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corrected leaf lamina abaxial epidermis definition.

added definitions for the following new terms:

leaf lamina epidermis, PO:0000047
Def: Epidermal layer of a leaf blade.

leaf lamina vascular system, PO:0000048
Def: Vascular system of the leaf lamina.

leaf lamina abaxial epidermis, PO:0000049
Def: The epidermal layer of the abaxial/lower surface of the leaf blade.

leaf lamina adaxial epidermis, PO:0000050
Def: The epidermal layer of the adaxial/upper surface of the leaf blade.

petiole epidermis, new term, PO:0000051
Def: Epidermal layer of a leaf petiole.

petiole vascular system PO:0000052
Def: Vascular system of the leaf petiole.

petiole cortex, PO:0000053
Def: The primary tissue located between the vascular system and the epidermis of the petiole.

New term: shoot borne root (synonym: adventitious root, stilt root) PO:0000042
New definition: Post-embryonic root developed from stem.
Note: (PO:0020129) adventitious root is merged to this term, and became its synonym.

Term: nodal root (PO:0003005)
New definition: Adventitious root that forms at a shoot node.

New term: crown root PO:0000043
Definition: Adventitious root formed at the base of the growing stem (known as a crown).

New term: prop root (syn. brace root) PO:0000044
New Def: Adventitious root formed at stem nodes above the ground and growing directly into the soil.
Comment: This term is perhaps best defined functionally: these roots serve to prop the plant up.

New term: embryonic root PO:0000045
Definition: Root that is initiated in developing embryo.

New term: seminal root PO:0000046
Definition: Root formed at the scutelar node of the embryo in some monocotyledonous plants.

New terms:
1. stem vascular system	PO:0000039
Def: Vascular tissues in their specific arrangements in the stem.

2. primary endsperm cell	PO:0000038
Def: Cell produced by the fusion of sperm cell nucleus and two polar nuclei of the central cell (or diploid secondary endosperm nucleus, in cases where two polar nuclei fuse together before double fertilization). The first cell of the endosperm, often tripoid.

3. Renamed term 'nodule' to 'root nodule' and adding a new structure
for the term 'nodule:

New term: adventitious root nodule (syn. stem nodule)	PO:0000040
Def: Enlargement or swelling at position of dormant adventitious root primordium (on the stem), inhabited by nitrogen-fixing bacteria.

Comment: Unlike the root nodules, these contain functioning chloroplasts in the nodule cortex and are therefore capable of carbon fixation. Note: stem nodule is commonly used term for this structure, although the nodules are formed at positions of dormant adventitious root primordia.

Changed def in term: articulated laticifer PO:0006221
New def: Latex-containing cells in which the walls between contiguous cells may partly or completely disappear.

Cork cell (sensu Poaceae) PO:0000041
Def: One of the two types of short cells in the epidermis of grasses and bamboos. It is usually paired with silica cell.
Comment: Developmentally different from periderm cork cell (i.e., phellem), produced by cork cambium.

- Corrected error in the definition of term: stem cortex
Definition (new): The primary tissue located between the vascular system and the epidermis of the stem.

This version is based on po_anatomy.obo ver 1.3

Following term definition deleted. THis was committed accidently in the last version.

term: plant growth and development
goid: PO:0009012
definition: Any growth and developmental stage of a plant.
definition_reference: Poc:curators

Fixed character problem

added definitions:

Term: vascular system
Def: The total of the vascular tissues in their specific arrangement in a plant or plant organ.

Term: leaf vascular system
Def: Vascular system of the leaf.

Term: cotyledon vascular system
Def: Vascular system formed in cotyledons.

Term: shoot apex
Def: The topmost part of the shoot, situated at the distal extremity of the shoot axis, consists of apical meristem the youngest leaf primordia.


Also, added in Comment section of 'root vascular system' (PO:0003011):
This term was brought back from OBSOLETE node (original reason for OBSOLETE: synonym of term 'stele'). Since stele encompasses both, vascular system and the pith, in roots with pith, vascular system and stele are not synonymous.

Twelve new terms in PO:
Term: cuticle
Def: A layer of fatty material, cutin, rather impervious to water, located on the outer walls of epidermal cells.

Term: casparian strip
Def: A band-like wall formation within primary walls that contains suberin and lignin; typical of endodermal cells in roots, in which it occurs in radial and transverse anticlinal walls.

Term: filiform apparatus
Def: A complex of cell wall invaginations in a synergid cell similar to those in transfer cells.

Term: root tip
Def:  Top portion of the root including meristem and root cap.

