query=PO%3A0020125&search_constraint=terms 36 annotations from ''Arabidopsis'', 1 from rice] Replaced by root elongation zone (PO:0025181).
 +
 
 +
* secretory trichome (PO:0004509) was renamed glandular trichome (PO:0004509)
 +
 
 +
* seed hair (PO:0004511) was renamed 'seed trichome' (formerly a synonym), made 'seed hair' an exact synonym, added 'pubescence' as related synonym.
 +
 
 +
* valve (PO:0000033) was renamed fruit valve, with updated definition and new parent valve (PO:0025228).
 +
 
 +
* hull (PO:0006000) was renamed Poaceae hull to distinguish it from other types of hulls [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&query=PO:0006000&session_id=6293b1294429276 11 annotations from Oryza gene and QTL]
 +
 
 +
* old microsporangium (PO:0009070) was renamed pollen sac and made a child of new microsporangium (PO:0025202)
 +
 
 +
==List of replacement terms==
 +
These terms were made obsolete and replaced by new terms with the same name but new definitions, because the old definitions were incorrect:
 +
 +
* elongation zone (PO:0020125) replaced by root elongation zone (PO:0025181)
 +
 
 +
* obsolete lateral root elongation zone (PO:0003014) replaced by lateral root elongation zone (PO:0025256)
 +
 
 +
* obsolete primary root elongation zone (PO:0003003) replaced by primary root elongation zone (PO:0025257)
 +
 
 +
* obsolete basal endosperm transfer layer (PO:0009019) replaced by basal endosperm transfer layer (PO:0025196)
 +
 
 +
==List of New Terms-general:==
 +
* plant anatomical entity (PO:0025131): An anatomical entity (CARO:0000000) that is or was part of a plant.
 +
* plant anatomical space (PO:0025117): An anatomical space (CARO:0000005) that is part of a plant.
 +
* portion of plant substance (PO:0025161)
 +
 
 +
 
 +
 
 +
* embryonic plant structure PO:0025099
 +
 
 +
 
 +
* axil id: PO:0025224
 +
* branch axil PO:0025226
 +
* bract axil PO:0025225
 +
 
 +
 
 +
* reproductive shoot system PO:0025082
  
−
Consider carpel epidermis (PO:0025096), petal epidermis (PO:0006041), sepal epidermis (PO:0006040), stamen epidermis (PO:0025097), or tepal epidermis (PO:0025184)
 
  
 +
* gynoecium ridge PO:0025088
 +
* Poaceae gynoecium ridge PO:0025086
 +
* Zea gynoecium ridge PO:0025087
  
−
* elongation zone (PO:0020125) (replaced by root elongation zone (PO:0025181) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=1646b1294179675&view=assoc&query=PO%3A0020125&search_constraint=terms ~40 annotations, all from ''Arabidopsis'']
 
  
−
Replaced by root elongation zone (PO:0025181).
+
* dehiscence zone PO:0025092
  
−
* papillae (PO:0002001) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=1797b1294180398&view=assoc&query=PO%3A0002001&search_constraint=terms 6 annotations from ''Arabidopsis'']
 
  
−
Consider: PO:0025166 papilla cell, PO:0025167 leaf papilla cell, PO:0025168 stigma papilla cell, or  GO:0090395 plant cell papilla, GO:0090396 leaf papilla, GO:0090397 stigma papilla
+
* primordium PO:0025127
 +
* phyllome primordium PO:0025128
  
−
* trichome branch (PO:0008031) (replaced by 'multicellular trichome branch cell' in PO plus unicellular trichome branch in GO):No Annotations
 
  
−
* differentiation zone (PO:0020135)-(replaced by root differentiation zone; PO:0020135)
+
* root parenchyma PO:0025095
  
−
* basal endosperm transfer layer (PO:0009019) (created new term with same name, but new def'n and id) No annotations
 
  
−
* primary root elongation zone (PO:0003003) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=4638b1294180703&view=assoc&query=PO%3A0003003&search_constraint=terms ~40 annotations from ''Arabidopsis'', 1 from ''Oryza'']
+
* stele PO:0025197
 +
* shoot axis stele PO:0025198
 +
* branch stele PO:0025199
 +
* stem stele PO:0025200
  
−
Replaced by new term primary root elongation zone (PO:0025257).
 
  
−
* lateral root elongation zone (PO:0003014) [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0003014&session_id=5563b1294180915&show_associations=list 4 annotations from ''Arabidopsis'']
+
* sporangium PO:0025094 (added during last release, but didn’t have definition),
 +
* microsporangium PO:0025202
 +
* megasporangium PO:0025201
  
−
Replaced by new term lateral root elongation zone (PO:0025256).
 
