New terms and obsolete terms-April 2012 Release

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New plant anatomical entity terms

phyllome plate meristem: (PO:0025428)

leaf plate meristem: (PO:0025429)

phyllome anlagen: (PO:0025430)

leaf anlagen (PO:0025431)

cotyledon anlagen (PO:0025432)

root anlagen: (PO:0025433)

phyllome adaxial meristem (PO:0025400)

leaf adaxial meristem (PO:0025401)

phyllome abaxial meristem (PO:0025402)

leaf abaxial meristem (PO:0025403)

phyllome marginal meristem (PO:0025404)

leaf marginal meristem (PO:0025405)

intercellular space (PO:0025379)

leaf mesophyll intercellular space (PO:0025380)

spongy mesophyll intercellular space (PO:0025381)

palisade mesophyll intercellular space (PO:0025397)

substomatal cavity (PO:0025382)

phyllome substomatal cavity (PO:0025398)

leaf substomatal cavity (PO:0025399)

phyllome sinus (PO:0025383)

leaf sinus (PO:0025384)

cutin (PO:0025385)

cuticular wax (PO:0025386)

plant cuticle proper (PO:0025387)

epicuticular wax(PO:0025388)

intercuticular wax (PO:0025389)

palea awn (PO:0025350)

glume awn (PO:0025351)

tubercle (PO:0025352)

bud areole (PO:0025353) (maybe should be areole bud)

cladode (PO:0025354)

corm (PO:0025355)

bulb (PO:0025356)

pneumatophore (PO:0025357)

pneumatorhiza (PO:0025358)

sorus (PO:0025359)

coenosorus (PO:0025360)

leaf tendril (PO:0025361)

leaflet tendril (PO:0025362)

leaf apex tendril (PO:0025363)

branch tendril (PO:0025364)

stem apex tendril (PO:0025365)

leaf rachis tendril (PO:0025366)

prophyll tendril (PO:0025367)

arillode (PO:0025378)

intercellular space (PO:0025379)

leaf mesophyll intercellular space (PO:0025380)

spongy mesophyll intercellular space (PO:0025381)

substomatal cavity (PO:0025382)

phyllome sinus (PO:0025383)

leaf sinus (PO:0025384)

cutin (PO:0025385)

cuticular wax (PO:0025386)

plant cuticle proper (PO:0025387)

epicuticular wax (PO:0025388)

intercuticular wax (PO:0025389)

free ending veinlet (PO:0025390)

lamina areole (PO:0025391)

leaf lamina areole (PO:0025392)

pappus (PO:0025393)

pappus element (PO:0025394)

floral organ (PO:0025395)

phyllome lamina (PO:0025396)

palisade mesophyll intercellular space (PO:0025397)

phyllome substomatal cavity (PO:0025398)

leaf substomatal cavity (PO:0025399)

phyllome adaxial meristem (PO:0025400)

leaf adaxial meristem (PO:0025401)

phyllome abaxial meristem (PO:0025402)

leaf abaxial meristem (PO:0025403)

phyllome marginal meristem (PO:0025404)

leaf marginal meristem (PO:0025405)

sieve element (PO:0025406)

fiber cell (PO:0025407)

primary vascular tissue (PO:0025408)

secondary vascular tissue (PO:0025409)

axial system (PO:0025410)

ray system (PO:0025411)

albuminous cell (PO:0025412)

primary vein (PO:0025413)

secondary thickening meristem (PO:0025414)

sieve cell (PO:0025415)

sieve tube (PO:0025416)

vessel (PO:0025417)

sclerid (PO:0025418)

septate fiber tracheid (PO:0025419)

septate libriform fiber cell (PO:0025420)

septate phloem fiber cell (PO:0025421)

gelatinous fiber (PO:0025422)

petiole vascular bundle (PO:0025434)

shoot axis cork cambium (PO:0025435)

root cork cambium (PO:0025436)

shoot axis vascular cambium (PO:0025437)

root vascular cambium (PO:0025438)

cambial zone (PO:0025439)

shoot axis cambial zone (PO:0025440)

root cambial zone (PO:0025441)

stem secondary thickening meristem (PO:0025442)

root secondary thickening meristem (PO:0025443)

primary xylem tracheary element (PO:0025444)

