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add following terms:
PO:0008028 reproductive shoot apical meristem
PO:0008016 vegetative shoot apical meristem

added terms
id: PO:0005028 | name: inflorescence vascular system
id: PO:0005029 | name: root primordium
added additional IS_A parent PO:0005029 for PO:0000016 | lateral root primordium

destroyed the scrupulous term

[Term]
id: PO:0008016
name: <new term>
namespace: plant_structure
is_obsolete: true

delete PO:0008016

add several new PO terms
PO:0008033: phyllome whorl
PO:0008034: leaf whorl
PO:0008018: transition leaf
PO:0008019: leaf lamina base
PO:0008020: central zone of the leaf lamina
PO:0008021: tertiary vein
PO:0008022: quaternary vein
PO:00080023: higher order vein
PO:00080024: petiole proximal end
PO:00080025: central zone of the petiole
PO:00080026: petiole distal end
PO:00080027: petiole adaxial epidermis
PO:00080029: petiole abaxial epidermis
PO:00080030: trichome cell
PO:00080031: trichome branch
PO:00080032: stomatal pore

Modify PO:0002000: stomatal complex" definition

fixed
pollen tube tip PO:0000028 part_of pollen tube PO:0006345

add PO:0008017 leaf sheath pulvinus

add "vein" as synonym to "vascular system" in few cases

add "is a" relationship to various vascular system.

Add new terms:
embryo vascular system
stigma vascular system
filament vascular system
anther vascular system
hypocotyl vascular system

remove PO:0009093

Delete PO:0009012 from file

Add a new term: silk scar

fixed the duplicate use of ID [PO: PO:0009012] by the term
[Term]
id: PO:0009012
name: petiole pulvinus
namespace: plant_structure

The asme ID existed for
id: PO:0009012
name: plant growth and development stages
namespace: plant_growth_and_development_stage

The new ID for the term name: petiole pulvinus from namespace: plant_structure is PO:0009111

modify "Pulvinus" definition

Add following new terms:
stylar ridge of lower floret of pedicellate spikelet of ear
stylar ridge of lower floret of sessile spikelet of ear
stylar ridge of upper floret of pedicellate spikelet of ear
stylar ridge of upper floret of sessile spikelet of ear

Add new terms: pulvinus, petiole pulvinus, inflorescence branch pulvinus, basal endosperm transfer cell, basal endosperm transfer layer

added CL:0000366 sperm cell (sensu Viridiplantae) to PO:0000084 sperm cell Xref

added cell-type ontology [from OBO] xref

added synonyms

various changes

added several new terms

Added synonym ' seed trichome' for PO:0004511
added new term PO:0005003 stem trichome

added the flag in header
version: $Revision: xxxx $

Following new terms were added and many terms have their term to term relationships added and/or updated.

id: PO:0009101
name: long lateral tassel branch

id: PO:0009102
name: short tassel branch

id: PO:0009103
name: short tassel branch meristem

id: PO:0009104
name: long lateral tassel branch meristem

id: PO:0009105
name: inflorescence lateral meristem

id: PO:0009106
name: tassel meristem

id: PO:0009107
name: tassel lateral meristem

id: PO:0009108
name: inflorescence apical meristem

id: PO:0009109
name: ear meristem

id: PO:0009110
name: ear lateral meristem

modified the definition of PO:0006382 by deleting ..outside the stamens statement.

Changed term name 'somatic embryo' to 'cultured somatic embryo' PO:0000011.

Modifications made to version 1.30 of po_anatomy.obo  include.


PO:0009049 inflorescence
	Added synonym : capitulum

PO:0009045 phyllary
	renamed to 'involucral bract'.
	synonym 'phyllary' added to renamed term
	Definition. modified to add the word 'Compositeae'

	is_a: PO:0009054 ! inflorescence bract
	relationship: part_of PO:0009100 ! involucre

PO:0009100 involucre -->new term
	Definition: A whorl of bracts at the base of a cluster of
	flowers as found in Asteraceae or Compositae." [POC:curators]

	Comment: The burs or bristles in Cenchrus and Pennisetum are
	not involucres because the fused structures are branches and
	not bracts.

	relationship: part_of PO:0009049 ! inflorescence

propagated 'root initial cell' terms from cell node to 'root apical meristem' node.