Term: primary root tip
Def: The portion of the primary root including the meristem and root cap

Term: lateral root tip
Def: The portion of the lateral root including the meristem and root cap.

Term: pollen tube tip
Def: Tip portion of the pollen tube that is rapidly growing.

Term: root hair tip
Def: Tip portion of an outgrowth of a root epidermal cell.

Term: septum
Def: A thin partition or membrane that divides a cavity or a mass of tissue, e.g., in anther, ovary or fruit.

Term: lenticel
Def: Loosely-packed mass of cork cells occurring especially in the young stem, bark or even leaf of a plant, visible on the surface as a raised, often powdery-appearing spot, through which gaseous exchange occurs.

Term: tetrad of microspores
Def: A group of four haploid cells that remained joined together shortly after meiosis. Each cell will give rise to the male gametophyte.

Term: valve
Def: valve: a portion of an organ that is fragmented; in capsule, theportions into which the pericarp splits at maturity.

Term: Whole plant
Def: The entire plant, including roots, shoots and leaves, at any stage of its life cycle.
Comment: This term is so general that it should be avoided whenever possible.

Term: in vitro cell, tissue and organ culture
Definition: Isolated and grown plant protoplast, cell, tissue and organ, involving, as a common factor, growth of microbe-free plant material in sterile environment, such as sterilized nutrient medium in a test tube or petri dish.

Term: cultured protoplast
Def: In vitro isolated cells from which the entire cell wall has been enzymatically removed.

Term: cultured cell
Synonym: cell suspension
Def: In vitro grown isolated cells and small cell aggregates that proliferate while suspended in liquid sterile medium or spread on a solid agar medium.
Comment:  In cell cultures, the cells are no longer organized into tissues.

Term: cultured leaf cell
Def: In vitro grown isolated cells and small cell aggregates that originated from isolated leaf protoplasts (after they re-established cell wall, or from callus that was induced from leaf tissue).

Term: cultured root cell
Def: In vitro grown isolated cells and small cell aggregates that originated from isolated protoplasts after they re-established cell wall, or from callus that was induced from segment of root.

Term: somatic embryo
Def: An embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote.

Term: cultured callus
Def: In vitro grown cell aggregates that originated from isolated protoplasts, cell suspensions, or from callus that was induced in sterile medium the supplemented by plant growth regulators.

Term: cultured embryo
Def: In vitro isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte).

Term: Cauline leaf
Def: Leaf or pairs/whorls of leaves borne on the stem.
Comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.

Term: Rosette leaf
Def: One of multiple leaves borne in a rosette. Rosette - a group of leaves, generally borne at the base of the plant, that are separated by very short internodes.

Comment: In Arabidopsis, vegetative development is characterized by the production of the rosette leaves.

Term: apical hook
Synonym: hypocotyl hook
Def: hook-like structure which develops at the apical part of the
hypocotyl in dark-grown seedlings in dicots.

Term: cotyledon primordium
Def: An organized group of cells that will differentiate into a cotyledon.

Term: lateral root primordium
Def: An organized group of cells derived from the root pericycle that will differentiate into a new root.

Term: leaf primordium
Def: An organized group of cells that will differentiate into leaf that are emerging as an outgrowth in the shoot apex (flanking the meristem).

Term: ovule primordium
Def The very first appearance of ovule.
Term: gynoecium primordium
Def: The very first appearance of gynoecium.

Term: petal primordium
Def: The very first appearance of a petal.

Added Felipe's new definitions:
Stem: the axial system of plants that bears leaves and buds.
Comment: it is usually above ground and more or less negatively geotropic, is exogenous in origin, often indeterminate in growth and with secondary thickening.

Inflorescence: That part of the axial system of plants above the uppermost foliage leaf/pair of foliage leaves that bears flowers.

Peduncle: The stalk of an inflorescence; that part of the inflorescence below the first flower or inflorescence branch and above the last foliage leaf/pair of foliage leaves.

added word OBSOLETE to the PO:0006067 definition
modified the text "obsolete" in definitions to upper case "DEFINITION"
in order to allow AmiGO to detect correctly that obsolete terms are to be displayed in grey color.

Coments for pericycle  PO:0006203  suggesting "In seed plants it is regularly present in roots and absent in most stems and leaves" was deleted. Thus avoiding confusion of a generic Vs a tissue/organ specific pericycle. The term preicycle PO:0006203 now stands as present in flowering plant as part_of root only.

No changes in def file.

1. Corrected typo, mesotome sheath to mestome sheath

2. Changed  definitions for terms epicotyl and plumule:

Epicotyl: The first internode of the stem above the hypocotyl. In literature also used for the entire embryonic axis, consisting of several internodes, above the cotyledonary node. Equals: first internode.

