POC Conf. Call 10-25-11 - Revision history

Rwalls at 19:40, 1 November 2011

2011-11-01T19:40:29Z

Rwalls: Replaced content with ''''POC meeting, Webex Conference Call; Date: Tuesday Oct 25th, 2011 10am (PDT)''' In attendance: POC members: Absent: Collaborators: none Any changes or correction…'

2011-10-19T13:40:50Z

Replaced content with ''''POC meeting, Webex Conference Call; Date: Tuesday Oct 25th, 2011 10am (PDT)''' In attendance: POC members: Absent: Collaborators: none Any changes or correction…'

Rwalls: /* Old user requests on Source Forge */

2011-10-19T13:39:35Z

Old user requests on Source Forge

Rwalls: /* PGDSO revisions */

2011-10-17T12:57:55Z

PGDSO revisions

Rwalls: /* new mid-level terms for mosses */

2011-10-17T12:50:02Z

new mid-level terms for mosses

Rwalls at 12:49, 17 October 2011

2011-10-17T12:49:20Z

Rwalls at 23:49, 13 October 2011

2011-10-13T23:49:26Z

Rwalls at 23:46, 13 October 2011

2011-10-13T23:46:49Z

Cooperl: Created page with ''''POC meeting, Webex Conference Call; Date: Tuesday Oct 25th, 2011 10am (PDT)''' In attendance: POC members: Absent: Collaborators: none Any changes or corrections (a…'

2011-10-13T05:34:57Z

Created page with ''''POC meeting, Webex Conference Call; Date: Tuesday Oct 25th, 2011 10am (PDT)''' In attendance: POC members: Absent: Collaborators: none Any changes or corrections (a…'

New page

'''POC meeting, Webex Conference Call; Date: Tuesday Oct 25th, 2011 10am (PDT)'''

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_10-18th-11]]?

Back to [[POC Meetings Minutes]]

← Older revision		Revision as of 13:40, 19 October 2011
Line 13:		Line 13:
	Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC Conf. Call 10-18-11]]?		Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC Conf. Call 10-18-11]]?

−	~~=PGDSO revisions=~~
−	~~===sub-types of whole plant development stage===~~
−	~~====vegetative, reproductive, senescent, and dormant stages====~~
−
−	Existing terms for vegetative, reproductive, senescent and dormant stages are actually referring only to the sporophyte stage, so they will be made subtypes of sporophyte development stage, and renamed sporophyte vegetative development stage, etc. Corresponding stages will be created as subtypes of gametophyte stage.
−
−	~~We had an extensive discussion of what senescence is, and how to define the landmarks for the beginning and end of the senescent development stage. Some key points:~~
−
−	~~-Need different definitions for a senescent stage in a whole plant and a senescent stage in a part of a plant (like a leaf).~~
−
−	~~-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.~~
−
−	'''proposed definition, senescent stage:''' A plant structure development stage that is (1) initiated by an event of cell death within the plant structure, (2) terminated in the death of the plant structure in such a way that (3) the former is connected to the latter by processes of dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism. [source: POC:curators, BS]''
−
−	~~This definitions can be modified for specific structures (like sporophyte, gametophyte, leaf, etc.).~~
−
−
−	'''proposed definition, gametophyte reproductive development stage:''' A gametophyte development stage that is initiated with the development of a gamete producing structure and terminated with fertilization.
−
−	~~''Comment: Some gametophytes may dies before fertilization.''~~
−
−	~~'''proposed definition, gametophyte vegetative development stage:''' A gametophyte development stage that succeeds spore germination and ends with the formation of gametangia.~~
−
−
−	''Worked on new children of gametophyte reproductive development stage and gametophyte vegetative development stage. Whole plant development stages that are named after a plant structure that is not a whole plant will need to have the words "whole plant" in their name, to distinguish them from other structure development stages. For example, gametophore reproductive whole plant development stage is a whole plant development stage, while gametophore development stage is a stage in the development of an individual gametophore.''
−
−	'''''proposed definition, gametophore reproductive whole plant development stage''' (needs work): A gametophyte reproductive development stage in which gametophores and gametangia are being produced.''
−
−	'''''proposed definition, gametophore vegetative whole plant development stage''' (needs work): A gametophyte vegetative whole plant development stage during which a gametophore is being produced but no gametangia are being produced. Succeeds a protonema stage.''
−
−	'''''proposed definition, protonema whole plant development stage (PO:0030006)''': A gametophyte development stage during which a gametophyte undergoes filamentous growth. This succeeds spore germination and precedes a thalloid development stage (planar growth) or gametophore development stage.''
−
−	~~''Can also add new terms for '''thalloid reproductive whole plant development stage''' and '''thalloid vegetative whole plant development stage'''.''~~
−
−
−	~~=Upcoming meetings and Presentations 2011/2012:=~~


