POC Conf. Call 12-13-11 - Revision history

Cooperl at 19:43, 8 March 2012

2012-03-08T19:43:58Z

Cooperl: /* PSDSO Revisions: Whole plant development stages */

2011-12-29T21:23:25Z

PSDSO Revisions: Whole plant development stages

Cooperl: Reverted edits by Cooperl (Talk) to last revision by Rwalls

2011-12-29T21:22:40Z

Reverted edits by Cooperl (Talk) to last revision by Rwalls

Cooperl: /* review of definitions for embryo stage and plant embryo */

2011-12-29T21:19:05Z

review of definitions for embryo stage and plant embryo

Cooperl: /* GO terms */

2011-12-28T19:37:39Z

GO terms

Cooperl: /* GO terms */

2011-12-28T19:37:21Z

GO terms

Cooperl: /* PSDSO Revisions: Whole plant development stages */

2011-12-28T19:36:04Z

PSDSO Revisions: Whole plant development stages

Rwalls at 19:43, 20 December 2011

2011-12-20T19:43:21Z

Rwalls: /* GO terms */

2011-12-20T15:02:33Z

GO terms

Rwalls: /* gametophyte/sporophyte senescent stage */

2011-12-14T16:16:59Z

gametophyte/sporophyte senescent stage

← Older revision		Revision as of 19:43, 8 March 2012
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	Collaborators: none		Collaborators: none
−
−
−	~~Streaming recording link:~~
−
−	~~https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=60302387&rKey=f3cad8ca3f7a5d22~~
−	~~Download recording link:~~
−
−	~~https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=60302387&rKey=ab45ea8538532405~~

	Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_11-29-11]]? ''No additions, deletions, or changes.''		Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_11-29-11]]? ''No additions, deletions, or changes.''

@@ Line 27: / Line 27: @@
 ''Comments: Looks good, suggest having a search box, if it is possible''
-=PSDSO Revisions: Whole plant development stages=
+=PSDS Revisions: Whole plant development stages=
 ==[https://sourceforge.net/tracker/?func=detail&aid=3435050&group_id=76834&atid=835555 gametophyte/sporophyte dormant stage]==
 ===GO terms===

@@ Line 27: / Line 27: @@
 ''Comments: Looks good, suggest having a search box, if it is possible''
-=PSDS Revisions: Whole plant development stages=
+=PSDSO Revisions: Whole plant development stages=
 ==[https://sourceforge.net/tracker/?func=detail&aid=3435050&group_id=76834&atid=835555 gametophyte/sporophyte dormant stage]==
 ===GO terms===
@@ Line 68: / Line 68: @@
 ''We may also want to request GO terms like bud dormancy process and spore dormancy process.''
 ===PO terms===
@@ Line 131: / Line 129: @@
 Seems like they should be synonyms of seed dormant stage, but we do not have a term for that, which is why they probably got stuck here.
 ==[https://sourceforge.net/tracker/?func=detail&aid=3439450&group_id=76834&atid=835555 zygote stage]==

← Older revision		Revision as of 21:19, 29 December 2011
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	Seems like they should be synonyms of seed dormant stage, but we do not have a term for that, which is why they probably got stuck here.		Seems like they should be synonyms of seed dormant stage, but we do not have a term for that, which is why they probably got stuck here.
−
−	==review of definitions for [https://sourceforge.net/tracker/?func=detail&aid=3439459&group_id=76834&atid=835555 embryo stage] and [https://sourceforge.net/tracker/?func=detail&aid=2982384&group_id=76834&atid=835555 plant embryo]==
−	~~===embryo stage===~~
−	~~We already had a term PO:0007631, embryo development stages, is_a seed development stage. This term was renamed '''embryo stage''' and made is_a sporophyte vegetative stage.~~
−
−	~~proposed def.:~~
−
−	'''embryo stage (PO:0007631):''' A sporophyte vegetative stage that occurs during the interval between the first cell division and one of the following: germination in seed plants, formation of the first true leaf after the cotyledon(s) in pteridophytes, cessation of division of the apical cell and initiation of development of the sporangium in bryophytes, or the beginning of the formation of organs (roots, shoot axes, or leaves) in cultured plant embryos.
−
−	Comment: An embryo stage generally starts after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it begins after the division of a single cell that is not a zygote. The end of an embryo stage varies among taxa.
−
−	~~===plant embryo===~~
−	~~Now that we have a working term for embryo stage, we can define '''plant embryo''' in terms of the stage.~~
−
−	~~'''existing def. plant embryo (PO:0009009):''' A whole plant in the early part of a sporophytic phase after the first cell division.~~
−
−	~~'''proposed def. plant embryo (PO:0009009):''' A whole plant that participates in the embryo stage (PO:0025369).~~
−
−	comment (basically the same as existing comment): An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. In seed plants, the embryo stage ends with germination. In pteridophytes, the embryo stage ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryo stage ends when the apical cell stops dividing and the sporangium begins to develop. In cultured plant embryos, the embryo stage ends when organs (roots, shoot axes, or leaves) begin to form.
−
−	~~-change from participates_in sporophyte development stage to participates_in embryo stage~~
−
−	''We had a discussion a few weeks ago whether is better to define stages in terms of structures or structures in terms of stages. We agreed that in general, it is better to define stages in terms of structures. This works well for terms like trichome development stage which have a trichome as a primary participant. However, in the case of embryo stage (and other whole plant growth stages), the primary participant is a whole plant that is undergoing certain processes, and the stage is a more fundamental term that defines what those processes are. It would be circular to define the embryo stage as a stage that has as participant an embryo, then define the embryo as a whole plant during a certain time. Better to define the embryo stage as a stage that has as participant a whole plant that is undergoing certain processes (in this case, everything between first cell division and the other events that mark the end of embryo stage).''
−
−	~~''We agreed that in the case of embryo and zygote (and probably other whole plant stages), it is better to define the stage first, then define the whole plant as participating in that stage.''~~