  
 +
* gametangium PO:0025124
 +
* antheridium PO:0025125
 +
* archegonium PO:0025126
  
−
Others??
 
  
−
* floral stomatal complex (PO:0008044): No Annotations
+
* pericarp vascular bundle PO:0025203
  
−
floral guard cell (PO:0008045): no annotations
 
  
−
floral stomatal pore (PO:0008046): no annotations
+
* shoot system vascular system PO:0025205 - Made different vascular systems of above ground parts child of this.
 +
* phyllome vascular system PO:0025206
 +
* tepal vascular system PO:0025207
  
−
==List of New Terms-general:==
+
* reproductive shoot apex PO:0025222
−
* '''plant anatomical entity''' (PO:0025131): An anatomical entity (CARO:0000000) that is or was part of a plant.
+
* vegetative shoot apex PO:0025223
−
*''' plant anatomical space''' (PO:0025117): An anatomical space (CARO:0000005) that is part of a plant.
 
  
−
* '''axil''' (child of plant anatomical space)
 
−
* '''leaf axil''' (PO:0009023) ''not a new term''
 
−
* '''branch axil''' (PO#)
 
−
* '''bract axil''' (PO#) (children of axil).
 
  
−
* '''reproductive shoot system''' (PO:0025082): A shoot system in the sporophytic phase that has as part at least one sporangium.
+
* columella PO:0025230
−
* '''gynoecium ridge''' (PO:0025088): A gynoecium in the early stages of development, characterized as a ridge on the abaxial surface of the floral meristem that develops from a gynoecium primordium.
+
* moss capsule columella PO:0025231
−
* '''dehiscence zone''' (PO:0025092): A portion of plant tissue that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure.
+
* PO:0004540 was renamed fruit columella
  
−
* '''primordium''' (PO:0025127)
 
−
* '''phyllome primordium'''
 
−
* '''root parenchyma''' (PO:0025095): A portion of parenchyma tissue that is part of a root system.
 
  
−
* '''stele'''
+
* canal  PO:0025132
−
* '''shoot axis stele'''
+
* petiole canal PO:0025133
−
* '''branch stele'''
+
* abaxial petiole canal PO:0025238
−
* '''stem stele'''
+
* adaxial petiole canal PO:0025239
  
−
* '''sporangium (already there, but didn’t have definition),
 
−
* '''microsporangium'''
 
−
* '''megasporangium'''
 
  
−
* pericarp vascular bundle
+
* phyllome apex PO:0025139
 +
* phyllome base PO:0025140
 +
* phyllome tip PO:0025141
  
−
* shoot system vascular system. Made different vascular systems of above ground parts child of this.
 
  
−
* phyllome vascular system
+
* valve PO:0025228
−
* sepal vascular system
+
* moss capsule valve PO:0025229
−
* flower vascular system
+
* PO:0000033 was renamed fruit valve
−
* tepal vascular system new
 
  
 
==New terms- cells==
 
==New terms- cells==
−
* '''pollen tube cell''' (PO:0025195): A plant cell that develops from a vegetative cell and forms a tubular extension of the pollen grain. [source: POC:rw]  Comment: Carries the male gametes to into or near the ovule. May be branched in gymnosperms. See GO for pollen tube and pollen tube tip. (need to add GO term ids)
+
*antheridium sperm cell (PO:0025120)
−
* '''papilla cell''' (PO:0025166): An epidermal pavement cell with a short protuberance. [source: POC:curators]  Comment: See GO for the subcellular component papilla.(need to add GO term ids)
+
 