	Back to [[POC Meetings Minutes]]		Back to [[POC Meetings Minutes]]

← Older revision		Revision as of 13:39, 19 October 2011
Line 12:		Line 12:

	Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC Conf. Call 10-18-11]]?		Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC Conf. Call 10-18-11]]?
−
−	~~=Old user requests on Source Forge=~~
−	~~==TraitNet requests==~~
−	~~===[https://sourceforge.net/tracker/?func=detail&aid=3080906&group_id=76834&atid=835555 corm]===~~
−
−	~~'''proposed def:''' A short, enlarged stem in which the internodes do not elongate.~~
−
−	~~Comment: May serve as a storage and/or perennating organ. Usually underground.~~
−
−	~~child of stem (PO:0009047).~~
−
−	~~===[https://sourceforge.net/tracker/?func=detail&aid=3080913&group_id=76834&atid=835555 pneumatophore]===~~
−
−	~~definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves~~
−
−	~~'''proposed def:''' A lateral root that is erect and protrudes above the soil.~~
−
−	~~Comment: Pneumatophores are found in trees that live in flooded habitats such as mangroves. May provide oxygen to below ground roots growing in flooded soils.~~
−
−	~~is_a lateral root~~
−
−	~~===[https://sourceforge.net/tracker/?func=detail&aid=3080925&group_id=76834&atid=835555 tendril]===~~
−
−	~~Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.~~
−
−	~~tendrils can be (evolutionarily) derived from multiple types of structures. Suggest we make separate terms:~~
−
−	~~'''branch tendril''' (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.~~
−
−	~~'''leaf tendril''' (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.~~
−
−	~~'''leaflet tendril''' (child of leaflet): A leaflet that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.~~
−
−	~~'''leaf apex tendril''' (child of leaf apex): A leaf apex that is slender and coiling. Comment: Found at the apex of a leaf lamina, but the leaf apex tendril is not laminar. Aids plant in climbing.~~
−
−	~~Can add other types of tendrils if they come up or users need them.~~
−
−	~~This is the way we defined spine (no parent class spine, only leaf spine and stipule spine with is_a relations to leaf and stipule).~~
−
−
−
−	~~Alternative is to create a parent 'tendril'(is_a plant structure) with children that are part_of the other structures:~~
−
−	~~'''tendril''': A plant structure that is slender and coiling. Comment: Aids plant in climbing.~~
−
−	~~'''branch tendril''' is_a tendril part_of branch~~
−
−	~~'''leaf tendril''' is_a tendril part_of leaf~~
−
−	~~'''leaflet tendril''' is_a leaf tendril part_of leaflet~~
−
−	~~'''leaf apex tendril''' is_a leaf tendril part_of leaf apex~~
−
−
−	~~The part_of relations are technically correct (not proper part), but I'm not sure it conveys the proper meaning.~~
−
−
−	~~''also add petiole tendril and maybe root tendril. German: Ranke''~~

	=PGDSO revisions=		=PGDSO revisions=

← Older revision		Revision as of 12:57, 17 October 2011
Line 106:		Line 106:


		+	=Upcoming meetings and Presentations 2011/2012:=


	Back to [[POC Meetings Minutes]]		Back to [[POC Meetings Minutes]]

← Older revision		Revision as of 12:50, 17 October 2011
Line 105:		Line 105:
	''Can also add new terms for '''thalloid reproductive whole plant development stage''' and '''thalloid vegetative whole plant development stage'''.''		''Can also add new terms for '''thalloid reproductive whole plant development stage''' and '''thalloid vegetative whole plant development stage'''.''