1. Obsoleted following 13 subcellular terms and added comment for each referring to the corresponding GO subcellular term
PO:0020014 columella	GO:0043674
PO:0020009 ectexine	GO:0043669
PO:0020010 endexine	GO:0043671
PO:0020008 exine	GO:0043668
PO:0020016 foot layer	GO:0043670
PO:0020017 intine	GO:0043678
PO:0020011 nexine	GO:0043672
PO:0020059 pollen wall	GO:0043667
PO:0020015 sculpture element GO:0043675
PO:0020012 sexine	GO:0043673
PO:0020013 tectum	GO:0043676
PO:0020018 germination pore	GO:0043677
PO:0000024 filiform apparatus	GO:0043680
PO:0000023 Casparian strip	GO:0048226
PO:0020095 polar nucleus	GO:0043078

2. added new terms under initial cell, and also under root meristem:

'root initial cell' PO:0000059, synonym: root stem cell
def: Cell in the root apical meristem that by division gives rise to two cells one of which remains in the meristem, the other is added produces different root cells.

'root cortex-endodermis initial cell', PO:0000060, synonym: root cortex-endodermis stem cell
def: Cell that produces root cortex and endodermis. In direct contact with quiescent center.

'lateral root-cap-epidermal initial' PO:0000061, synonym: lateral root cap-epidermal stem cell
Def: Cell that produces lateral root-cap cells and root epidermis.

3. Added four new terms under 'shoot' node:

' bud', PO:0000055; def: Undeveloped shoot

'floral bud'; PO:0000056, def: Bud that develops into a flower.

'inflorescence bud' PO:0000057, def: Bud that develops into an inflorescence.

'vegetative bud'PO:0000058, def: Bud that develops into a long or short shoot.

4. new term added: petal vascular system, PO:0000054. def: Vascular system of the petal.

5. Added meiocyte as synonym of the term 'sporocyte'.

modified relationships for children of PO:0004709 : axillary bud, PO:0004713 : terminal bud to IS_A.

Added subsets reference for creation suggesting which terms are
1-reference -->for reference ontology
2-Arabidopsis
3-Poaceae
4-rice
5-maize
6-citrus
7-tomato

2-7 were be added only for the fruit section

modified the definition of prop root and organogenic callus by deleting the special characters. The content is the same.

Added terms

[Term]
id: PO:0006090
name: organogenic callus
namespace: plant_structure
def: "A type of cultured callus that has competence to form any organ such as root\, leaf\, shoot\, leafless\nshoot/bare stem\, etc." [POC:curators]
synonym: "meristematic callus" []
is_a: PO:0000009 ! cultured callus

[Term]
id: PO:0006091
name: embryogenic callus
namespace: plant_structure
def: "A type of cultured callus that form embryo-like structures such as somatic embryos." [POC:curators]
is_a: PO:0000009 ! cultured callus

Added additonal parent for somatic embryo PO:0000011

embryogenic callus PO:0006091
--developsfrom--somatic embryo PO:0000011

PO:0000046 : seminal root
  Additional parent PO:0003005 nodal root
  Added synonyms
	lateral seminal roots,
	secondary roots,
	scutellar nodal roots
  Modified definition
  	"...at the scutellar node.." to "within the scutellar node"

Modifed term names for

apical meristem of lateral root  PO:0006020
new term name: lateral root apical meristem

apical meristem of primary root	PO:0006081
new term name: primary root apical meristem


Modified parents for

Primary root PO:0020127. By definition it is a root that
develops from the radicle which is a type of embryonic root.

root
--isa--embryonic root
-----isa--radicle
--------developsfrom--primary root
--isa--primary root

modified the header to include the revision number

Terms and definitions added

PO:0006089 anther primordium
PO:0006000 hull (sensu Poaceae)
PO:0006005 carpel anlagen
PO:0006006 primary parietal cell layer
PO:0006007 secondary parietal cell layer
PO:0006008 inner secondary parietal cell layer
PO:0006009 outer secondary parietal cell layer
PO:0006010 primary parietal cell
PO:0006013 juice sac
PO:0006014 male archesporial cell
PO:0006015 female archesporial cell

