2-16-10 Agenda and Minutes - Revision history

Cooperl at 22:02, 18 February 2010

2010-02-18T22:02:33Z

Cooperl at 21:54, 18 February 2010

2010-02-18T21:54:59Z

Cooperl at 21:49, 18 February 2010

2010-02-18T21:49:56Z

Cooperl at 21:22, 18 February 2010

2010-02-18T21:22:48Z

Cooperl at 21:22, 18 February 2010

2010-02-18T21:22:29Z

Cooperl at 20:35, 18 February 2010

2010-02-18T20:35:50Z

Cooperl at 20:33, 18 February 2010

2010-02-18T20:33:46Z

Cooperl at 20:27, 18 February 2010

2010-02-18T20:27:11Z

Cooperl at 00:37, 18 February 2010

2010-02-18T00:37:20Z

Cooperl at 00:35, 18 February 2010

2010-02-18T00:35:43Z

@@ Line 98: / Line 98: @@
 TAIR: 0000001-0005000
-Gramene: 0005001-0010000
+Gramene/OSU: 0005001-0010000
 IRIS-IRRI: 0010001-0015000
@@ Line 108: / Line 108: @@
 Proposed:
-'''0025000-0030000 PO curators'''
+'''0025001-0030000 PO Consortium'''
 '''0030001-0035000 NYBG'''
-.  '''Next conference call- Tues Feb 23rd at 11 am PST'''

@@ Line 28: / Line 28: @@
 -A plant structure that is a functional unit, is a proper part of a plant and includes portions of tissues of at least two different types which derive from a common developmental path.
   (reworded slightly for readability)
-Comments: May include individual cell types that are not part of tissues. example: guard cells which are part of the leaf,idioblasts
+Comments: May include individual cell types that are not part of tissues.
 "proper" refers to not being the whole plant

@@ Line 26: / Line 26: @@
 New def:
--is an anatomical structure that is a functional unit, is a proper part of a plant and includes portions of tissues of at least two different types which derive from a common developmental path.
+-A plant structure that is a functional unit, is a proper part of a plant and includes portions of tissues of at least two different types which derive from a common developmental path.
   (reworded slightly for readability)
-Comments: May include individual cell types that are not part of tissues. example: stomatal cells which are part of the leaf,
+Comments: May include individual cell types that are not part of tissues. example: guard cells which are part of the leaf,idioblasts
 "proper" refers to not being the whole plant
 Examples: stem, leaf,  root

@@ Line 5: / Line 5: @@
 Agenda:
-.'''Discuss the Plant Structure parent terms that were defined at the meeting in Ithaca- these have been posted on Sourceforge for people to comment:
+. '''Discuss the Plant Structure parent terms that were defined at the meeting in Ithaca- these have been posted on Sourceforge for people to comment:
 '''
 * '''plant cell'''

@@ Line 11: / Line 11: @@
 New def:
-A cell, which is the basic functional unit of a plant, and that has as its parts a maximally connected lumen, the contents of this lumen and the surrounding plant cell wall.
+A cell, the basic functional unit of a plant, that has as its parts a maximally connected lumen, the contents of this lumen and the surrounding plant cell wall.
 Comments:  Reference the definition of cell in GO(GO:0005623), see GO for definition of cell

@@ Line 48: / Line 48: @@
 -Does this include single-celled plants?  Can something be a plant cell and a whole plant?
-(Chris made a comment about disjoints in OBO-Edit- not too sure about this)
+(Chris made a comment about making these disjoints in OBO-Edit)
 - PJ- problem of having some terms that should be under both gametophyte and sporophyte- example is a leaf like structure- phyllome.  Also, root-like structures eg. rhizoids
@@ Line 64: / Line 64: @@
 - figure out how to cross reference between the PO Structure and Development ontologies.
-Note:  Make sure that gametophytic stage and sporophytic stage are defined in the developmental stage ontology.
+Note:  Gametophytic stage and sporophytic stage should be defined in the developmental stage ontology (not currently in it).

@@ Line 38: / Line 38: @@
 New def:
--is an anatomical structure in a plant that consists of one or more cell types, organized into a structural and functional unit, and may include an intercellular matrix.
+-A plant structure that consists of one or more cell types, organized into a structural and functional unit, and may include an intercellular matrix.
 Comment:  intercellular matrix- def: middle lamella- "layer of intercellular (between the cells) chiefly, pectic substances, cementing together the primary walls of contiguous cells ( ref: Evert, 3rd ed 2006)
@@ Line 71: / Line 71: @@
 -tabled for next discussion.
-. New parent terms proposed by Ramona:
+.'''New parent terms proposed by Ramona:'''
 *cardinal organ part
 def: A plant structure that is a direct or immediate part of an organ that is often maximal(?) but is smaller than the organ itself. Examples include lobe, operculum, neck, petiole?, leaflet.
 -tabled for next discussion.
 * collective plant structure
 A plant structure that is composed of multiple organs but is not an organ. (Maybe something about a bona fide boundary, some way to distinguish it from whole plant).
 Examples: flower, perianth, inflorescence. collective structure or compound organ?
 -tabled for next discussion.
-. Term request from TAIR for "gamete"- proposed (RW): add gamete to the ontology (is_a parent, plant cell), with sperm cell and egg cell as siblings under a common parent 'gamete'.
+. '''Term request from TAIR for "gamete"'''
 -tabled for next discussion.
-Assignment of Term numbers:
+. '''Assignment of Term numbers:'''
 We need a set of numbers for the POC curators ( Lol and Ramona, mostly)- existing:
@@ Line 91: / Line 94: @@
 identifier range (from-to)
-TAIR 0000001-0005000
+TAIR: 0000001-0005000
-Gramene 0005001-0010000
+Gramene: 0005001-0010000
-IRIS-IRRI 0010001-0015000
+IRIS-IRRI: 0010001-0015000
-MaizeGDB 0015001-0020000
+MaizeGDB: 0015001-0020000
-UMSL 0020001-0025000
+UMSL: 0020001-0025000
 Proposed:
-	0025000-0030000 PO curators
-	0030001-0035000 NYBG
+'''0025000-0030000 PO curators'''
-.  Next conference call- Tues Feb 23rd at 11 am PST?
+.  '''Next conference call- Tues Feb 23rd at 11 am PST'''

@@ Line 1: / Line 1: @@
 Minutes from the POC Conference Call  2-16-10
 present: Laurel Cooper, Pankaj Jaiswal, Ramona Wells, Chris Mungall
@@ Line 10: / Line 11: @@
 New def:
-...is a cell, which is the basic functional unit of a plant, and that has as its parts a maximally connected lumen, the contents of this lumen and the surrounding plant cell wall.
+A cell, which is the basic functional unit of a plant, and that has as its parts a maximally connected lumen, the contents of this lumen and the surrounding plant cell wall.
-Comments:  Reference the definition of cell in GO, as a cross-product,  see GO for definition of cell
+Comments:  Reference the definition of cell in GO(GO:0005623), see GO for definition of cell
 also: applies to living or dead cells
-Note: There is no "lumen" term in GO- so it should be added.
+Note: There is no "lumen" term in GO- Ramona will request it.
 Raven, Evert and Eichhorn define the lumen as: "the space bounded by the cell wall".