secondary xylem tracheary element (PO:0025445)

primary xylem tracheid (PO:0025446)

secondary xylem tracheid (PO:0025447)

primary xylem vessel member (PO:0025448)

secondary xylem vessel member (PO:0025449)

primary xylem vessel (PO:0025450)

secondary xylem vessel (PO:0025451)

primary phloem sieve element (PO:0025452)

secondary phloem sieve element (PO:0025453)

primary phloem sieve cell (PO:0025454)

primary phloem sieve tube element (PO:0025455)

secondary phloem sieve cell (PO:0025456)

secondary phloem sieve tube element (PO:0025457)

transfer companion cell (PO:0025458)

ordinary companion cell (PO:0025459)

intermediary companion cell (PO:0025460)

Renamed terms: PAE

cuticle (PO:0000022) to plant cuticle (PO:0000022)

awn (PO:0006032) > lemma awn

spore (PO:0025017) > plant spore

inflorescence lateral meristem (PO:0009105) > inflorescence branch meristem

ear lateral meristem (PO:0009110) > ear inflorescence branch meristem

tassel lateral meristem (PO:0009107) > tassel inflorescence branch meristem

leaf vein (PO:0020138) > leaf lamina vein (plus other leaf veins)

vessel member (PO:0002003) > xylem vessel member

vessel (PO:0025417) > xylem vessel

wood parenchyma (PO:0004532)>secondary xylem parenchyma

axial wood parenchyma (PO:0004533)>ray secondary xylem parenchyma

ray wood parenchyma (PO:0004534)>axial secondary xylem parenchyma

wood parenchyma cell (PO:0004525)>secondary xylem parenchyma cell

ray wood parenchyma cell (PO:0004527)>ray secondary xylem parenchyma cell

upright wood ray parenchyma cell (PO:0004528)>upright ray secondary xylem parenchyma cell

procumbent wood ray parenchyma cell (PO:0004529)>procumbent ray secondary xylem parenchyma cell

axial wood parenchyma cell (PO:0004526)>axial secondary xylem parenchyma cell

New plant structure development stage terms

life of whole plant (PO:0025337)

collective plant structure development stage (PO:0025338)

plant organ development stage (PO:0025339)

gametophyte vegetative development stage (PO:0025340)

gametophyte reproductive development stage (PO:0025341)

gametophyte dormant stage (PO:0025342)

gametophyte senescent stage (PO:0025343)

gametophore reproductive whole plant development stage (PO:0025344)

gametophore vegetative whole plant development stage (PO:0025345)

thallus reproductive whole plant development stage (PO:0025346)

thallus vegetative whole plant development stage (PO:0025347)

spore germination stage (PO:0025348)

trichome development stage (PO:0025368)

seed trichome development stage (PO:0025369)

seed trichome initiation stage (PO:0025370)

seed trichome elongation stage (PO:0025371)

seed trichome secondary wall biosynthesis stage (PO:0025372)

seed trichome maturation stage (PO:0025373)

seed dormant stage (PO:0025374)

plant spore stage (PO:0025375)

plant spore dormant stage (PO:0025376)

plant embryo dormant stage (PO:0025377)

plant tissue development stage (PO:0025423)

vascular tissue development stage (PO:0025424)

xylem development stage (PO:0025425)

phloem development stage (PO:0025426)

secondary xylem development stage (PO:0025427)

Renamed terms: PSDS

Changed all the terms that had "stages" in their names to "stage" and changed "developmental" to "development" for about 10 terms

whole plant growth stage (PO:0007033) > whole plant development stage

gametophyte phase (PO:0028003) > gamethophyte development stage

sporophyte phase (PO:0028002) > sporophyte development stage

A vegetative growth (PO:0007134) > sporophyte vegetative development stage

B reproductive growth (PO:0007130) > sporophyte reproductive development stage

C senescence (PO:0007017) > sporophyte senscent stage

D dormancy (PO:0007132) > sporophyte vegetative dormant stage

protonema phase (PO:0030006) > protonema whole plant development stage

New synonyms

This is only to highlight synonyms that are substantially different than the primary term name (e.g., cone as a synonym of strobilus).

working on 363 synonyms from FNA

Merged terms

plant structure development stage (PO:0007021) into plant growth and development stage (PO:0009012) -- plant structure development stage is primary name

