POC Conf. Call 8-14-12 - Revision history

Rwalls: /* Fruit development stage (PO:0001002) and subclasses */

2012-08-15T19:30:31Z

Fruit development stage (PO:0001002) and subclasses

2012-08-15T19:26:50Z

existing whole plant development stage terms

2012-08-15T19:24:28Z

New terms

2012-08-15T19:23:28Z

Aligning the top levels of plant structure development stage to plant structure

2012-08-15T18:42:13Z

PO-GO-PRO meeting- Summer 2013

2012-08-15T18:40:20Z

PAG 2013, San Diego, CA; January 12-16, 2013

2012-08-14T22:10:34Z

NSF Plant Genome PIs Meeting

2012-08-14T21:40:18Z

Fruit development stage (PO:0001002) and subclasses

2012-08-14T21:39:55Z

Fruit development stage (PO:0001002) and subclasses

2012-08-14T21:39:25Z

Aligning the top levels of plant structure development stage to plant structure

← Older revision		Revision as of 19:30, 15 August 2012
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	New sub-classes based on whole plant stages from above?		New sub-classes based on whole plant stages from above?
		+
		+	''We agreed that we should develop more specific subclasses for this term, but it may not be easy. PJ said that the reason there are not subclasses now is because there are not existing terminologies for comparing fruit development across all species.''
		+
		+	''After call: DWS suggested that we may be able to describe diverse types of fruit development by starting with the development of different parts of the fruit, like the mesocarp or endocarp, and then showing how development of different tissues leads to different types of fruits. Also, we could start with fertilization stage as a first stage in all fruit development (with parthenocarpy as an exception).''

	=Upcoming meetings and Presentations 2012-2013:=		=Upcoming meetings and Presentations 2012-2013:=

@@ Line 79: / Line 79: @@
 All of these definitions should be reworded to make it clear that they refer to development stages of a whole plant. Technically, saying that they are fruit formation stages does that, but it is not obvious to readers. Names should also be changed accordingly.
-''agreed after some discussion''
+''Agreed after some discussion. We will proposed names and revised definitions at a meeting in the near future.''
 For development stages of fruits (rather than whole plants with fruits), see [[Items_for_future_meetings#Fruit development stage (PO:0001002) and subclasses]]

← Older revision		Revision as of 19:24, 15 August 2012
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	==New terms==		==New terms==
		+	''In principle, we agreed on these definitions, but for now we are going to try to develop this part of the ontology without these upper level terms.''
		+
	===Multi-tissue plant structure development stage===		===Multi-tissue plant structure development stage===

@@ Line 32: / Line 32: @@
 ''We had a discussion about whether or not it is necessary to mirror all the upper level terms from the PAE or just the relevant parent categories for the classes such as "flower development" or "corolla development.  Decided that it needed additional study and  that for the mean time, we will develop the hierarchy with out them and compare the two approaches''
-''Plant tissue development stage refers to the development of a "portion of plant tissue" which is a child of plant structure''
+''Plant tissue development stage refers to the development of a "portion of plant tissue" which is a child of plant structure.''
-One way to deal with the 'unnatural sounding' upper level terms is through the development of slims and using [http://ontofox.hegroup.org/faqs.php OntoFox].  See their page for more details.
+''Currently we do not cover the development of plant cells, as this is more the area of GO.  Need to check with the GO if they have stages, or just processes described. RW: GO has terms for cell cycle phases like telophase and cytokenesis, but their definition sound like a mixtures of process and stage. They also have terms for oogenisis stages (GO:0022605 and children), but they have no is_a parent (part_of oogenesis).
 ''There was a comment about the integration of anatomy and development in the Zfin ontology, but in reality they have a simple list of stages as a separate branch along side the anatomy ontology.''

@@ Line 193: / Line 193: @@
 ''PJ will check with DW about Gramene involvement''
-=PO-GO-PRO meeting- Summer 2013=
+=PO-GO-PRO meeting- May 2013=
 Suggestion from BS:
 A PO meeting including representatives from the PRO and the GO. The main focus would be addressing how PRO can meet PO's present and future needs; a secondary focus might be to go over some of our high-level / definitional issues with the GO (e.g. as concerns senescence)
-The proposal is to hold this meeting in summer 2013.
+The proposal is to hold this meeting in May 2013.
 =Next meeting scheduled for Tuesday, Aug 28th, 2012 at 10am PDT/1pm EDT=
 See: [[POC_Conf._Call_8-28-12]]

@@ Line 183: / Line 183: @@
 ==[http://www.intlpag.org/ PAG 2013], San Diego, CA; January 12-16, 2013==
-The PO will be running a workshop again- Need suggestions for speakers.
+* The PO will be running a workshop again- Need suggestions for speakers.
-Want to focus on applications of the ontologies
+''PJ: Suggestions- someone from GO in Berkeley, Nigam Shaw''
 =PO-GO-PRO meeting- Summer 2013=

@@ Line 161: / Line 161: @@
 ==NSF Plant Genome PIs Meeting==
-Sept 5-6th?
+Arlington, VA, September 6-7, 2012
 Need 2 pager and poster

@@ Line 123: / Line 123: @@
 This term is a subtype of collective plant structure development stage, but will move to multi-tissue plant structure development stage. There are currently no subclasses for this term.
-'''fruit development stage (PO:0001002), current def.:''' Stages of development of a fruit defined by characteristic morphological, structural, histological or other visible features.
+'''fruit development stage (PO:0001002):''' Stages of development of a fruit defined by characteristic morphological, structural, histological or other visible features.
 '''proposed def.:''' A multi-tissue plant structure development stage (PO:new term) that has as primary participant a fruit (PO:0009001).

← Older revision		Revision as of 21:39, 14 August 2012
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	Currently we do not cover the development of plant cells, as this is more the area of GO. Need to check with the gO if they have stages, or just processes described. Some cases are specific to plants such as secondary xylem development.''		Currently we do not cover the development of plant cells, as this is more the area of GO. Need to check with the gO if they have stages, or just processes described. Some cases are specific to plants such as secondary xylem development.''

−	One way to deal with the 'unnatural' upper level terms is through the development of slims and using [http://ontofox.hegroup.org/faqs.php OntoFox]. See their page for more details.	+	One way to deal with the 'unnatural sounding' upper level terms is through the development of slims and using [http://ontofox.hegroup.org/faqs.php OntoFox]. See their page for more details.
		+
		+	''There was a comment about the integration of anatomy and development in the Zfin ontology, but in reality they have a simple list of stages as a separate branch along side the anatomy ontology.''