 +
*pollen sperm cell (PO:0025121)
 +
 
 +
*archegonium egg cell (PO:0025122)
 +
 
 +
*embryo sac egg cell (PO:0025123)
 +
 
 +
*multicellular trichome branch cell (PO:0025163)
 +
 
 +
*root epidermal cell (PO:0025164)
 +
 
 +
*shoot epidermal cell (PO:0025165)
 +
 
 +
*papilla cell (PO:0025166)
 +
 
 +
*leaf papilla cell (PO:0025167)
 +
 
 +
*stigma papilla cell (PO:0025168)
 +
 
 +
*pollen tube cell (PO:0025195)
 +
 
 +
*leaf pavement cell (PO:0025212)
 +
 
 +
*leaf abaxial pavement cell (PO:0025213)
 +
 
 +
*leaf adaxial pavement cell (PO:0025214)
 +
 
 +
*phyllome guard cell (PO:0025236)
 +
 
 +
*leaf guard cell (PO:0025237)
 +
 
 +
==List of new terms: trichome, epidermis, and related==
 +
 
 +
 
 +
carpel epidermis PO:0025096
 +
 
 +
stamen epidermis PO:0025097
 +
 
 +
bract trichome PO:0025098
 +
 
 +
cigar leaf lamina abaxial epidermis PO:0025135
 +
 
 +
peduncle epidermis PO:0025152
 +
 
 +
peduncle trichome PO:0025153
 +
 
 +
phyllome epidermis PO:0025157
 +
 
 +
bract epidermis PO:0025158
 +
 
 +
bract abaxial epidermis PO:0025159
 +
 
 +
bract adaxial epidermis PO:0025160
 +
 
 +
multicellular trichome PO:0025162
 +
 
 +
multicellular trichome branch cell PO:0025163
 +
 
 +
root epidermal cell PO:0025164
 +
 
 +
shoot epidermal cell PO:0025165
 +
 
 +
papilla cell PO:0025166
 +
 
 +
leaf papilla cell PO:0025167
 +
 
 +
stigma papilla cell PO:0025168
 +
 
 +
prickle PO:0025169
 +
 
 +
root prickle PO:0025170
 +
 
 +
shoot axis prickle PO:0025171
 +
 
 +
thorn PO:0025172
 +
 
 +
leaf spine PO:0025173
 +
 
 +
stipule spine PO:0025174
 +
 
 +
leaf prickle PO:0025175
 +
 
 +
stem trichome PO:0025176
 +
 
 +
branch trichome PO:0025177
 +
 
 +
stem epidermis PO:0025178
 +
 
 +
branch epidermis PO:0025179
 +
 
 +
sepal trichome PO:0025182
 +
 
 +
tepal epidermis PO:0025184
 +
 
 +
phyllome trichome PO:0025186
 +
 
 +
petal trichome PO:0025187
 +
 
 +
tepal trichome PO:0025188
 +
 
 +
tepal abaxial epidermis PO:0025192
 +
 
 +
tepal adaxial epidermis PO:0025193
  
−
* '''stigma papilla cell''' (PO:0025168):
+
carpel trichome PO:0025208
−
* '''leaf papilla cell''' (PO:0025167):
 
−
* '''archegonium egg cell'''
 
−
* '''embryo sac egg cell'''
 
−
* '''antheridium sperm cell'''
 
−
* '''pollen sperm cell'''
 
  
−
==List of new terms: trichome==
+
stamen trichome PO:0025209
−
* '''trichome''' (PO:0000282) not new?
 
−
* '''multicellular trichome'''
 
−
* '''trichome cell'''
 
−
* '''multicellular trichome branch'''
 
−
* '''multicellular trichome branch cell''' (replaces trichome branch)
 
−
* '''bract trichome'''
 
−
* '''carpel trichome'''
 
−
* '''stem trichome'''
 
−
* '''branch trichome'''
 
−
* '''phyllome trichome (PO:0025186)''' (parent to leaf trichome; existing?)
 
−
* '''sepal trichome (PO:0025182)'''
 
−
* '''petal trichome (PO:0025187)'''
 
−
* '''tepal trichome (PO:0025188)'''
 
  
−
* '''phyllome epidermis'''
+
leaf abaxial trichome PO:0025210
−
* '''stem epidermis'''
 
−
* '''branch epidermis'''
 
−
.
 
  
−
* '''thorn'''
+
leaf adaxial trichome PO:0025211
  
−
* '''prickle''' (PO:0025169)
+
leaf pavement cell PO:0025212
−
* leaf prickle (PO:0025175)
 
−
* root prickle (PO:0025170)
 
−
* shoot axis prickle (PO:0025171)
 
  
−
* '''spine'''
+
leaf abaxial pavement cell PO:0025213
 +
 
 +
leaf adaxial pavement cell PO:0025214
  
 
==new terms- elongation and differentiation zones:==
 
==new terms- elongation and differentiation zones:==
 
* plant axis differentiation zone (PO:0025119)
 