(Old definition: The node between the cotyledon(s) and the first foliage leaf of a young sporophyte)

Plumule: The somewhat differentiated terminal bud in several embryo types above the cotyledonary node, in which one or more internodes and leaves or scales can be discerned in a primordial stage.

(Old def: The growing point of the stem of a young sporophyte).

Felipe made changes in the following definitions:

bundle sheath extension:  add "one or" after: " It may be present on..."

cotyledon abaxial epidermis: rephrase to: The abaxial/lower epidermal
cell layer of the cotyledon.

cotyledon adaxial epidermis: rephrase to: The adaxial/upper epidermal
cell layer of the cotyledon.

cotyledon epidermis: rephrase to: The epidermal cell layer of the
cotyledon.

floral meristem: get rid of "Apical or the primary  shoot" and
capitalize M in meristem.

floret meristem (sensu Poaceae): get rid of "Apical or the primary
shoot", capitalize M in meristem and get rid of "It terminates into
carpel primordum."

root procambium: change "A primary cambium" to "A derivative of the
apical mersitem"...

subsidiary cell: get rid of: "composing the groundmass of the tissue"

suspensor: change from "A nearly always uniserrate extension at the
base of the embryo." to "A nearly always single file of cells at the
base of the embryo derived from the basal cell."

Peter and Felipe changed MANY definitions and so it's impossible to list them all.

Additionally, I changed definitions for the following terms:

1. Term cell: (PO:0009002):
Structural and physiological unit of a living organism; it (i.e., plant cell) consists of protoplast and cell wall; in nonliving state, of cell wall only, or cell wall and some nonliving inclusions.

2. term: sperm cell
id: PO:0000084
A haploid male reproductive cell (usually two in number); during double fertilization, one fuses with the female gamete (egg cell) to produce a zygote while another fusses with the two polar nuclei of the central cell to give rise to endosperm.

T3. erm: apical meristem
id: PO:0020144
term: apical meristem (suggested definition - Pankaj):
Def: new: The meristems located at the apices of the main and lateral shoots and
roots.

4. term: primary shoot
id: PO:0006341
(suggested definition -Pankaj):
The shoot developing from the embryonic shoot apical meristem.

5. term: sterile lemma
id: PO:0009040
Suggested def -Toby
sterile lemma:  A bract in the position of a lemma, but not enclosing floral organs.  (Comment: An undeveloped androecium or gynoecium may or may not be detectable.)

6. term: fertile lemma
id: PO:0009041
Suggested def -Toby
fertile lemma:  A lemma that encloses a functional flower, with androecium, gynoecium or both.

7. Changed definition of 'central cell' back to my revision 1.25 (fro the reason I explained lat week, to
term: central cell
goid: PO:0020090
definition: The largest cell of the mature embryo sac. Contains two polar nuclei, which (after double fertilization) will develop into the endosperm.
definition_reference: TAIR:ki

Changed definition for central cell: The largest cell of the mature embryo sac. Contains two polar nuclei, which (after double fertilization) will develop into the endosperm.

Added Pankaj's definitions
For PO:0006378 ear spikelet meristem
Def: Apical or the primary shoot meristem that gives rise to the upper
and lower florets of the maize ear spikelets. [GR:pj]

for PO:0006377 tassel spikelet meristem
Def: Apical or the primary shoot meristem that gives rise to the upper
and lower florets of the maize tassel spikelets. [GR:pj]

Added definitions for the three relationship types (that somehow didn't get saved last time):
[[Typedef]
id: is_a
def: 'Instance of' relationship means that the term is a subclass of its parent, It should not be confused with an 'instance', meaning a specific example.
name: instance_of


[Typedef]
id: part_of
def: It indicates a subpart/part relationship within a tissue or organ. Used in a non-restrictive manner, i.e., the parent may or may not have the child as a part, and the child may or may not be a part of the parent. Therefore, a child is sometimes part of its parent and not necessarily always part of a parent term.
name: part of

[[Typedef]
id: develops_from
def: It indicates that cell/tissue/organ develops from its parent term. Implies both, develops from and a more indirect relationship, derived from.
name: develops from

1. Corrected the mistake in definitions of the term
Ear spikelet meristem, which is now:
Apical or the primary shoot meristem that gives rise to the ear spikelet and its parts.
Similarly, changed tassel spikelet meristem


2. Changed capital M in Maize to lower case m, (except in MaizeGDB, which I left as it was)

3. Double-checked spelling of botanical terms for the cell type node, root and gametophyte node  (including all the definitions). Changed wording, punctuation and similar in some terms under the three nodes assigned to me.

