POC Conf. Call 11-6-12 - Revision history

Cooperl: /* Add new synonyms for grapes */

2012-11-13T19:16:40Z

Add new synonyms for grapes

Cooperl: /* Sub-classes of whole plant fruit ripening stage (PO:0007010) */

2012-11-13T19:16:09Z

Sub-classes of whole plant fruit ripening stage (PO:0007010)

Cooperl: /* FF.00 fruit size up to 10% stage (PO:0007032) */

2012-11-13T06:25:43Z

FF.00 fruit size up to 10% stage (PO:0007032)

Cooperl: /* FF.01 fruit size 10 to 30% stage (PO:0007009) */

2012-11-13T06:19:34Z

FF.01 fruit size 10 to 30% stage (PO:0007009)

Cooperl: /* FF.00 fruit size up to 10% stage (PO:0007032) */

2012-11-13T06:19:07Z

FF.00 fruit size up to 10% stage (PO:0007032)

Cooperl: /* whole plant fruit formation stage (PO:0007042) */

2012-11-13T05:43:55Z

whole plant fruit formation stage (PO:0007042)

Cooperl: /* Plans for Upcoming Release #19 */

2012-11-13T05:41:48Z

Plans for Upcoming Release #19

Cooperl: /* Plans for Upcoming Release #19 */

2012-11-13T05:39:12Z

Plans for Upcoming Release #19

Cooperl: /* Plans for Upcoming Release #19 */

2012-11-13T05:38:03Z

Plans for Upcoming Release #19

Cooperl: /* Phenotype RCN meeting, Oct 26-29th 2012 */

2012-11-13T05:35:23Z

Phenotype RCN meeting, Oct 26-29th 2012

@@ Line 132: / Line 132: @@
 related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79
-==Add new synonyms for grapes==
+Add new synonyms for grapes:
 ''Add related synonym: BBCH principle growth stage 77; Berries beginning to touch''

@@ Line 146: / Line 146: @@
 The current definitions are very vague and circular! For now, propose just rewording them so it is clear that they refer to whole plants, but we will need to develop some more specific boundaries for these stages at some point.
-==FR.00 beginning of fruit ripening stage (PO:0007036)==
+''Tabled for a future meeting, as they have not been worked on yet- moved to [[Items_for_future_meetings]] page.
 =Upcoming meetings and Presentations 2012-2013:=

@@ Line 91: / Line 91: @@
 '''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 ''expected'' final size.
+'''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) enters a fruit initiation stage (PO:0025503) and ends when the average size of fruits (PO:0009001)  has reached 10% of ''expected'' final size.
 comment: This terms is best used for plants with more or less synchronous fruit development and can only be used if the ''expected'' 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).
-'can only be used if the normal size of the fruit is known'.  healthy plants, must have a knowledge of he
+''can only be used if the normal size of the fruit is known.  healthy plants, must have a knowledge of the expected final size.''
-what is a normal size?  Could depend on the environment e.g. fruits in OR vs CA
+''what is a normal size?  Could depend on the environment e.g. fruits in OR vs CA''
 ====FF.01 fruit size 10 to 30% stage (PO:0007009)====

@@ Line 104: / Line 104: @@
 '''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)====

@@ Line 91: / Line 91: @@
 '''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.
+'''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 ''expected'' 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).
+comment: This terms is best used for plants with more or less synchronous fruit development and can only be used if the ''expected'' 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)====

@@ Line 86: / Line 86: @@
 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.''
+''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 their 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)====

@@ Line 74: / Line 74: @@
 - fruit development stages
-- grape data set
+- New datasets: grape, cotton, rice
-LC: will send MAG a list of the new terms that we need
+LC: will send MAG a list of the new terms that we need translation.
 =Stage terms continued from last meeting:=

@@ Line 66: / Line 66: @@
 =Plans for Upcoming Release #19=
-Timeline for Release: Goal is mid November 2012
+Timeline for Release: Goal is Mid-December 2012
 [[Release_19]]

@@ Line 37: / Line 37: @@
 PJ: were there missing Po entities?  Recommend using the dev version.  Document of recommendations
-e.g. tomato flesh-
+e.g. tomato flesh- center core and material around seeds- variation in placentation
 ''PJ: All phenotype annotation to anatomical entity needs an annotation to the stage, whether you think you need it or not.  It is critical. In the GAF column 16 can be used for this.  Should use the more generic stage if it is not known''
@@ Line 51: / Line 51: @@
 ''PJ recommends that the EQs statements should include the growth stage, even it is not dependent on the gs. Try with a mandatory aspect and then it could be relaxed.''
-Whole plant vs plant structure development; leaf development
+Whole plant vs plant structure development; could use more than one leaf development
 =PO "Aspect" vs. "Ontology Branch"=