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

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 vascular shoot system

PO:0030017 non-vascular shoot system

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

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)

week of 4/12/11

callus parenchyma PO:0025285

embryonic coleoptile PO:0025286

seedling coleoptile PO:0025287

embryonic coleorhiza PO:0025288

seedling coleorhiza PO:0025289

embryonic hypocotyl PO:0025290

seedling hypocotyl PO:0025291

portion of axial tissue (PO:0030046)

hydrome (PO:0030047)

leptome (PO:0030048)

portion of plant fiber (PO:0030049)

week of 4/19/11

embryonic coleoptile PO:0025286

seedling coleoptile PO:0025287

embryonic coleorhiza PO:0025288

seedling coleorhiza PO:0025289

embryonic hypocotyl PO:0025290

seedling hypocotyl PO:0025291

epicotyl (PO:0025292)

seedling epicotyl (PO:0025293)

embryonic mesocotyl (PO:0025294)

seedling mesocotyl (PO:0025295)

embryonic radicle (PO:0025296)

seedling radicle (PO:0025297)

stereid (PO:0030045)

stereome (PO:0030050)

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