Added several synonyms:
flavedo = epicarp
albedo = mesocarp
rind = pericarp
pulp  (sensu Citrus) = endocarp
flesh  (sensu Citrus) = endocarp

deleted synonym archesporial cell from megasporocyte.
A new term female archesporial cell was created. see above

additional relationships assigned to existing and new terms.
significant being
floret is_a flower
ovary part-of carpel

1. New terms: long cell and short cell (is_a epidermal cell)

(i) epidermal cell
	(i) long cell (PO:0004717)
	(i) short cell (PO:0004718)
		(i) epidermal cork cell
		(i) silica cell

Definitions:
long cell - a more or less rectangular epidermal cell in which the proximo-distal dimension is several times longer than the transverse dimension.

short cell - an isodiametric epidermal cell.

To make it consistent with its sibling, 'epidermal cork cell', I modified the definition of silica cell to:
"Cells with deposits of silica in them. One of the two types of short cells in the epidermis of grasses and bamboos. It is usually paired with epidermal cork cell."

Comment (for both cell types): In the leaf epidermis of Poaceae and Joinvilleaceae, long cells and short cells often alternate in longitudinal rows.

2. New term - hilum groove
Def: longitudinal groove in the testa through the prominent hilum of the seed.
Synonym: faboid split

3. Stem cell terms
Added stem cell as synonym of 'initial cell, and also, added 'columella root cap stem cell' as synonym of 'columella root cap initial'

4. New term - paraclade and paraclade cortex
Stem
 (p) paraclade (PO:0004720)
	(p) paraclade cortex (PO:0004721)

paraclade (PO:0004720)
Def: lateral branch which ends in an inflorescence that repeats the main inflorescence (used both refs: APWeb and Weberling, ISBN: 0521251346
Morphology of Flowers and Inflorescences.

paraclade cortex (PO:0004721
Def The primary tissue located between the vascular system and the epidermis of the paraclade.

5. Inflorescence stem added as synonym of 'peduncle'.

6. New terms - pedicel cortex and sepal vascular system,

pedicel cortex PO:0004722
Def: The primary tissue located between the vascular system and the epidermis of the pedicel.

sepal vascular system, PO:0004723
Def: Vascular system of the sepal.

7. New term - hypocotyl-root junction PO:0004724

Def: Junction point of the embryonic root and hypocotyl.
Note: the decision was to add this term under 'embryo axis' and also propagate it under shoot.

8. New terms: abaxial and adaxial leaf primorduim

abaxial side of leaf primorduim PO:0004725
Def: The abaxial/outer side of the leaf primordium that becomes the abaxial/lower leaf blade

adaxial side of leaf primorduim PO:0004726
Def: The adaxial/inner side of the leaf primordium that becomes adaxial/upper leaf blade.

added Poaceae and Solanaceae fruit terms

Changes made by Katica:

1.	Added following primordium terms:

carpel primordium PO:0004703
	Def: The very first appearance of a carpel.

sepal primordium, PO:0004704
	Def: The very first appearance of a sepal.

stamen primodium, PO:0004705
	Def: The very first appearance of a stamen.

flower primordium, PO:0004706
	Def: The very first appearance of a flower.

2.	Added fruit term ‘dehiscence zone’, also added ‘fruit wall’ as synonym to existing term ‘pericarp’
fruit dehiscence zone PO:0004707
Def: A narrow band of cells that extends along the entire length of the fruit. Upon fruit maturation, cell separation within the dehiscence zone allows the valves to detach from the replum and for the seeds to be dispersed.

3.	Added new term, scutellar node PO:0004708 (as a child of ‘embryo’)
Def The region in the embryo between the primary root (enclosed in the coleorhiza) and the plumule (enclosed in the coleoptile) to which the scutellum is attached.