* plant axis differentiation zone (PO:0025119)
−
* plant axis differentiation zone (PO:0025119)
+
* differentiation zone (PO:0020135) was renamed root differentiation zone. Existing children lateral root differentiation zone (PO:0003016) and primary root differentiation zone (PO:0003015) remained, but got standardized definitions
−
* root differentiation zone (PO:0020135); renamed (obsoleted?) old term differentiation zone (PO:0020135)
+
* shoot internode differentiation zone (PO:0025102)
 +
* branch internode differentiation zone (PO:0025103)
 +
* old term "stem internode differentiation zone" (PO:0008042) remained, but got standardized definition
 +
 
 +
* plant axis elongation zone (PO:0025180)
 +
* root elongation zone (PO:0025181). Old term elongation zone (PO:0020125) was made obsolete, because definition of was incorrect.
 +
* lateral root elongation zone (PO:0025256) Old term lateral root elongation zone (PO:0003014) was made obsolete, because definition of was incorrect.
 +
* primary root elongation zone (PO:0025257) Old term primary root elongation zone (PO:0003003) was made obsolete, because definition of was incorrect.
 +
* shoot internode elongation zone (PO:0025100)
 +
* branch internode elongation zone (PO:0025101)
 +
* old term "stem internode elongation zone" (PO:0008041) remained, but got standardized definition
 +
 
 +
==List of Terms stomatal complex:==
  
 +
phyllome stomatal complex PO:0025215
  
−
'''On dev browser 1-4-11:'''
+
leaf stomatal complex PO:0025183
−
new:
 
−
* '''branch internode differentiation zone''' (PO:0025103): A shoot internode differentiation zone that is part of a branch internode.
 
−
* '''plant axis differentiation zone''' (PO:0025119): A cardinal organ part that is part of a plant axis and is located behind the
 
−
* '''shoot internode differentiation zone''' (PO:0025102): A plant axis differentiation zone that is part of a shoot axis.
 
−
* '''root differentiation zone''' (PO:0020135): A plant axis differentiation zone that is the part of a root and is located behind a root elongation zone.(renamed)
 
  
−
Old:
+
leaf lamina stomatal complex PO:0025185
−
* '''lateral root differentiation zone''' (PO:0003016): A root differentiation zone that is part of a lateral root elongation zone and contains cells that are differentiating into their final form and function.
 
−
* '''primary root differentiation zone''' (PO:0003015): A root differentiation zone that is part of a primary root.
 
  
−
* '''stem internode differentiation zone''' ; PO:0008042 [show def][view annotations]
+
petiole stomatal complex PO:0025189
  
 +
leaf abaxial stomatal complex PO:0025190
  
 +
leaf adaxial stomatal complex PO:0025191
  
 +
bract stomatal complex PO:0025216
  
−
* '''root elongation zone''' (PO:0025181): (because definition of elongation zone was incorrect and added new term, new id) 
+
carpel stomatal complex PO:0025217
−
* '''elongation zone'''
 
−
* '''plant axis elongation zone'''(PO:0025180)
 
  
−
Questions about:
+
petal stomatal complex PO:0025218
−
* '''differentiation zone''' not new??? (see PO:0020135)
 
  
−
==List of Terms stomatal complex:==
+
sepal stomatal complex PO:0025219
−
* stomatal complex
 
−
* phyllome stomatal complex
 
−
* leaf stomatal complex
 
−
* petiole stomatal complex
 
  
−
* leaf lamina stomatal complex
+
stamen stomatal complex PO:0025220
−
* leaf lamina abaxial stomatal complex
 
−
* leaf lamina adaxial stomatal complex
 
  
−
* petiole abaxial stomatal complex
+
tepal stomatal complex PO:0025221
−
* petiole adaxial stomatal complex
 
  
−
* root nodule meristem (PO:0025194): A root meristem that gives rise to a root nodule.
 
−
* basal endosperm transfer layer (PO:0025196) (replaces PO:0009019, with same name): A portion of plant tissue that is part of an endosperm and is composed of basal endosperm transfer cells. [source:POC:rw]
 
  
−
==List of Renamed Terms==
+
plus:
−
* secretory trichome was renamed glandular trichome
 
−
* seed trichome was made the primary name for PO:0004511, (changed seed hair to exact synonym, added pubescence as related synonym)
 
−
* root differentiation zone (PO:0020135; renaming of old term differentiation zone)
 
−
* valve (PO:0000033) was renaned fruit valve, with updated definition and new parent valve (PO:0025228).
 
