2-16-10 Conf Call Agenda - Revision history

Cooperl at 00:30, 17 February 2010

2010-02-17T00:30:26Z

Cooperl at 00:28, 17 February 2010

2010-02-17T00:28:40Z

Cooperl at 01:57, 16 February 2010

2010-02-16T01:57:52Z

Cooperl at 00:43, 10 February 2010

2010-02-10T00:43:42Z

Cooperl: Created page with ''''2-16-10 Conf Call Agenda''' ===Future Meetings Schedule=== * March 9, 2010 * April 6, 2010 * May 4, 2010 *[[POC_6-8-10| Ju…'

2010-02-09T22:44:27Z

Created page with ''''2-16-10 Conf Call Agenda''' ===Future Meetings Schedule=== * March 9, 2010 * April 6, 2010 * May 4, 2010 *[[POC_6-8-10| Ju…'

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 Minutes from the POC Conference Call  2-16-10
 Items for discussion:
 .Discuss the Plant Structure parent terms that were defined at the meeting in Ithaca- these have been posted on Sourceforge for people to comment:
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 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)
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-.  Next conference call- Tues Feb 23rd at 10 am PST?
+.  Next conference call- Tues Feb 23rd at 11 am PST?

← Older revision		Revision as of 00:28, 17 February 2010
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−	===2-16-10 Conference Call ~~Agenda~~===	+	===2-16-10 Conference Call Minutes===
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		+	Minutes from the POC Conference Call 2-16-10
		+	Items for discussion:
		+	1.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
		+	def: An anatomical structure that is or was part of a plant and that has as its parts a maximally connected lumen, the contents of this lumen and the surrounding cell wall.
		+
		+	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.
		+	Comments: applies to living or dead cells
		+
		+	Note: There is no "lumen" term in GO- so it should be added.
		+	Raven, Evert and Eichhorn define the lumen as: "the space bounded by the cell wall".
		+	Def: maximally connected lumen ?? is there a simpler way to word this?
		+
		+	* plant organ
		+	def: "A maximal anatomical structure which is a proper part of a plant and which derives from a single ontogenetic event and includes as parts portions of tissues of at least two different types. Examples: stem, leaf, root."
		+
		+	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.
		+	(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, "proper" refers to not being the whole plant
		+	Examples: stem, leaf, root
		+
		+	Note: in 2-11-10 talk, Barry Smith suggested having child terms of plant organ: simple, compound and complex plant organs- tabled for next discussion.
		+
		+	*portion of plant tissue
		+	def: "An anatomical structure in a plant that consists of cells and intracellular matrix." comment: See Esau on simple and compound tissue. **This still needs to be fixed.
		+
		+	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.
		+
		+	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)
		+
		+
		+
		+
		+
		+	2. Whole plant was redefined as "A plant structure which is a whole organism." and gametophyte and sporophyte were moved under it.
		+
		+	There was much discussion about this one and several good points were raised:
		+	-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)
		+	- 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
		+	-also the problem of having term inflation if all the plant structures have to be qualified as either gametophytic or sporophytic
		+	- gametophyte and sporophyte are really phases of development not plant structures, although botanists are used to referring to the "gametophyte and sporophyte"
		+	-should gametophyte and sporophyte actually be siblings of 'whole plant', so that terms like microphyll can have multiple parentages.
		+	- there was discussion about actually dissolving the gametophyte and sporophyte terms, but we decided not to disrupt the ontology right now and do the following:
		+	-move all terms that are currently under gametophyte and sporophyte under whole plant,
		+	- then worry about populating gametophyte and sporophyte with specific terms
		+	- 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.
		+
		+
		+
		+	3. in vitro cultured cell, tissue and organ was moved out the Plant Structure class and made a separate class.
		+	def: "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."
		+	-tabled for next discussion.
		+
		+	4. 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.
		+
		+	5. 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'.
		+	-tabled for next discussion.
		+
		+	6 Assignment of Term numbers:
		+
		+	We need a set of numbers for the POC curators ( Lol and Ramona, mostly)- existing:
		+
		+	Group
		+	identifier range (from-to)
		+	TAIR
		+	0000001-0005000
		+	Gramene
		+	0005001-0010000
		+	IRIS-IRRI
		+	0010001-0015000
		+	MaizeGDB
		+	0015001-0020000
		+	UMSL
		+	0020001-0025000
		+
		+	Proposed:
		+	0025000-0030000 PO curators
		+	0030001-0035000 NYBG
		+
		+
		+	7. Next conference call- Tues Feb 23rd at 10 am PST?
		+
		+
		+
		+
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		+
		+
		+

	'''Future Meetings Schedule'''		'''Future Meetings Schedule'''

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	'''Future Meetings Schedule'''		'''Future Meetings Schedule'''
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−	*[[POC_3-9-10\| March 9, 2010]]
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−	*[[POC_4-6-10\| April 6, 2010]]
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−	*[[POC_5-4-10\| May 4, 2010]]
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−	*[[POC_6-8-10\| June 8, 2010 ]]
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−	*[[POC_7-6-10\| July 6, 2010]]
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−	*[[POC_8-10-10\| Aug 10, 2010]]

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-'''2-16-10 Conf Call Agenda'''
+===2-16-10 Conference Call Agenda===
-===Future Meetings Schedule===
 *[[POC_3-9-10| March 9, 2010]]
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 *[[POC_7-6-10| July 6, 2010]]
-*[[POC_8-10-10| Aug 10,2010]]
+*[[POC_8-10-10| Aug 10, 2010]]