Felipe's revision:
-I checked definitions and relationships for my assigned nodes.
-I moved infructescence from part of sporophyte to part of shoot (also
to make it parallel with inflorescence).
-I checked for 5 terms needing definition: pollen wall, primary shoot
and the 3 relationships. Pollen wall and primary shoot DONE.
-I changed endotegmen and exotegmen as parts of seed coat epidermis to
instance of seed coat epidermis (to make it consistent with other parts
in the same node).
-I corrected various typos and added words to various terms under the
inflorescence node.
-I changed the definitons of the various instances of glume.
-I would recommend to be consistent with the use of the word Maize or
maize (capital M).  I changed many to Maize but perhaps I missed some
(an automatic review of this would be nice).
-I added filament (sensu Zea) as an instance of the generic filament. I
propagated it where necessary taking care of checking for the right
type of relationship.
-I corrected a typo in scale leaf definition.

Katica corrected mis-spelled definition for the following terms:

adventitious root epidermis
bundle sheath
embryo axis
exodermis
lateral root cap of the primary root
plant ontology
primary root elongation zone
spongy mesophyll cell
upper floret of pedicellate spikelet of ear

I. Cell type node
Changed relationship type wherever needed: Most terms in this node now have 'instance_of' in addition to develops_from relationship. Few terms still have 'part_of' in addition to 'develops_from'. No term has only develops_from relationship.
Added definitions for
1.articulated laticifer cell (PO:0006221) and synonym (laticiferous vessel)
2. non-articulated laticifer cell (PO:0006222) and synonym (simple laticifer)
3. endodermal passage cell (PO:0006208)
4. exodermal passage cell (PO:0006207)

II. Gametyphyte node
Added definition to pollen tube (PO:0006345)

III. Root node
Obsoleted term haustorial root (reason: this term is specific for parasitic plants mostly, which we are not on our plate right now)
Merged crown root and seminal root to the main term nodal root (these are now synonyms of nodal root). We agreed on this in STL.

Instantiated terms elongation zone and differentiation zone into primary root elongation zone and lateral root elongation zone (same with diff zone), and also added these new terms under appropriately under primary root and lateral root.

I instantiated term root cap (with its two children terms) for primary and lateral root, by adding 6 terms (and propagating them under all appropriate nodes):
Root cap (existing term)
 (p) central root cap (existing term)
	(i) central root cap of the primary root (PO:00030121
	(i) central root cap of the lateral root (PO:0003019)

 (p) lateral root cap (existing term)
		(p) lateral root cap of the primary root (PO:0003022)
		(p) lateral root cap of the lateral root (PO:0003020)

 (i) root cap of the primary root (PO:0003017)
	(p) central root cap of the primary root (PO:00030121
	(p) lateral root cap of the primary root (PO:0003022)

 (i) root cap of the lateral root (PO:0003018)
	(p) central root cap of the lateral root (PO:0003019)
	(p) lateral root cap of the lateral root (PO:0003020)

IV. added definitions to most of the terms with missing defs (to all of the above and to terms central endosperm and embryo proper) and also for the three relationship types.

Obsolete node
added 'Obsolete' in definitions (wherever it was missing), and removed the 'left-over' obsoleted terms from various nodes in the ontology.

added definitions for the new terms. Also defined the root terms and the growth stage term

modified the structure and added new terms. Extensive modification of fruit and inflo section

changes made by POC developers in ST Louis, May 19.
(saved in legacy style)

changes made by POC developers in STL, May 19

Legacy style

felipe's update, may 12

File edited by Leszek: clarified locations of terms - integument, chalaza, tegmen, testa & perisperm. Not able to indicate tegmen as developed from (~) outer integument as this violates TPR in that integument is no longer part of seed (only part of ovule).

added term vesel member (PO:0002003)
obsoleted term sieve tube
merged sieve element and sieve tube member

instances of collenchyma and aerenchyma made obsolete

modified the parents for vascular cambium and its instances

1. Added root node
2. Obsoleted Apical cell (PO:0004000)

Added word "Obsolete" to teh definition of the terms that became obsolete. Also added a comment to these terms.

Added definitions to the new terms in leaf section.

Added definitions to the terms in seed section. The terms came from Leszek.

Added the full blown tissue node definitions to the previous version. All the tissue terms have definitions.

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new version with children of cell PO:0009002

new version from UMSL

updated version of the plant ontology with more bits of the hierarchy filled in and also
definitions for everything so far

Plant ANATOMY ONTOLOGY DEFINITION file.
The alpha version.
The ontology itself is under development and is NOT FOR IMPLEMENTATION