CVS log for Poc/ontology/GO_format/po_anatomy.ontology
	Help

Request diff between arbitrary revisions

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo by oboedit/obo2flat

converted from po_anatomy.obo using oboedit

converted from obo format files of release 0805 using oboedit obo2flat script

no changes

added granular terms under petiole, and instantiated leaf epidermis and leaf vascular system into leaf lamina epidermis and leaf lamina vascular system.

1. New structure of teh root node:
root
 (i) shoot borne roots (syn: adventitious)
        (i) nodal root
              (i) crown root
              (i) prop root (syn. brace root)
 (i) embryonic root
        (i) primary root
              (i) radicle
        (i) seminal root
 (i) lateral

2. Merged 'adventitious root' to 'shoot borne root', and 'tap root to 'primary root'.

Added 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:

addedew term: adventitious root nodule (syn. stem nodule)	PO:0000040

4. Deleted 'laticifer' from cell node
5. Added new term 'cork cell (sensu Poaceae)' PO:0000041

6.- Corrected typos and minor errors in the ontology file:
1. Term:

7. Corrected sillica cell to silica cell

8. Also, several minor typos in the text of the following:
Terms: Cotyledon vascular system, stem cortex, stolon, valve, phloem, chlorenchyma, and shoot procambium.

This version is based on po_anatomy.obo ver 1.3

added new terms:

Term: vascular system
Term: leaf vascular system
Term: cotyledon vascular system
Term: shoot apex

Moved back from OBSOLETE node term: root vascular system (PO:0003011).

New terms added:

Term: cuticle
Term: casparian strip
Term: filiform apparatus
Term: root tip
Term: primary root tip
Term: lateral root tip
Term: pollen tube tip
Term: root hair tip
Term: septum
Term: lenticel
Term: tetrad of microspores
Term: valve

added following terms:

Term: Whole plant
Term: in vitro cell, tissue and organ culture
Term: cultured protoplast
Term: cultured cell (Synonym: cell suspension)
Term: cultured leaf cell
Term: cultured root cell
Term: somatic embryo
Term: cultured callus
Term: cultured embryo
Term: cauline leaf
Term: apical hook (Synonym: hypocotyl hook)
Term: cotyledon primordium
Term: lateral root primordium
Term: leaf primordium
Term: ovule primordium
Term: gynoecium primordium
Term: petal primordium

The following changes were made in the term-term relationships
PO:0000252 : endodermis is part_of PO:0005708 : cortex
PO:0005051 : hypodermis  is part_of PO:0005708 : cortex

PO:0006203 : pericycle is part_of PO:0020124 : root stele
Coments for pericycle 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 as part_of root only.

Removed 'embryo' node from sporophyte. Term 'embryo' is now always a child of 'seed'.

Propagated pericycle under the root cortex.

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

8. I obsoleted: term: cambium-like transitional zone
id: PO:000606C
Comment: If found, this zone is a temporary feature mostly in Gymnosperms.

9. Following our conference call, I made following changes:

- Infructescence node is now PART_OF sporophyte.

- Protoderm is now PARTOF meristem (instead of instance of apical meristem)

1. Added synonyms to:
added megagametophyte as synonym of female gametophyte

2. Added guard cell and guard mother cell as children of meristemoid (dev_from). Couldn't add epidermal initial, because of its multiple children, that would wrongly end up under the term meristemoid.

3. 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.


4.. 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]


5. 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 changed:

-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.

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 new terms instatiating for maize ear and tassel. Also added few more to the tree.

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

changed made by POC developers in St Louis on May 19.
(saved in legacy style)

changes made by POC developers in St Louis, 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
changed relationship in the root node:
	- crown root and seminal root are now children of nodal root, and nodal 	root is a child of adventitious root

Katica added cell types to the tissues. Pankaj added tissues to various organs
Modified teh parentage of vascular cambium, cork cambium and others.

modified the parents for vascular cambium and its instances

1. Added root node
2. Obsoleted apical cell PO:0004000

Added new terms to the leaf section with a major revision of the structure. Some of the phenotype terms like simple leaf and compound leaf became obsolete

Added more terms to the seed section. The terms came from Leszek.

Added the full blown tissue node to the previous version

*** empty log message ***

1. Merged  the existing PO term sperm nuclei (PO:0020098) to the
cell type term sperm cell (PO:0000084).

2. Changed  term antipodals to antipodal cell (to avoid
plurals).

3.Deleted embryo sac from the cell type node; this term is still
present in the gametophyte node.

4. Made term pollen a synonym of the male gametophyte. This way, pollen was gone
from my cell type node, and male gametophyte is still present as a child
of the gametophyte.

5. Obsoleted term synergids (PO:0020096); term synergid is still in the ontology (PO:0000191)

new version with children of cell PO:0009002

changed the ide of the root term to PO:0009075. Earlier it was GO:0000000

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 file.
The very alpha version.
The ontology is under development and is NOT FOR IMPLEMENTATION