−
* hull (PO:0006000) was renamed Poaceae hull to distinguish it from other types of hulls
 
−
* old microsporangium (PO:0009070) was renamed pollen sac and made a child of new microsporangium (PO:0025202)
 
  
−
==List of replacement terms==
+
phyllome stomatal pore PO:0025234
  
−
These terms were made obsolete and replaced by new terms with the same name but new definitions, because the old definitions were incorrect:
+
leaf stomatal pore PO:0025235
  
 
==List of new terms in numerical order==
 
==List of new terms in numerical order==
Line 644: Line 758:
  
 
id: PO:0025240
 
id: PO:0025240
−
name: secondary inflorescence
+
name: second order inflorescence
  
 
id: PO:0025241
 
id: PO:0025241

Latest revision as of 17:34, 24 January 2011

Back to Jan 2011 Release Page

Back to Summary of Changes to PO Jan2011

List of Obsoleted Terms

  • pollen tube tip (PO:0000028) 9 annotations from Arabidopsis. Consider pollen tube cell (PO:0025195). New term pollen tube tip was requested in GO; GO ID (GO:0090404) has been added to the obsoleted term.
  • floral epidermis (PO:0008043) 1 annotation from Arabidopsis. Consider carpel epidermis (PO:0025096), petal epidermis (PO:0006041), sepal epidermis (PO:0006040), stamen epidermis (PO:0025097), or tepal epidermis (PO:0025184)
  • papillae (PO:0002001) 6 annotations from Arabidopsis. Consider: papilla cell (PO:0025166), leaf papilla cell (PO:0025167), stigma papilla cell ( PO:0025168) or plant cell papilla (GO:0090395), leaf papilla (GO:0090396) or stigma papilla

Others: No Annotations associated with them:

  • basal endosperm transfer layer (PO:0009019) (created new term with same name, but new def'n and id). No annotations
  • trichome branch (PO:0008031). replaced by 'multicellular trichome branch cell (PO:0025163)' in PO, plus unicellular trichome branch in GO- waiting for ID#): No Annotations
  • floral stomatal complex (PO:0008044): no annotations
  • floral guard cell (PO:0008045): no annotations
  • floral stomatal pore (PO:0008046): no annotations

List of Renamed Terms

  • root hair (PO:0000256) ~100 annotations from Arabidopsis, maize, rice and S.lycopersicum. The name was changed to 'root hair cel'l (PO:0000256), because the definition of the term was for a cell, not just for the hair. Annotations that belong only to the cell extension should be moved to root hair (GO:0035618) or root hair tip (GO:0035619).
  • differentiation zone (PO:0020135)- Renamed 'root differentiation zone', (PO:0020135), 6 annotations from Arabidopsis. These should not need to be moved.
  • secretory trichome (PO:0004509) was renamed glandular trichome (PO:0004509)
  • seed hair (PO:0004511) was renamed 'seed trichome' (formerly a synonym), made 'seed hair' an exact synonym, added 'pubescence' as related synonym.
  • valve (PO:0000033) was renamed fruit valve, with updated definition and new parent valve (PO:0025228).
  • old microsporangium (PO:0009070) was renamed pollen sac and made a child of new microsporangium (PO:0025202)

List of replacement terms

These terms were made obsolete and replaced by new terms with the same name but new definitions, because the old definitions were incorrect:

  • elongation zone (PO:0020125) replaced by root elongation zone (PO:0025181)
  • obsolete lateral root elongation zone (PO:0003014) replaced by lateral root elongation zone (PO:0025256)
  • obsolete primary root elongation zone (PO:0003003) replaced by primary root elongation zone (PO:0025257)
  • obsolete basal endosperm transfer layer (PO:0009019) replaced by basal endosperm transfer layer (PO:0025196)

List of New Terms-general:

  • plant anatomical entity (PO:0025131): An anatomical entity (CARO:0000000) that is or was part of a plant.
  • plant anatomical space (PO:0025117): An anatomical space (CARO:0000005) that is part of a plant.
  • portion of plant substance (PO:0025161)


  • embryonic plant structure PO:0025099


  • axil id: PO:0025224
  • branch axil PO:0025226
  • bract axil PO:0025225


  • reproductive shoot system PO:0025082


  • gynoecium ridge PO:0025088
  • Poaceae gynoecium ridge PO:0025086
  • Zea gynoecium ridge PO:0025087


  • dehiscence zone PO:0025092


  • primordium PO:0025127
  • phyllome primordium PO:0025128


  • root parenchyma PO:0025095


  • stele PO:0025197
  • shoot axis stele PO:0025198
  • branch stele PO:0025199
  • stem stele PO:0025200


  • sporangium PO:0025094 (added during last release, but didn’t have definition),
  • microsporangium PO:0025202
  • megasporangium PO:0025201


