POC Conf. Call 9-25-12 - Revision history

Cooperl: /* PO/TO Crop Annotation Workshop at OSU; Sept. 13-15th, 2012 */

2012-09-28T17:15:52Z

PO/TO Crop Annotation Workshop at OSU; Sept. 13-15th, 2012

2012-09-26T17:45:06Z

Update on SIA

2012-09-26T17:29:13Z

Phenotype RCN meeting, Oct 26-29th 2012

2012-09-26T17:28:18Z

Update from Cornell

2012-09-26T17:27:25Z

PO/TO Crop Annotation Workshop at OSU; Sept. 13-15th, 2012

2012-09-26T17:25:26Z

Genome Informatics 2012

2012-09-26T17:25:19Z

Genome Informatics 2012

2012-09-26T17:24:49Z

Recent Meeting reports

2012-09-26T17:21:31Z

2012-09-26T17:21:12Z

@@ Line 63: / Line 63: @@
 Outcomes:
--preparing a short new item for circulation
+-preparing a short news item for circulation
--preparing a "vision/white paper" to focus on the ref plant onotlogy concept
+-preparing a "vision/white paper" to focus on the ref plant ontology concept
 -follow up meeting will occur at PAG 2013, along with Ontology workshop

← Older revision		Revision as of 17:45, 26 September 2012
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	* Bug tracker is set up through the Jaiswal Lab tracker- this will be available to outside users through email- more details TBA		* Bug tracker is set up through the Jaiswal Lab tracker- this will be available to outside users through email- more details TBA

		+	==New item from BS: GO Cell Development Working Group==
		+	The GO is establishing a working group to focus on terms for cell development and it would be good to a representative for plants

		+	Currently, the people involved are Judy Blake, Jane Lomax, David OS, Chris Mungall

	==Cont. from last meeting:==		==Cont. from last meeting:==

@@ Line 157: / Line 157: @@
 LC is going and has been working with LM to compile EQ statemnts to describe ~100 rice mutants.  These are going to be compiled with similar statements from maize, Arabidopsis, Soybean, SGN- tomato, and  Medicago.
-Will be combining the mutants with similar E and Q and looking at the genes and if they are othologs.
+The project (headed by EH) be combining the mutants with similar E and Q and looking at the genes and if they are othologs.
 ==[http://www.intlpag.org/ PAG 2013], San Diego, CA; January 12th - 16th, 2013==

@@ Line 83: / Line 83: @@
 RW visited Cornell and MAG and RW started adding keywords in the beginning of Sept, and came up with a way to add PO's to all the images then link them to the PO pages, but it will probably be a few weeks before Kevin is able to implement the links.
-News: The website is up again (but was not available during the call). Cornell had a major servers crash the last two weeks and it took them several days to figure out what it was wrong.
+News: The website is up again. Cornell had a major servers crash the last two weeks and it took them several days to figure out what it was wrong.
-MAG will be talking with PJ about having a technician work on labeling the images using the SIA tool
+''MAG will be talking with PJ about having a technician work on labeling the images using the SIA tool''
 =Update on SIA=

← Older revision		Revision as of 17:27, 26 September 2012
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	-Many new and enhanced collaborations		-Many new and enhanced collaborations
		+
		+
		+	''Discussion with BS about the name of the reference ontology for plants: CROP''
		+	''BS will join the next conf call to discuss with the group''

	=Update from Cornell=		=Update from Cornell=

@@ Line 37: / Line 37: @@
 *: [http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html ENCODE Summary Paper]
 *: "The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions."
 * interesting talks:

@@ Line 33: / Line 33: @@
 JP attended and submitted a poster representing the PO:  ''Put in link to poster on Outreach page..''
 * conference was tilted towards biomedical and mammalian research
 * lots of buzz about the ENCODE release and its implications for changing research methods in other organisms
 *: [http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html ENCODE Summary Paper]
 *: "The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions."
 * interesting talks:
 ** Josh Stein (Gramene) - iPlant Discovery Environment (data cloud and analysis applications)
@@ Line 43: / Line 44: @@
 ** Pavel Pezner: new de Bruijn graph assembly model utilizing an extra dimension of network relatedness (represented by color); built for single-cell assembly
 ** a couple of talks about single-cell sequencing; there seems to be growing interest in that approach
 ==PO/TO Crop Annotation Workshop at OSU; Sept. 13-15th, 2012==

@@ Line 19: / Line 19: @@
 Back to [[POC Meetings Minutes]]
-=Recent Meeting reports=
+=Recent Meeting Reports=
 ==NSF Plant Genome PIs Meeting==
@@ Line 25: / Line 25: @@
 PJ presented a 2 pager and poster
 ==[https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=296 Genome Informatics 2012]==
@@ Line 30: / Line 31: @@
 Robinson College, Cambridge, UK
-JP attended and submitted a poster representing the PO
+JP attended and submitted a poster representing the PO:  ''Put in link to poster on Outreach page..''
 * made contact with Remco Ursem (bioinformatics @ Rijk Zwaan - Dutch vegetable and seed company); he is interested in PO

@@ Line 3: / Line 3: @@
 In attendance:
-POC members: ''Laurel Cooper (OSU), Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY), Justin Elser (OSU), Justin Preece (OSU)''
+POC members: ''Laurel Cooper (OSU), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY), Justin Elser (OSU), Justin Preece (OSU)''
-Absent: ''Dennis Stevenson (NYBG),  Ramona Walls (NYBG), Chris Mungall (Lawrence Berkeley National Lab)''
+Absent: '' Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG),  Ramona Walls (NYBG), Chris Mungall (Lawrence Berkeley National Lab)''
@@ Line 15: / Line 15: @@
 Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=68559652&rKey=2372f53c53e0133c
- Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=68559652&rKey=c5053bcfd32d7d2e
+Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=68559652&rKey=c5053bcfd32d7d2e
 Back to [[POC Meetings Minutes]]

← Older revision		Revision as of 17:21, 26 September 2012
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	Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_9-04-12]]?		Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_9-04-12]]?
		+
		+
		+	Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=68559652&rKey=2372f53c53e0133c
		+
		+	Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=68559652&rKey=c5053bcfd32d7d2e

	Back to [[POC Meetings Minutes]]		Back to [[POC Meetings Minutes]]