Obsolete terms

axial cell (PO:0000081), consider fiber cell (PO:0025407), sieve element (PO:0025406), tracheary element (PO:0000290)

xylem element (PO:0000273), consider tracheary element (PO:0000290) and xylem fiber cell (PO:0000274)

septate fiber (PO:0004521), consider septate fiber tracheid (PO:0025419), septate libriform fiber cell (PO:0025420), septate phloem fiber cell (PO:0025421)

Other Changes:

(These will be summarized on the "Summary of changes page" before the release.)

carpel anlagen (PO:0006005) (revised)

added a comment to leaf intercalary meristem: The leaf intercalary meristem does not include a leaf plate meristem (PO:0025429)

-made flower meristem is_a reproductive shoot apical meristem, revised def'n

-made phyllome marginal meristem part_of phyllome

-added exact synonym to leaf marginal meristem: leaf margin blastozone

added has_participant relations between the following terms:

-trichome development stage (PO:0025368) and trichome (PO:0000282)

-seed trichome development stage (PO:0025369) and seed trichome (PO:0004511)

-leaf trichome development stage (PO:0007039) and leaf trichome (PO:0006504)

Changed the aspect (namespace) from plant_growth_and_development_stage to plant_structure_development_stage

Moved leaf trichome development stage (PO:0007039) to be is_a trichome development stage. new def'n: A trichome development stage that has as primary participant a leaf trichome. (POC:Curators)

Modified def'n: seed trichome: (PO:0004511): A trichome that develops from seed coat epidermis.

Got rid of old GRO synonyms on sporophyte dormant stage.

Made seed is_a plant structure. Updated definition. Removed seed part_of fruit and added develops_from ovule, has_part embryo

Added seed dormant stage has_part plant embryo dormant stage

As part of a general overhaul of the definitions of vascular tissue and cell types, updated definitions of: vascular tissue, vascular bundle, phloem, primary phloem, secondary phloem, protophloem, metaphloem, plant spore, xylem, primary xylem, protoxylem, metaxylem, secondary xylem, tracheid bar, leaf vein, midvein, primary vein, lateral meristem, cambium, vascular cambium, cork cambium, sieve tube member, tracheary element, xylem fiber cell, fiber tracheid, libriform fiber cell, axial system, ray system, wood parenchyma, axial wood parenchyma, ray wood parenchyma, wood parenchyma cell, ray wood parenchyma cell, upright wood parenchyma cell, procumbent wood parenchyma cell, axial wood parenchyma cell, tracheary element, tracheid, vessel member, schlerencyma cell, companion cell, sapwood, heartwood, early wood, late wood, growth ring, growth ring boundary.

Changed cambial initial from part_of vascular cambium to part_of cambium, because that is how it is defined.

Made growth ring boundary part_of growth ring, instead of is_a. This means it has no is_a parent for the moment.

Added comment to all leaf vein orders that they should only not be used with dichotomously branching vein patterns.

Updated definitions of second through higher order veins, renamed them leaf lamina veins

Updated definition of carpel anlagen.

Set up shoot and root lateral meristems as XPs

Changed phellem and phelloderm to part_of periderm, from part_of shoot axis periderm.

Made root meristem and shoot mersitem into cross-products (is_a meristem and part_of root or shoot system), also ear meristem and tassel meristem.

Changed definition of fruit nucellus (PO:0008005). Removed comment about filter that shouldn't have been there. Udated definitions of intercalary meristem (PO:0006073), leaf intercalary meristem (PO:0006346), stem intercalary meristem (PO:0006347), lateral meristem (PO:0020145), vascular cambium (PO:0005598), and secondary thickening meristem (PO:0025414). Renamed tassel branch meristem to tassel inflorescence branch meristem.

Added synonyms: lateral meristem - lateral growth meristem shoot lateral meristem - shoot lateral growth meristem root lateral meristem - root lateral growth meristem

Updated definition of companion cell (PO:0000071), sclerenchyma cell (PO:0000077) and sclerid cell (PO:0025418), sapwood (PO:0004513), heartwood (PO:0004512), early wood (PO:0004515), late wood (PO:0004516), growth ring (PO:0004514), plus wood parenchyma types and wood parenchyma cell types.