  • gametangium PO:0025124
  • antheridium PO:0025125
  • archegonium PO:0025126


  • pericarp vascular bundle PO:0025203


  • shoot system vascular system PO:0025205 - Made different vascular systems of above ground parts child of this.
  • phyllome vascular system PO:0025206
  • tepal vascular system PO:0025207
  • reproductive shoot apex PO:0025222
  • vegetative shoot apex PO:0025223


  • columella PO:0025230
  • moss capsule columella PO:0025231
  • PO:0004540 was renamed fruit columella


  • canal PO:0025132
  • petiole canal PO:0025133
  • abaxial petiole canal PO:0025238
  • adaxial petiole canal PO:0025239


  • phyllome apex PO:0025139
  • phyllome base PO:0025140
  • phyllome tip PO:0025141


  • valve PO:0025228
  • moss capsule valve PO:0025229
  • PO:0000033 was renamed fruit valve

New terms- cells

  • antheridium sperm cell (PO:0025120)
  • pollen sperm cell (PO:0025121)
  • archegonium egg cell (PO:0025122)
  • embryo sac egg cell (PO:0025123)
  • multicellular trichome branch cell (PO:0025163)
  • root epidermal cell (PO:0025164)
  • shoot epidermal cell (PO:0025165)
  • papilla cell (PO:0025166)
  • leaf papilla cell (PO:0025167)
  • stigma papilla cell (PO:0025168)
  • pollen tube cell (PO:0025195)
  • leaf pavement cell (PO:0025212)
  • leaf abaxial pavement cell (PO:0025213)
  • leaf adaxial pavement cell (PO:0025214)
  • phyllome guard cell (PO:0025236)
  • leaf guard cell (PO:0025237)

List of new terms: trichome, epidermis, and related

carpel epidermis PO:0025096

stamen epidermis PO:0025097

bract trichome PO:0025098

cigar leaf lamina abaxial epidermis PO:0025135

peduncle epidermis PO:0025152

peduncle trichome PO:0025153

phyllome epidermis PO:0025157

bract epidermis PO:0025158

bract abaxial epidermis PO:0025159

bract adaxial epidermis PO:0025160

multicellular trichome PO:0025162

multicellular trichome branch cell PO:0025163

root epidermal cell PO:0025164

shoot epidermal cell PO:0025165

papilla cell PO:0025166

leaf papilla cell PO:0025167

stigma papilla cell PO:0025168

prickle PO:0025169

root prickle PO:0025170

shoot axis prickle PO:0025171

thorn PO:0025172

leaf spine PO:0025173

stipule spine PO:0025174

leaf prickle PO:0025175

stem trichome PO:0025176

branch trichome PO:0025177

stem epidermis PO:0025178

branch epidermis PO:0025179

sepal trichome PO:0025182

tepal epidermis PO:0025184

phyllome trichome PO:0025186

petal trichome PO:0025187

tepal trichome PO:0025188

tepal abaxial epidermis PO:0025192

tepal adaxial epidermis PO:0025193

carpel trichome PO:0025208

stamen trichome PO:0025209

leaf abaxial trichome PO:0025210

leaf adaxial trichome PO:0025211

leaf pavement cell PO:0025212

leaf abaxial pavement cell PO:0025213

leaf adaxial pavement cell PO:0025214

new terms- elongation and differentiation zones:

  • plant axis differentiation zone (PO:0025119)
  • differentiation zone (PO:0020135) was renamed root differentiation zone. Existing children lateral root differentiation zone (PO:0003016) and primary root differentiation zone (PO:0003015) remained, but got standardized definitions
  • shoot internode differentiation zone (PO:0025102)
  • branch internode differentiation zone (PO:0025103)
  • old term "stem internode differentiation zone" (PO:0008042) remained, but got standardized definition
  • plant axis elongation zone (PO:0025180)
  • root elongation zone (PO:0025181). Old term elongation zone (PO:0020125) was made obsolete, because definition of was incorrect.
  • lateral root elongation zone (PO:0025256) Old term lateral root elongation zone (PO:0003014) was made obsolete, because definition of was incorrect.
  • primary root elongation zone (PO:0025257) Old term primary root elongation zone (PO:0003003) was made obsolete, because definition of was incorrect.
  • shoot internode elongation zone (PO:0025100)
  • branch internode elongation zone (PO:0025101)
  • old term "stem internode elongation zone" (PO:0008041) remained, but got standardized definition