4. Added axillary and terminal bud terms as children of ‘shoot’:

PO:0009006 : shoot
(p) axillary bud PO:0004709
(i) axillary floral bud PO:0004710
(i) axillary inflorescence bud PO:0004711
(i) axillary vegetative bud PO:0004712
(p) terminal bud PO:0004713
(i) terminal floral bud PO: 0004714
(i) terminal inflorescence bud PO: 0004715
(i) terminal vegetative bud PO: 0004716

Definitions:
axillary bud: Bud formed in the axil of a leaf or shoot.

axillary floral bud: Bud formed in the axil of a leaf or shoot that develops into a flower.

axillary inflorescence bud: Bud formed in the axil of the a leaf or shoot that develops into an inflorescence.

axillary vegetative bud: Bud formed in the axil of the a leaf or shoot that develops into a long or short shoot and/or leaf(s).

terminal bud: Bud formed at the apex of shoot.

teminal floral bud: Bud formed at the apex of shoot that develops into a flower.

terminal inflorescence bud: Bud formed at the apex of shoot that develops into an inflorescence.

terminal vegetative bud: Bud formed at the apex of shoot that develops into a long or short shoot.

5. Changed synonym of shoot, crown (sensu trees) to ‘tree crown’.

6. Changed relationship type of the term 'bark' changed, now bark (develops_from) ‘secondary phloem’, also added ‘bark’ as instance of tissue. in PSO.

7. Removed ‘phellem’ from cell type node, and added it as instance of tissue. Note: ‘phellem’ was already a child of ‘bark’.

1.	Brought back 'organ' from the obsolete node and added 28 terms as its  children with is_a relationship type.

2.	Change definition for the term 'cambial initial'

Old: Cell localized in the vascular cambium or phellogen that their periclinal divisions can contribute cells either to the outside or to the inside of the axis; in vascular cambium, classified into fusiform initials (source of axial cells of xylem and phloem) and ray initials (source of the ray cells).

New def: Cell in the vascular or cork cambium which by periclinal divisions produce cells to the outside or inside of the cambial axis.

3.	Propagated 'apical hook' under 'hypocotyl' (part_of)

4.	Added  new term 'middle layer'

PO:0000002 : anther wall
(p) new term: middle layer (PO:0004700)

Def: Usually a single cell layer between tapetum and endothecium which almost invariably degenerates early during angiosperm anther  development and is eventually absorbed by adjacent cells.

5.	added two new terms under 'axillary shoot'

short shoot  (PO:0004701)
Def: Shoot in which the internodes elongate little or at all, bearing reproductive structures and/or leaves.
Synonyms: brachyblast, bud spur,

long shoot  (PO:0004702)
Def: Shoot in which all or most of the internodes elongate.

PO:0004545: shoot borne shoot
   (i) PO:0006343 axillary shoot
                (i) long shoot
                (i) short shoot

6. Obsoleted subcellular terms

PO:0000023 casparian strip
PO:0020095 polar nucleus
Added comments: this term is available in the Cellular component aspect of the Gene Ontology (GO:0048226 and GO:0043078).

Manually changed IDs for the following terms (duplicated entries in dev stages file):

rhizome, PO:0004501, new ID is PO:0004542

tuber, PO:0004502, new ID is PO:0004543

root borne shoot, PO:0004503,  new ID is PO:0004544

shoot borne shoot, PO:0004504, new ID is PO:0004545

epicomic shoot, PO:0004505, new ID is PO:0004546

subterranean tuber, PO:0004506, new ID is PO:0004547

aerial tuber, PO:0004507, new ID is PO:0004548

Ontology file changes from the developer's meeting at Carnegie, November 03-05, 2005

1.  Changed definition of the term 'shoot'

Def: Part of the sporophyte composed of the stems and leaves, and includes shoot apical meristems.

Old def: def: "All the parts developed that can trace their origin to the apical cell of the two celled embryo."

2. Added three synonyms to the term 'shoot'

crown (sensu tree)
crown (sensu Poaceae)
branch

3. Added New term: rhizome
rhizome, PO:0004501
def: Underground shoot

4. Added new terms: tuber. aerial tuber and subterranean tuber

New term: tuber, PO:0004502
Def: Swollen storage shoot with determinate growth

New term: aerial tuber, PO:0004507
Def: An axillary shoot with a swollen stem.