	==[https://sourceforge.net/tracker/?func=detail&aid=3439450&group_id=76834&atid=835555 zygote stage]==		==[https://sourceforge.net/tracker/?func=detail&aid=3439450&group_id=76834&atid=835555 zygote stage]==

@@ Line 69: / Line 69: @@
 ''We may also want to request GO terms like bud dormancy process and spore dormancy process.''
-Link to discussion on [https://sourceforge.net/tracker/index.php?func=detail&aid=3462990&group_id=36855&atid=440764 GO SF Tracker]
+''Link to discussion on [https://sourceforge.net/tracker/index.php?func=detail&aid=3462990&group_id=36855&atid=440764 GO SF Tracker]''
 ===PO terms===

← Older revision		Revision as of 19:37, 28 December 2011
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	''We may also want to request GO terms like bud dormancy process and spore dormancy process.''		''We may also want to request GO terms like bud dormancy process and spore dormancy process.''
		+
		+	Link to discussion on [https://sourceforge.net/tracker/index.php?func=detail&aid=3462990&group_id=36855&atid=440764 GO SF Tracker]

	===PO terms===		===PO terms===

@@ Line 17: / Line 17: @@
 https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=60302387&rKey=ab45ea8538532405
-Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_11-29-11]]?
+Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_11-29-11]]? ''No additions, deletions, or changes.''
 Back to [[POC Meetings Minutes]]

← Older revision		Revision as of 15:02, 20 December 2011
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	''should be called "multicellular organism dormancy process''		''should be called "multicellular organism dormancy process''

−	''New comment: Multicellular organism dormancy is a suspension of most physiological activity and growth that can be reactivated. In plants, multicellular organism dormancy may involve the formation of dormant buds and may be preceded by the senescence of plant parts such as leaves in woody plants or most of the shoot system herbaceous perennials. The end of organism dormancy in vascular plants is marked by resumed growth of buds and/or growth of vascular cambium. May be response to environmental conditions such as seasonality or extreme heat, drought, or cold''.	+	''New comment: Multicellular organism dormancy is a suspension of most physiological activity and growth that can be reactivated. In plants, multicellular organism dormancy may involve the formation of dormant buds and may be preceded by the senescence of plant parts such as leaves in woody plants or most of the shoot system herbaceous perennials. The end of organism dormancy in vascular plants is marked by resumed growth of buds and/or growth of vascular cambium. May be a response to environmental conditions such as seasonality or extreme heat, drought, or cold''.

@@ Line 210: / Line 210: @@
 Note: [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0008150#lineage GO:biological process] already states that this applies is "pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms", and [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0032502#lineage GO:developmental process]  states that it is a "progression of an integrated living unit... over time from an initial condition to a later condition".
-====cell aging (GO:0007569)====
+''We only had time for a quick discussion of senescence. Will go over it more next week.''
-'''current definition:''' Progression of the cell from its inception to the end of its lifespan.
+''We agreed that comment about sterility should probably come out.''
-'''proposed definition:''' An aging process that has as participant a cell.
+====cell aging (GO:0007569)====
+''Postponed until the 12-20-11 meeting.''
 ====cellular senescence (GO:0090398)====
+''Postponed until the 12-20-11 meeting.''
 ====multicellular organismal aging (GO:0010259):====
+''Postponed until the 12-20-11 meeting.''
 ====organ senescence (GO:0010260)====
-'''current definition:''' The process that occurs in an organ near the end of its active life that is associated with the dismantling of cell components and membranes, and an overall decline in metabolism. An example of this process is found in Arabidopsis thaliana. Source: GOC:mtg_sensu, GOC:sm
+''Postponed until the 12-20-11 meeting.''
 ====leaf senescence (GO:0010150)====
-'''current definition:''' The process that occurs in a leaf near the end of its active life that is associated with the dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism. Source: ISBN:0387987819
+''Postponed until the 12-20-11 meeting.''
 ====ripening (GO:0009835)====
-GO has the term '''ripening''': The series of events causing changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) to make it more attractive to animals and/or aid in seed dispersal.
+''Postponed until the 12-20-11 meeting.''
 ===PO senescent stage terms===
-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.
+''Postponed until the 12-20-11 meeting.''
 =Updating PO relations=