List of Terms stomatal complex:

phyllome stomatal complex PO:0025215

leaf stomatal complex PO:0025183

leaf lamina stomatal complex PO:0025185

petiole stomatal complex PO:0025189

leaf abaxial stomatal complex PO:0025190

leaf adaxial stomatal complex PO:0025191

bract stomatal complex PO:0025216

carpel stomatal complex PO:0025217

petal stomatal complex PO:0025218

sepal stomatal complex PO:0025219

stamen stomatal complex PO:0025220

tepal stomatal complex PO:0025221


plus:

phyllome stomatal pore PO:0025234

leaf stomatal pore PO:0025235

List of new terms in numerical order

id: PO:0025086 name: Poaceae gynoecium ridge

id: PO:0025087 name: Zea gynoecium ridge

id: PO:0025088 name: gynoecium ridge

id: PO:0025092 name: dehiscence zone

id: PO:0025093 name: moss capsule annulus

id: PO:0025094 name: sporangium

id: PO:0025095 name: root parenchyma

id: PO:0025096 name: carpel epidermis

id: PO:0025097 name: stamen epidermis

id: PO:0025098 name: bract trichome

id: PO:0025099 name: embryonic plant structure

id: PO:0025100 name: shoot internode elongation zone

id: PO:0025101 name: branch internode elongation zone

id: PO:0025102 name: shoot internode differentiation zone

id: PO:0025103 name: branch internode differentiation zone

id: PO:0025104 name: first order inflorescence axis

id: PO:0025105 name: forth order inflorescence axis

id: PO:0025106 name: fifth order inflorescence axis

id: PO:0025107 name: sixth order inflorescence axis

id: PO:0025108 name: seventh order inflorescence axis

id: PO:0025109 name: eighth order inflorescence axis

id: PO:0025110 name: ninth order inflorescence axis

id: PO:0025111 name: tenth or higher order inflorescence axis

id: PO:0025112 name: second order infructescence axis

id: PO:0025113 name: third order infructescence axis

id: PO:0025114 name: forth order infructescence axis

id: PO:0025115 name: fifth order infructescence axis

id: PO:0025116 name: sixth order infructescence axis

id: PO:0025117 name: plant anatomical space

id: PO:0025118 name: anther pore

id: PO:0025119 name: plant axis differentiation zone

id: PO:0025120 name: antheridium sperm cell

id: PO:0025121 name: pollen sperm cell

id: PO:0025122 name: archegonium egg cell

id: PO:0025123 name: embryo sac egg cell

id: PO:0025124 name: gametangium

id: PO:0025125 name: antheridium

id: PO:0025126 name: archegonium

id: PO:0025127 name: primordium

id: PO:0025128 name: phyllome primordium

id: PO:0025129 name: petiole lamina

id: PO:0025130 name: cigar leaf

id: PO:0025131 name: plant anatomical entity

id: PO:0025132 name: canal

id: PO:0025133 name: petiole canal

id: PO:0025134 name: inflorescence branch crown

id: PO:0025135 name: cigar leaf lamina abaxial epidermis

id: PO:0025136 name: free tepal

id: PO:0025137 name: fused tepal

id: PO:0025138 name: fused collective tepal structure

id: PO:0025139 name: phyllome apex

id: PO:0025140 name: phyllome base

id: PO:0025141 name: phyllome tip

id: PO:0025142 name: leaf tip

id: PO:0025143 name: tepal apex

id: PO:0025144 name: petal apex

id: PO:0025145 name: sepal apex

id: PO:0025146 name: petal base

id: PO:0025147 name: sepal base

id: PO:0025148 name: tepal base

id: PO:0025149 name: petal tip

id: PO:0025150 name: sepal tip

id: PO:0025151 name: tepal tip

id: PO:0025152 name: peduncle epidermis

id: PO:0025153 name: peduncle trichome

id: PO:0025154 name: bract apex

id: PO:0025155 name: bract base

id: PO:0025156 name: bract tip

id: PO:0025157 name: phyllome epidermis

id: PO:0025158 name: bract epidermis

id: PO:0025159 name: bract abaxial epidermis

id: PO:0025160 name: bract adaxial epidermis

id: PO:0025161 name: portion of plant substance

id: PO:0025162 name: multicellular trichome

id: PO:0025163 name: multicellular trichome branch cell

id: PO:0025164 name: root epidermal cell

id: PO:0025165 name: shoot epidermal cell

id: PO:0025166 name: papilla cell

id: PO:0025167 name: leaf papilla cell