New term: subterranean tuber, PO:0004506
Def: A swollen rhizome or a part of the rhizome with determinate growth.
Comment: This has nothing to do with the underground swollen storage organ of Ipomoea which is swollen.

(p) Shoot
(i) tuber
(i) aerial tuber
(i) subterranean tuber

5. New terms: root borne shoot, shoot borne shoot, epicomic shoot

New term: root borne shoot, PO:0004503
Def: Shoot that is initiated from a root.
synonym: sucker shoot

New term: shoot borne shoot, PO:0004504
def: "Shoot that is initiated from a shoot." [POC:curators]
synonym:branch

New term: epicomic shoot, PO:0004505
Def: Shoot developing from a trunk.

6. Term 'trunk' added as synonym to existing term 'stem'

7. Term 'catkin' added as synonym to the term 'inflorescence'

8. Term 'gland' added as synonym of 'secretory tissue'.
Added comment for this term 'secretory tissue'
Comment: The synonym gland does not imply non-secretory 'glands'.

9. Under 'trichome' node, added terms: secretory trichome, non- secretory trichome, and seed hair.

new term: secretory trichome, PO:0004509
def: A trichome that secretes or sequesters a substance.

new term: non-secretory trichome, PO:0004510
def: Trichome that does not have secretory function.

new term: seed hair, PO:0004511
def: Trichome that develops from seed coat epidermis and is often long with putative dispersal function.

10. Under 'secondary xylem' added terms: heartwood, sapwood, growth ring, growth ring boundary, early wood and late wood

New term: heartwood, PO:0004512
def: "The inner layers of secondary xylem that have largely ceased to function in storage and conduction and in which reserve materials have been removed or converted into heartwood substances; generally darker colored than the functioning sapwood.

New term: sapwood, PO:0004513
def: Outer part of the wood of stem or root containing living cells and reserves and in which conduction of water takes place. Generally lighter colored than the heartwood.

New term: growth ring, PO:0004514
def: A growth layer of secondary xylem or secondary phloem as seen in transection of stem or root; may be an annual ring or a false annual ring.

New term: growth ring boundary, PO:0004517
def: Boundary between two growth rings.

New term: early wood, PO:0004515
def: The wood formed in first part of a growth ring and characterized by a lower density and larger cells than the late wood.
synonym: "spring wood

New term: late wood, PO:0004516
def: The secondary xylem formed in the later part of a growth ring; denser and composed of smaller cells than the early wood.
synonym: summer wood

11. Added new term 'bark' under 'secondary phloem'

New term: bark. PO:0004518
Def: All tissues outside the vascular cambium or the xylem; in older trees may be divided into dead outer bark and living inner bark, which consists of secondary phloem.

12. Added new terms, libriform fiber, septate fiber as children of 'xylem fiber', and added 'phloem fiber' under 'secondary phloem'.,

New term: phloem fiber, PO:0004519
def: A fiber in phloem.

PO:0004520
New term: libriform fiber
def: A xylem fiber commonly with thick walls and simple pits.

New term: septate fiber, PO:0004521
def: A fiber with thin transverse walls (septa)\, which are formed after the cell develops a secondary wall thickening.

13. Added terms: outer vascular cambium, included vascular cambium as children of 'vascular cambium'.

New term: outer vascular cambium, PO:0004522
def: Cambium at the outer margin of the xylem cylinder.

New term: included vascular cambium, PO:0004523
def: Cambium occurring within xylem.

new term: included phloem, PO:0004524
def: Phloem produced by included vascular cambium.

14. changed definition for the term 'phloem mother cell'
New definition: A cell derived from vascular cambium which is destined to differentiate into secondary phloem.

15. Added new terms under 'cell' node: wood parenchyma cell, axial wood parenchyma cell, ray wood parenchyma cell, upright wood ray parenchyma cell, procumbent wood ray parenchyma cell, tile cell and sheath cell as children of 'parenchyma cell'

New term: wood parenchyma cell, PO:0004525
def: Parenchyma cell occurring within secondary xylem.

New term: axial wood parenchyma cell, PO:0004526
def: Parenchyma cell in the axial system of secondary xylem.

New term: ray wood parenchyma cell, PO:0004527
def: Parenchyma cell of a ray in secondary xylem.

