new ontology files in the cvs (rev 1.34 and 1.38)

[Katica Ilic]

Hi all,

The new ontology files are in the cvs. I updated GO flat file
anatomy.ontology and ontology.definition and committed them back to cvs as
GO flat files (till we solve problem with obo2 flat conversion script).

The following changes to the Plant Structure Ontology are made:

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

2. primary endosperm 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 triploid.

3. Renaming the 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.

Ontology structure:

root
 (p) root nodule
 (i) adventitious root
     (p) adventitious root nodule (synonym: stem nodule)

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

Added new term: cork cell (sensu Poaceae)

(i) PO:0004013 : epidermal cell
    (i) PO:0004009 : silica cell
    (i) cork cell (sensu Poaceae)

and

  PO:0009007 : tissue
      (i) PO:0009014 : dermal tissue
        (i) PO:0005679 : epidermis
            (p) PO:0004013 : epidermal cell
                (i) cork cell (sensu Poaceae)
                (i) silica cell

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: The primary tissue located between the vascular system and the
epidermis of the stem.

Also, I corrected typos in the text of several terms.

Thanks and have a nice weekend.

Katica


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Katica Ilic             		katica at acoma.stanford.edu
The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington 	FAX: (650) 325-6857
Department of Plant Biology 		URL: http://arabidopsis.org/
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Stanford, CA 94305
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