id: PO:0025168 name: stigma papilla cell

id: PO:0025169 name: prickle

id: PO:0025170 name: root prickle

id: PO:0025171 name: shoot axis prickle

id: PO:0025172 name: thorn

id: PO:0025173 name: leaf spine

id: PO:0025174 name: stipule spine

id: PO:0025175 name: leaf prickle

id: PO:0025176 name: stem trichome

id: PO:0025177 name: branch trichome

id: PO:0025178 name: stem epidermis

id: PO:0025179 name: branch epidermis

id: PO:0025180 name: plant axis elongation zone

id: PO:0025181 name: root elongation zone

id: PO:0025182 name: sepal trichome

id: PO:0025183 name: leaf stomatal complex

id: PO:0025184 name: tepal epidermis

id: PO:0025185 name: leaf lamina stomatal complex

id: PO:0025186 name: phyllome trichome

id: PO:0025187 name: petal trichome

id: PO:0025188 name: tepal trichome

id: PO:0025189 name: petiole stomatal complex

id: PO:0025190 name: leaf abaxial stomatal complex

id: PO:0025191 name: leaf adaxial stomatal complex

id: PO:0025192 name: tepal abaxial epidermis

id: PO:0025193 name: tepal adaxial epidermis

id: PO:0025194 name: root nodule meristem

id: PO:0025195 name: pollen tube cell

id: PO:0025196 name: basal endosperm transfer layer

id: PO:0025197 name: stele

id: PO:0025198 name: shoot axis stele

id: PO:0025199 name: branch stele

id: PO:0025200 name: stem stele

id: PO:0025201 name: megasporangium

id: PO:0025202 name: microsporangium

id: PO:0025203 name: pericarp vascular bundle

id: PO:0025204 name: rhizome internode

id: PO:0025205 name: shoot system vascular system

id: PO:0025206 name: phyllome vascular system

id: PO:0025207 name: tepal vascular system

id: PO:0025208 name: carpel trichome

id: PO:0025209 name: stamen trichome

id: PO:0025210 name: leaf abaxial trichome

id: PO:0025211 name: leaf adaxial trichome

id: PO:0025212 name: leaf pavement cell

id: PO:0025213 name: leaf abaxial pavement cell

id: PO:0025214 name: leaf adaxial pavement cell

id: PO:0025215 name: phyllome stomatal complex

id: PO:0025216 name: bract stomatal complex

id: PO:0025217 name: carpel stomatal complex

id: PO:0025218 name: petal stomatal complex

id: PO:0025219 name: sepal stomatal complex

id: PO:0025220 name: stamen stomatal complex

id: PO:0025221 name: tepal stomatal complex

id: PO:0025222 name: reproductive shoot apex

id: PO:0025223 name: vegetative shoot apex

id: PO:0025224 name: axil

id: PO:0025225 name: bract axil

id: PO:0025226 name: branch axil

id: PO:0025227 name: tetrad of megaspores

id: PO:0025228 name: valve

id: PO:0025229 name: moss capsule valve

id: PO:0025230 name: columella

id: PO:0025231 name: moss capsule columella

id: PO:0025232 name: moss capsule

id: PO:0025233 name: embryonic plant tissue

id: PO:0025234 name: phyllome stomatal pore

id: PO:0025235 name: leaf stomatal pore

id: PO:0025236 name: phyllome guard cell

id: PO:0025237 name: leaf guard cell

id: PO:0025238 name: abaxial petiole canal

id: PO:0025239 name: adaxial petiole canal

id: PO:0025240 name: second order inflorescence

id: PO:0025241 name: second order infructescence

id: PO:0025242 name: infructescence axis

id: PO:0025243 name: infructescence branch

id: PO:0025244 name: first order infructescence axis

id: PO:0025245 name: persistent sepal

id: PO:0025246 name: persistent tepal

id: PO:0025247 name: persistent stamen

id: PO:0025248 name: pseudostem

id: PO:0025249 name: leaf sheath epidermis

id: PO:0025250 name: leaf sheath abaxial epidermis

id: PO:0025251 name: leaf sheath adaxial epidermis

id: PO:0025252 name: seventh order infructescence axis

id: PO:0025253 name: eighth order infructescence axis

id: PO:0025254 name: ninth order infructescence axis

id: PO:0025255 name: tenth or higher order infructescence axis

id: PO:0025256 name: lateral root elongation zone

id: PO:0025257 name: primary root elongation zone

Retrieved from "http://wiki.plantontology.org/index.php?title=New_terms_and_obsolete_terms_for_Jan2011_release&oldid=5348"