POC Conf. Call 12-20-11 - Revision history

Rwalls at 19:42, 3 January 2012

2012-01-03T19:42:25Z

2011-12-29T21:46:54Z

Senescence and aging in GO

2011-12-21T17:47:17Z

Wood Anatomy and Forest Trees

2011-12-21T17:19:11Z

organ senescence (GO:0010260)

2011-12-21T16:45:12Z

Wood Anatomy and Forest Trees

2011-12-21T16:42:52Z

Vascular tissue terms

2011-12-21T16:40:03Z

Wood Anatomy and Forest Trees

2011-12-21T16:39:38Z

Wood Anatomy and Forest Trees

2011-12-21T16:33:37Z

Physcomitrella Annotations

2011-12-21T15:46:04Z

PO senescent stage terms

← Older revision		Revision as of 19:42, 3 January 2012
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	Collaborators: none		Collaborators: none
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−	~~Streaming recording link:~~
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−	~~https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=60554252&rKey=ad566621977ab67f~~
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−	~~Download recording link:~~
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−	~~https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=60554252&rKey=da91a208b5aa8084~~

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 The POC needs a term for whole organism senescence, and we feel that the existing definitions of aging is not appropriate for plants, or even for GO:cell aging and GO:cellular senescence.
 ===Revisions to existing GO terms===
 '''GO tree view:'''

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 Invitation letter went out 12/15/11 from DWS, to experts (below) signed by all three Co-PIs, along with Jill Wegrzyn of the [http://dendrome.ucdavis.edu/treegenes/ TreeGenes] Database at UCDavis (Bioinformatics) and Andrew Groover Geneticist, USDA Forest Service, Institute of Forest Genetics, Davis CA.
-*Frederic Lens: (new faculty at [http://www.nhn.leidenuniv.nl/index.php/nhn/institute/nlcb/ Netherlands Centre for Biodiversity Naturalis])
+*Frederic Lens: [http://www.nhn.leidenuniv.nl/index.php/nhn/institute/nlcb/ Netherlands Centre for Biodiversity Naturalis]
 *Barb Lachenbruch [http://woodscience.oregonstate.edu/people/faculty/lachenbruch-barb link]
 *Elisabeth Wheeler (paleobotanist and wood anatomist at [http://cnr.ncsu.edu/fb/about/faculty/wheeler.php NC State]

← Older revision		Revision as of 17:19, 21 December 2011
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	''Is there organ senescence in animals? Perhaps in things that metamorphosize.''		''Is there organ senescence in animals? Perhaps in things that metamorphosize.''
		+
		+	''PO will also need a term for anther senescence, is_a organ senescence, to correspond to the PO stage term.''

	====leaf senescence (GO:0010150)====		====leaf senescence (GO:0010150)====

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 ''Tentative dates are Feb. 5-7 (Sun-Tues).''
-''BS is available to give his presentation on Sunday morning. He suggested that this presentation may be of interest to others in the NYC area. He will advertise it, and RW will advertise it on the NYBG list. If we need a bigger room, we can get a classroom. DWS (after meeting) said that it would be okay to invite other people.''
+''BS is available to give his presentation on Sunday morning. He suggested that this presentation may be of interest to others in the NYC area. He will advertise it to a wider audience, and RW will advertise it on the NYBG list. If we need a bigger room, we can get a classroom. DWS (after meeting) said that it would be okay to invite other people.''
 ''RW will send out travel forms to domestic invitees for them to sign and make sure they get to LC.''

← Older revision		Revision as of 16:42, 21 December 2011
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	These terms will need to be fixed before the Wood Ontology meeting in February. Proposed definitions and structures are almost ready, so we can start working on them during the POC meetings in January.		These terms will need to be fixed before the Wood Ontology meeting in February. Proposed definitions and structures are almost ready, so we can start working on them during the POC meetings in January.
		+
		+	''Okay to start adding these synonyms to the ontology. Don't need group discussion, since they are just synonyms of existing terms. Will have FNA:glossary as reference. Link to Google Doc listing them is on the [http://sourceforge.net/tracker/?func=detail&aid=3376762&group_id=76834&atid=835555 SF tracker for FNA].''

	=FNA=		=FNA=

@@ Line 353: / Line 353: @@
 ''BS is available to give his presentation on Sunday morning. He suggested that this presentation may be of interest to others in the NYC area. He will advertise it, and RW will advertise it on the NYBG list. If we need a bigger room, we can get a classroom. DWS (after meeting) said that it would be okay to invite other people.''
-''RW will send out travel forms to domestic invitees for them to sign.''
+''RW will send out travel forms to domestic invitees for them to sign and make sure they get to LC.''
 ==Vascular tissue terms==

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 Would be nice to set tentative dates before leaving for the holiday.
-''*Maybe it would be appropriate at this point to set up a Doodle type poll?''
+''Elisabeth Wheeler has been out of town. LC will follow up with Barb Lachenbruch and RW will ask Jill to follow up with John Carlson.''
 ==Vascular tissue terms==

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 These are available for preview on the [http://beta.plantontology.org:8080/amigo/go.cgi?xpand=PO:0009011&search_constraint=terms&query=PO:0009011&session_id=3244b1324320775&view=details&show_associations=list beta browser]
 Outstanding issues: we are still sorting out a few problems with linking and displaying the new annotations. Hopefully these can be resolved when JE returns in a week.  Waiting for a response from DL @ the links.
 Then these could be uploaded to the main database for a data release, as all the necessary terms are in the current live file.
 ==Cotton (Gossypium)==

← Older revision		Revision as of 15:46, 21 December 2011
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	See initial discussion at [[Saturday_Sept_10th,_2011#Task_4._Work_existing_upper-_to_mid-level_terms_into_the_hierarchy_determined_in_task_3.]], where we decided that even though a plant may die from other causes before the end of normal senescence, the senescent stage of a whole plant ends with death.		See initial discussion at [[Saturday_Sept_10th,_2011#Task_4._Work_existing_upper-_to_mid-level_terms_into_the_hierarchy_determined_in_task_3.]], where we decided that even though a plant may die from other causes before the end of normal senescence, the senescent stage of a whole plant ends with death.

		+	''Even though the existing GO terms are not perfect for our needs, we will go ahead with the new definitions, and add a comment that we have reqested new definitions from GO, which we can get rid after GO updates their definitions.''

	'''sporophyte senescent stage (PO:0007017):''' A sporophyte development stage during which a sporophyte participates in multicellular organism senescence (GO:0010259).		'''sporophyte senescent stage (PO:0007017):''' A sporophyte development stage during which a sporophyte participates in multicellular organism senescence (GO:0010259).