POC Conf. Call 9-24-13 - Revision history

Cooperl at 17:55, 23 October 2013

2013-10-23T17:55:12Z

Cooperl: /* Upcoming meetings and Presentations 2013-2014: */

2013-10-01T13:59:36Z

Upcoming meetings and Presentations 2013-2014:

Cooperl: /* Next meeting scheduled for Tuesday, Oct 8th, 2013 at 10:30am Pacific/1:30pm Eastern */

2013-09-30T21:28:35Z

Next meeting scheduled for Tuesday, Oct 8th, 2013 at 10:30am Pacific/1:30pm Eastern

Cooperl: /* Strawberry Genomics Annotation Project */

2013-09-27T17:12:11Z

Strawberry Genomics Annotation Project

Cooperl at 17:28, 26 September 2013

2013-09-26T17:28:18Z

Cooperl: /* vascular leaf anlagen formation stage (PO:0001003) */

2013-09-26T17:26:21Z

vascular leaf anlagen formation stage (PO:0001003)

Cooperl: /* vascular leaf initiation stage (PO:0007040) and child terms: */

2013-09-26T17:24:00Z

vascular leaf initiation stage (PO:0007040) and child terms:

Cooperl: /* vascular leaf initiation stage (PO:0007040) and child terms: */

2013-09-26T17:23:44Z

vascular leaf initiation stage (PO:0007040) and child terms:

Cooperl: /* Strawberry Genomics Annotation Project */

2013-09-25T18:00:04Z

Strawberry Genomics Annotation Project

Cooperl: /* vascular leaf anlagen formation stage (PO:0001003) */

2013-09-25T00:15:22Z

vascular leaf anlagen formation stage (PO:0001003)

← Older revision		Revision as of 17:55, 23 October 2013
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−	POC meeting, Skype Conference Call; Date: Tuesday Sept 24th, 2013 10:30am ~~PST~~/1:30pm ~~EST~~	+	POC meeting, Skype Conference Call; Date: Tuesday Sept 24th, 2013 10:30am PDT/1:30pm EDT

	In attendance: ''Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Pankaj Jaiswal (OSU), Barry Smith (OBO), Marie Alejandra Gandolfo (Cornell)''		In attendance: ''Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Pankaj Jaiswal (OSU), Barry Smith (OBO), Marie Alejandra Gandolfo (Cornell)''

← Older revision		Revision as of 13:59, 1 October 2013
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	** Registration is now open: [http://www.intlpag.org/2014/attend/registration-and-fees?utm_source=PAG+XXII+-+Newsletter+-+Attendee+%231&utm_campaign=PAG+XXII+Attendee+Newsletter+%231&utm_medium=email PAG 2014]. Early reg'n till Nov. 1st		** Registration is now open: [http://www.intlpag.org/2014/attend/registration-and-fees?utm_source=PAG+XXII+-+Newsletter+-+Attendee+%231&utm_campaign=PAG+XXII+Attendee+Newsletter+%231&utm_medium=email PAG 2014]. Early reg'n till Nov. 1st
−

	=Next meeting scheduled for Tuesday, Oct 1st, 2013 at 10:30am Pacific/1:30pm Eastern=		=Next meeting scheduled for Tuesday, Oct 1st, 2013 at 10:30am Pacific/1:30pm Eastern=

← Older revision		Revision as of 21:28, 30 September 2013
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−	=Next meeting scheduled for Tuesday, Oct ~~8th~~, 2013 at 10:30am Pacific/1:30pm Eastern=	+	=Next meeting scheduled for Tuesday, Oct 1st, 2013 at 10:30am Pacific/1:30pm Eastern=

@@ Line 7: / Line 7: @@
 =Strawberry Genomics Annotation Project=
-I have been working with Omar Darwish on annotating the samples and stages for their project.
+LC has been working with Omar Darwish on annotating the samples and stages for their project.
-You can view the annotations here:https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdHhObVd5UUZGT1BaalRKQ1FyMWx0dFE&usp=sharing
+You can view the annotations here: [https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdHhObVd5UUZGT1BaalRKQ1FyMWx0dFE&usp=sharing Strawberry Annotations]
-They have a nice page where you can view the samples they used: http://bioinformatics.towson.edu/strawberry/newpage/Tissue_Description.aspx see slide #2
+They have a nice page where you can view the samples they used: [http://bioinformatics.towson.edu/strawberry/newpage/Tissue_Description.aspx see slide #2 Strawberry Genomics]
 Suggest we need to create a specific term for receptacle cortex and receptacle pith:

@@ Line 1: / Line 1: @@
 POC meeting, Skype Conference Call; Date: Tuesday Sept 24th, 2013 10:30am PST/1:30pm EST
-In attendance:
+In attendance: ''Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Pankaj Jaiswal (OSU), Barry Smith (OBO), Marie Alejandra Gandolfo (Cornell)''
-Absent:
+Absent:  ''Brian Atkinson (OSU), Dennis W Stevenson (NYBG)''
 =Strawberry Genomics Annotation Project=

@@ Line 130: / Line 130: @@
 See also: [http://www.public.iastate.edu/~bot.512/papers/Eshed.pdf Eshed et al,
-''NOTE: Based on the 9-24 conference call we decided to change the name of vascular leaf anlagen formation stage (PO:0001003) back to vascular leaf founder cells formation stage (PO:0001003) with a revised def’n: The initial stage of leaf development when cells in the shoot apical meristem (PO:0020148) are already determined to form a leaf primordium, but the primordium itself is not distinguishable morphologically. We also realize the def'n needs some work. ''
+''NOTE: Based on the discussion, the founder cells are not the same as the anlagen so we will change the name of vascular leaf anlagen formation stage (PO:0001003) back to vascular leaf founder cells formation stage (PO:0001003) with a revised def’n: The initial stage of leaf development when cells in the shoot apical meristem (PO:0020148) are already determined to form a leaf primordium, but the primordium itself is not distinguishable morphologically. We also realize the def'n needs some work.   It is still not clear how to distinguish the two though. ''
 ''We also created a new term vascular leaf anlagen formation stage (PO:0025586): A vascular leaf initiation stage (PO:0007040) when the cells of the shoot apical meristem (PO:0020148) form a vascular leaf anlagen (PO:0025431).  ''
@@ Line 139: / Line 139: @@
 comment: The phyllome anlagen is only detectable by gene expression, not morphology.
-====references- analagen and founder cells====
+====references for anlagen and founder cells====
 "The development of a leaf begins with a regional shift in the polarity and rate of cell division and expansion within a group of leaf founder cells on the flank of shoot apical meristem." [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC160193/pdf/041017.pdf Smith and Hake 1992]

← Older revision		Revision as of 17:24, 26 September 2013
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	* Revised Comment: Localized cell divisions in the peripheral zone (PO:0000225) transition from anticlinal to periclinal divisions.		* Revised Comment: Localized cell divisions in the peripheral zone (PO:0000225) transition from anticlinal to periclinal divisions.
−

	-''def'n accepted, OK''		-''def'n accepted, OK''

@@ Line 101: / Line 101: @@
 * Revised Comment: Localized cell divisions in the peripheral zone (PO:0000225) transition from anticlinal to periclinal divisions.
 [[File:Vas_leaf_intiation.png]]
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 Comments: The vascular leaves (PO:0009025) of some plants may not have an obvious adaxial or abaxial side such as the leaves of many xerophytic (arid-adapted) species. The adaxial and abaxial side may appear considerably more rounded and this could be due to early activity of the vascular leaf adaxial meristem (PO:0025401) and/or leaf abaxial meristem (PO:0025401).
 ==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/572/ vascular leaf differentiation stage (new PO:0025574)]==

← Older revision		Revision as of 18:00, 25 September 2013
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	''revised: shoot axis pith: A pith (PO:0006109) which is part of a shoot axis (PO:0025029).''		''revised: shoot axis pith: A pith (PO:0006109) which is part of a shoot axis (PO:0025029).''
		+
		+	See continued discussion [[Items_for_future_meetings#Revisions_to_cortex_.28PO:0005708.29_and_other_portion_of_ground_tissue_.28PO:0025059.29_children]]

	Question about using the plant embryo stages, as these refer to the developmental stages of the whole plant. rather than an individual embryo (sporophyte development stage (PO:0028002)). I related the samples to the stages of development of the individual fruits- the achenes.		Question about using the plant embryo stages, as these refer to the developmental stages of the whole plant. rather than an individual embryo (sporophyte development stage (PO:0028002)). I related the samples to the stages of development of the individual fruits- the achenes.

@@ Line 134: / Line 134: @@
 comment: The phyllome anlagen is only detectable by gene expression, not morphology.
 "The development of a leaf begins with a regional shift in the polarity and rate of cell division and expansion within a group of leaf founder cells on the flank of shoot apical meristem." [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC160193/pdf/041017.pdf Smith and Hake 1992]
 See image: [http://www.nature.com/nrg/journal/v4/n3/fig_tab/nrg1002_F1.html founder-cell population (FC) that will give rise to the next leaf primordium]
-[http://dev.biologists.org/content/139/5/883.long Goh et al, 2012 Development]
+[http://brie4.cshl.edu/pipermail/po-dev/2006-February/000733.html PO-dev Feb.06]
 ===[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/556/ vascular leaf primordium formation stage (PO:0001019)]===