POC Conf. Call 10-9-12 - Revision history

Rwalls at 20:02, 11 October 2012

2012-10-11T20:02:40Z

Rwalls: /* Subclasses of whole plant fruit ripening stage (PO:0007010) */

2012-10-11T20:00:31Z

Subclasses of whole plant fruit ripening stage (PO:0007010)

Rwalls: /* new subclasses of fruit formation stage */

2012-10-11T19:55:50Z

new subclasses of fruit formation stage

Rwalls: /* New fruit development stages */

2012-10-11T19:55:11Z

New fruit development stages

Rwalls: /* whole plant fruit development stage (PO:0025500) */

2012-10-11T19:41:37Z

whole plant fruit development stage (PO:0025500)

Rwalls: /* whole plant fruit development stage (PO:0025500) */

2012-10-11T19:17:48Z

whole plant fruit development stage (PO:0025500)

Rwalls: /* Subclasses of whole plant fruit formation stage (PO:0007042) */

2012-10-11T19:15:40Z

Subclasses of whole plant fruit formation stage (PO:0007042)

Rwalls: /* Fruit development stages for whole plants */

2012-10-11T19:14:23Z

Fruit development stages for whole plants

Rwalls: /* Change to gametophyte development stage */

2012-10-11T19:12:37Z

Change to gametophyte development stage

Rwalls: /* Manuscripts in prep */

2012-10-11T18:57:14Z

Manuscripts in prep

@@ Line 3: / Line 3: @@
 In attendance:
-POC members:
+POC members: Laurel Cooper (OSU), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY), Justin Elser (OSU), Justin Preece (OSU), Pankaj Jaiswal (OSU), Ramona Walls (NYBG), Dennis Stevenson (NYBG)
 Collaborators: none
-Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_10-2-12]]?
+Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_10-2-12]]? ''no additions, deletions, or changes''
 Back to [[POC Meetings Minutes]]

@@ Line 121: / Line 121: @@
 =Subclasses of whole plant fruit ripening stage (PO:0007010)=
 ''postponed to future meeting''
 =Upcoming meetings and Presentations 2012-2013:=

← Older revision		Revision as of 19:55, 11 October 2012
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−	'''~~fruit size up to 10% stage (PO:0025504):~~'~~'' A fruit formation stage (PO:0025501) that begins after a fruit initiation stage (PO:0025503), and ends when the fruit (PO:0009001) has reached 10% of its final size.~~	+	''other stages postponed until next week''
−
−	Comment: Begins as soon as plant cells (PO:0009002) in a developing fruit begin to divide or expand. Succeeds a fruit initiation stage (PO:0025503) and proceeds a fruit size 10 to 30% stage (PO:0025505). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).
−
−
−	~~'''fruit size 10 to 30% stage (PO:0025505):''' A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 10% to 30% of its final size.~~
−
−	Comment: Succeeds a fruit size up to 10% stage (PO:0025504) and proceeds a fruit size 30 to 50% stage (PO:0025506). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 10 to 30% (PO:0007009).
−
−
−	~~'''fruit size 30 to 50% stage (PO:0025506):''' A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 30 to 50% of its final size.~~
−
−	Comment: Succeeds a fruit size 10 to 30% stage (PO:0025505) and proceeds a fruit size 50 to 70% stage (PO:0025507). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 30 to 50% (PO:0007029).
−
−
−	~~'''fruit size 50 to 70% stage (PO:0025507):''' A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 50 to 70% of its final size.~~
−
−	Comment: Succeeds a fruit size 30 to 50% stage (PO:0025505) and proceeds a fruit size 70% to final size stage (PO:0025508). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 50 to 70% (PO:0007007).
−
−
−	'''fruit size 70% to final size stage (PO:0025508):''' A fruit formation stage (PO:0025501) that spans begins when a fruit (PO:0009001) has reached 70% of its final size and ends when a fruit has reached its final size and a fruit ripening stage (PO:0025502) begins.
−
−	Comment: Succeeds a fruit size 50 to 70% stage (PO:0025507) and proceeds a fruit ripening stage. This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 70% to final size (PO:0007027).