−	~~====new mid-level terms for mosses====~~
−
−	~~We looked at the list of growth and development stages requested by the Moss Ontology, and started to work on the placement and definitions for some of them.~~
−
−	Terms like "gametangium development stage" (their gametangia development stages), "gametophore development stage", "protonema developmental stage", or "spore development stage" will be subtypes of "plant structure development stage".
−
−	~~Their term "gametophore growth" appears to be referring to what we have called the "gametophore whole plant vegetative development stage".~~



	Back to [[POC Meetings Minutes]]		Back to [[POC Meetings Minutes]]

@@ Line 13: / Line 13: @@
 Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC Conf. Call 10-18-11]]?
 ===sub-types of whole plant development stage===
 ====vegetative, reproductive, senescent, and dormant stages====

@@ Line 1: / Line 1: @@
 '''POC meeting, Webex Conference Call; Date: Tuesday Oct 25th, 2011 10am (PDT)'''
-In attendance:
+No meeting this week.
 Back to [[POC Meetings Minutes]]

@@ Line 11: / Line 11: @@
-Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_10-18th-11]]?
+Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC Conf. Call 10-18-11]]?
 ====vegetative, reproductive, senescent, and dormant stages====
@@ Line 44: / Line 45: @@
 ''Can also add new terms for '''thalloid reproductive whole plant development stage''' and '''thalloid vegetative whole plant development stage'''.''
 Back to [[POC Meetings Minutes]]

← Older revision		Revision as of 23:46, 13 October 2011
Line 12:		Line 12:

	Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_10-18th-11]]?		Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_10-18th-11]]?
		+
		+	====vegetative, reproductive, senescent, and dormant stages====
		+
		+	Existing terms for vegetative, reproductive, senescent and dormant stages are actually referring only to the sporophyte stage, so they will be made subtypes of sporophyte development stage, and renamed sporophyte vegetative development stage, etc. Corresponding stages will be created as subtypes of gametophyte stage.
		+
		+	We had an extensive discussion of what senescence is, and how to define the landmarks for the beginning and end of the senescent development stage. Some key points:
		+
		+	-Need different definitions for a senescent stage in a whole plant and a senescent stage in a part of a plant (like a leaf).
		+
		+	-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.
		+
		+	'''proposed definition, senescent stage:''' A plant structure development stage that is (1) initiated by an event of cell death within the plant structure, (2) terminated in the death of the plant structure in such a way that (3) the former is connected to the latter by processes of dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism. [source: POC:curators, BS]''
		+
		+	This definitions can be modified for specific structures (like sporophyte, gametophyte, leaf, etc.).
		+
		+
		+	'''proposed definition, gametophyte reproductive development stage:''' A gametophyte development stage that is initiated with the development of a gamete producing structure and terminated with fertilization.
		+
		+	''Comment: Some gametophytes may dies before fertilization.''
		+
		+	'''proposed definition, gametophyte vegetative development stage:''' A gametophyte development stage that succeeds spore germination and ends with the formation of gametangia.
		+
		+
		+	''Worked on new children of gametophyte reproductive development stage and gametophyte vegetative development stage. Whole plant development stages that are named after a plant structure that is not a whole plant will need to have the words "whole plant" in their name, to distinguish them from other structure development stages. For example, gametophore reproductive whole plant development stage is a whole plant development stage, while gametophore development stage is a stage in the development of an individual gametophore.''
		+
		+	'''''proposed definition, gametophore reproductive whole plant development stage''' (needs work): A gametophyte reproductive development stage in which gametophores and gametangia are being produced.''
		+
		+	'''''proposed definition, gametophore vegetative whole plant development stage''' (needs work): A gametophyte vegetative whole plant development stage during which a gametophore is being produced but no gametangia are being produced. Succeeds a protonema stage.''
		+
		+	'''''proposed definition, protonema whole plant development stage (PO:0030006)''': A gametophyte development stage during which a gametophyte undergoes filamentous growth. This succeeds spore germination and precedes a thalloid development stage (planar growth) or gametophore development stage.''
		+
		+	''Can also add new terms for '''thalloid reproductive whole plant development stage''' and '''thalloid vegetative whole plant development stage'''.''
		+

	Back to [[POC Meetings Minutes]]		Back to [[POC Meetings Minutes]]