New terms and obsolete terms for May2011 release
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New terms added
week of 02/02/2011
PO:0000062 stomatal initial (stomatal meristermoid, stomatal initial cell)
PO:0025258 procambial cell
PO:0025259 leaf procambium
PO:0025260 shoot axis procambium
PO:0000063 leaf procambial cell
PO:0025261 pericycle cell
PO:0000064 xylem pole pericycle cell
PO:0000065 phloem pole pericycle cell
week of 02/09/2011
PO:0025262 ovary septum
PO:0025263 locule
PO:0025265 sporangium locule
PO:0025264 anther locule
PO:0025266 ovary locule
PO:0025267 fruit replum
PO:0025268 fruit septum
PO:0025269 collective organ part structure
week of 02/16/2011
PO:0025270 fruit locule
PO:0025271 spore capsule locule
PO:0025272 ovary replum
PO:0025273 stem procambium
PO:0025274 branch procambium
week of 02/23/2011
PO:0025275 procambium
PO:0025276 shoot procambium
PO:0025277 pollen sac
PO:0025278 rhizome scale leaf
week of 3/8/11
PO:0030001 chloronema cell
PO:0030002 caulonema cell
PO:0030003 protonema
PO:0030004 chloronema
PO:0030005 caulonema
PO:0030006 protonema phase
week of 3/22/11
PO:0025279 megagametophyte
PO:0025280 microgametophyte
apical cell gametophytic apical cell, sporophytic apical cell, root apical cell, shoot apical cell, gametophore apical cell, thallus apical cell, leaf apical cell, non-vascular leaf apical cell, vascular leaf apical cell, shoot axis apical cell, gametophore axis apical cell, vascular shoot axis apical cell
Added vascular shoot system and non-vascular shoot system.
week of 3/29/11
PO:0025281 pollen
PO:0025282 archegonial megagametophyte
PO:0025283 antheridial microgametophyte
week of 4/12/11
gametophore bud (PO:0030026)
thallus (PO:0030027)
pergonial bract (PO:0030028)
sporphyte foot (PO:0030029)
perichaetal bract (PO:0030030)
gametophytic perianth (PO:0030031)
seta (PO:0030032)
antheridiophore (PO:0030033)
archegoniaphore (PO:0030034)
antheridium stalk (PO:0030035)
archegonium stalk (PO:0030036)
spore capsule calyptra (PO:0030037)
venter (PO:0030038)
archegonium neck(PO:0030039)
sporangium base (PO:0030040)
sporangium theca (PO:0030041)
peristome (PO:0030042)
peristome tooth (PO:0030043)
spore capsule operculum (PO:0030044)
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