	===fruit ripening stage===		===fruit ripening stage===

@@ Line 81: / Line 81: @@
 def.: A plant structure development stage (PO:0009012) that has as primary participant a single fruit (PO:0009001).
-comment: Defined by characteristic morphological, structural, histological or other visible features of a fruit. May have as part a seed development stage (PO:0001170). For development stages of a whole plant based on fruit development, use whole plant fruit development stage (PO:0025500) or its subclasses.
+comment: Defined by characteristic morphological, structural, histological or other visible features of a fruit. May have as part a seed development stage (PO:0001170). This stage applies to an individual fruit (PO:0009001).  For development stages of a whole plant based on fruit development, use whole plant fruit development stage (PO:0025500) or its subclasses.
 ==New proposed subclasses==
 ''still need to create SF tracker items and add xref to terms''
 ===fruit formation stage (PO:0025501)===
 Proposed def.: A fruit development stage (PO:0001002) that being with the formation of the plant zygote (PO:0000423) ''that is contained in that fruit'' and ends when ''its'' fruit ripening stage (PO:0025502) begins.
@@ Line 94: / Line 98: @@
-'''fruit initiation stage (PO:0025503)''': A fruit formation stage (PO:0025501) that begins with the formation of the plant zygote (PO:0000423) ''that is contained in that fruit (PO:0009001)'' and ends when the plant cells (PO:0009002) in the fruit begin to divide or expand (add GO terms)''.
+'''fruit initiation stage (PO:0025503)''': A fruit formation stage (PO:0025501) that begins with the formation of the plant zygote (PO:0000423) ''that is contained in that fruit (PO:0009001)'' and ends when the plant cells (PO:0009002) in the fruit begin to ''divide or expand (add GO terms)''.
 Comment: The fruit initiation stage may begin without fertilization or formation of a zygote in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This stage ends as soon as plant cells (PO:0009002) in a developing fruit begin to divide or expand. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).
-''Apply similar changes as for PO:0025501. Copy comment to PO:0025501.''
+''What about fruits that don't grow after fertilization? I guess they go right to ripening stage? Do we need a comment to this effect? Maybe say it ends when cells start to divide or expand or senesce, if it goes directly into the ripening stage.''
@@ Line 126: / Line 134: @@
 ===fruit ripening stage===
-Proposed def.: A fruit development stage (PO:0001002) during which a fruit (PO:0009001) participates in the process of fruit ripening (GO:0009835).
+''postponed until next week''
 =Subclasses of whole plant fruit formation stage (PO:0007042)=

@@ Line 59: / Line 59: @@
 New term
-'''proposed defintion:''' A sporophyte reproductive stage that begins when a fruit (PO:0009001) enters its fruit initiation stage (PO:0025503) on a whole plant (PO:0000003) ''that does not have any other fruits as part'', and ends with the earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.
+'''proposed defintion:''' A sporophyte reproductive stage that begins when a ''single'' fruit (PO:0009001) enters its fruit initiation stage (PO:0025503) on a whole plant (PO:0000003) ''that does not have any other fruits as part'', and ends with the earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.
 Comment: Sub-classes include whole plant fruit formation stage (PO:0007042) and whole plant fruit ripening stage (PO:0007010). An iteroparous plant will have a single whole plant fruit development stage during its life of whole plant (PO:0025337), while a semelparous plant may have multiple whole plant fruit development stages during its life, each of which will be part of the same instance of a sporophyte reproductive stage.
-''It doesn't work to say "it has not other fruits as part", because sometimes the fruits from the previous growing season are still present. Also, sounds like there is only one fruit made by the plant.''
+''It doesn't work to say "it has not other fruits as part", because sometimes the fruits from the previous fruiting cycle are still present. Also, sounds like there is only one fruit made by the plant.''
 ==[http://sourceforge.net/tracker/?func=detail&aid=3565057&group_id=76834&atid=835555 whole plant fruit formation stage (PO:0007042)]==

← Older revision		Revision as of 19:15, 11 October 2012
Line 128:		Line 128:

	''postponed to future meeting''		''postponed to future meeting''
−
−	At the meeting on 9/4/12, we agreed to modify the names slightly to emphasize that they belong to whole plants, and to remove numbers. Definitions should be changed to use updated name of the parent term, and to make it clearer that they refer to whole plant stages.
−
−	''What about plants with asynchronous fruit development? RW and MAG talked to Naama Menda about using these terms for tomato. She felt that these size classes were not useful for tomatoes, but in any case, they used the size classes only to describe individual fruits. They will need to go over all of there existing annotations and move them to fruit development stage and its new subtypes as necessary.''
−
−	~~====FF.00 fruit size up to 10% stage (PO:0007032)====~~
−	~~'''proposed new name and definition:'''~~
−
−	'''whole plant fruit formation stage up to 10%:''' A whole plant fruit formation stage (PO:0007042) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) and ends when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% of final size.
−
−	comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size up to 10% stage (PO:0025504).
−
−	~~====FF.01 fruit size 10 to 30% stage (PO:0007009)====~~
−	~~'''proposed new name and definition:'''~~
−
−	'''whole plant fruit formation stage 10 to 30%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% to 30% of final size.
−
−	comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 10 to 30% stage (PO:0025505).
−
−	~~====FF.02 fruit size 30 to 50% stage (PO:0007029)====~~
−	~~'''proposed new name and definition:'''~~
−
−	'''whole plant fruit formation stage 30 to 50%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 30% to 50% of its final size.
−
−	comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 30 to 50% stage (PO:0025506).
−
−	~~====FF.03 fruit size 50 to 70% stage (PO:0007007)====~~
−	~~'''proposed new name and definition:'''~~
−
−	'''whole plant fruit formation stage 50 to 70%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 50% to 70% of its final size.
−
−	comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 50 to 70% stage (PO:0025507).
−
−	~~====FF.04 fruit size 70% to final size stage (PO:0007027)====~~
−	~~'''proposed new name and definition:'''~~
−
−	'''whole plant fruit formation stage 70% to final size:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 70% of its final size to its final size.
−
−	comment: Succeeded by a whole plant fruit ripening stage (PO:0007010). This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 70% to final size stage (PO:0025508).
−
−	~~related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79~~
−
−	~~==Add new synonyms for grapes==~~
−
−	~~''Add related synonym: BBCH principle growth stage 77; Berries beginning to touch''~~
−
−	~~''Add related synonym: grape E-L stage: 31 Berries pea-sized (7mm dia), bunches hang, (BBCH 75)''~~
−
−	~~''Add related synonym: grape E-L stage: 32 Beginning of bunch closure, berries touching (if bunches are tight), Berries beginning to touch (BBCH 77)''~~
−
−	~~''Add related synonym: grape E-L stage: 33 Berries still hard and green, Majority of berries touching, (BBCH 79)''~~

	=Subclasses of whole plant fruit ripening stage (PO:0007010)=		=Subclasses of whole plant fruit ripening stage (PO:0007010)=

@@ Line 66: / Line 66: @@
 ''postponed to future meeting''
 ==[http://sourceforge.net/tracker/?func=detail&aid=3565059&group_id=76834&atid=835555 whole plant fruit ripening stage (PO:0007010)]==
 ''postponed to future meeting''
 =New fruit development stages=

← Older revision		Revision as of 19:12, 11 October 2012
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	'''New addition to comment (rest stays the same):''' In seed plants, the gametophyte may be transformed by fertilization but not strictly die, such as when pollen (PO:0025281) germinates or when a plant embryo (PO:0009009) begins to develop within an embryo sac (PO:0025074) of an angiosperms.		'''New addition to comment (rest stays the same):''' In seed plants, the gametophyte may be transformed by fertilization but not strictly die, such as when pollen (PO:0025281) germinates or when a plant embryo (PO:0009009) begins to develop within an embryo sac (PO:0025074) of an angiosperms.
		+
		+
		+	''After some discussion, we thought probably the best way would be to define the gds as ending when the gametophyte ceases to exist. Comment: ceasing to exist can either come about by death, at any point, or transformation, through fertilization.''
		+
		+	''Better to say "when pollen releases its sperm cells" than when it germinates. Germination of pollen is still in the gametophyte stage.''

	=Fruit development stages for whole plants=		=Fruit development stages for whole plants=

← Older revision		Revision as of 18:57, 11 October 2012
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	=Manuscripts in prep=		=Manuscripts in prep=
		+	''No discussion today''

	=Change to [https://sourceforge.net/tracker/index.php?func=detail&aid=3030027&group_id=76834&atid=835555 gametophyte development stage]=		=Change to [https://sourceforge.net/tracker/index.php?func=detail&aid=3030027&group_id=76834&atid=835555 gametophyte development stage]=