New terms and obsolete terms for May2011 release

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New terms added, 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 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

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.