New term: upright wood ray parenchyma cell, PO:0004528
def: Ray cell in secondary xylem oriented axially (vertically in the axis) with its longest dimension.

New term: procumbent wood ray parenchyma cell, PO:0004529
def: Ray cell within secondary xylem having its longest axis in radial direction.

New term: tile cell, PO:0004530
def: Empty upright ray cell of approximately the same height as the procumbent ray cell and occurring in indeterminate horizontal series usually  interspersed among the procumbent cells.

New term: sheath cell, PO:0004531
Def: Cell on the margin of, and tending to form a sheath around, the procumbent cells of a multi-seriate ray as seen in tangential section.

16. Added new terms under 'secondary xylem': wood parenchyma, axial wood parenchyma and ray wood parenchyma

New term: wood parenchyma, PO:0004532
def: Parenchymatous tissue occurring in the wood.

New term: axial wood parenchyma, PO:0004533
def: Parenchyma tissue in the axial system of secondary xylem.

name: ray wood parenchyma, PO:0004534
def: Radially oriented parenchyma tissue in secondary xylem.

17. Added new terms under 'fruit; node: fruit placenta, fruit pedicel and fruit columella

New term: fruit placenta, PO:0004535
def: A more or less localized region within a fruit to which seeds are attached.

New term: fruit pedicel, PO:0004536
def: Basal part of the ultimate branch of the infructescence.

New term: fruit columella, PO:0004540
def: Central axis of the fruit.

18. Added new term under 'embryo' node: adventitious embryo

New term: adventitious embryo, PO:0004537
def: Embryo derived directly from nucelus cells without involving embryo sac cells.

19. added synonym 'germ; to the term 'embryo'


20. Added new term, indeterminate nodule and determinate nodule

New term: indeterminate nodule, PO:0004538
def: Nodule characterized by a persistent meristem\, presence of vascular transfer cells\, and cell division in the inner cortex with non-dividing infected cells and bacteria. ISBN:1842460137
Comment: Nodule is persistent and may continue to grow after a physiological stress.

New term: determinate nodule, PO:0004539

def: Nodule characterized by a dividing infected cells and bacteria\, vascular transfer cells absent and cell division is in the outer cortex.
Comment: Nodules are not persistent.

21. Changed relationship of carpe and ovary, they are now both direct children of 'gynoecium':
(p) gynoecium
	(i) carpel
	(i) ovary

22. Changed the ID of the term 'floret (sensu Asteraceae), this term has duplicated ID entry (PO:0004500) to PO:0004541, and merged to the term 'flower'.

Reason: this term was introduced in PO following rationale that florets in Poaceae and in Asteraceae are different structures. However, after re-examination of these terms, the group agreed that floret in Asteraceae is basically a flower, hence, it was merged to the term 'flower' (becoming its synonym).

corrected the syntax problem in teh definition of PO:0005005

modified the definition of PO:0005007

added definitions for PO:0005004 and PO:0005005

corrected the ids for PO:0005004/5/6/7. Earlier version had a 6 digit id.

added new terms, additional parents to terms with no is-a relationships
that were resolved in the meeting on October 7 2005.

added term 'floret (sensu Asteraceae)'

Changed term 'In vitro cell tissue oand organ culture' to "In vitro cultured cell, tissue and organ'

Added new terms basal and cauline axillary shoots.

obsoleted PO:0006300

removed 3 terms which belong to plant_growth_and_developmental_stages aspect

fixed minor format problems

this version is based on the GO-format files po_anatomy.ontology (ver 1.37 ) and po_anatomy.defs (ver 1.41).

Added two new terms:

PO:0003023
name: nodule
def: "Enlargement or swelling on the roots of plants, particularly in the Fabaceae, inhabited by nitrogen-fixing bacteria.


PO:0003024
name: stolon
def: "A slender, prostrate or trailing above-ground stem which produces roots and sometimes erect shoots at its nodes.

namespace: plant_anatomy --> plant_structure

This version of the plant structure ontology file in OBO format is based on the anatomy.ontology (ver 1.32 ) and anatomy.definition (ver 1.36).