POC Conf. Call 4-27-10 - Revision history

Cooperl: /* Agenda: */

2010-09-16T20:00:36Z

Agenda:

Cooperl at 17:21, 29 April 2010

2010-04-29T17:21:01Z

Cooperl at 19:06, 28 April 2010

2010-04-28T19:06:57Z

Cooperl at 18:31, 28 April 2010

2010-04-28T18:31:47Z

Cooperl at 17:22, 28 April 2010

2010-04-28T17:22:27Z

Rwalls at 15:33, 28 April 2010

2010-04-28T15:33:34Z

Rwalls at 11:24, 28 April 2010

2010-04-28T11:24:39Z

Cooperl at 22:06, 27 April 2010

2010-04-27T22:06:39Z

Cooperl at 20:04, 27 April 2010

2010-04-27T20:04:50Z

Cooperl at 19:37, 27 April 2010

2010-04-27T19:37:45Z

← Older revision		Revision as of 20:00, 16 September 2010
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−	*The previously-used term: Leaf whorl (PO:0008034) was made obsolete, because its definition did not match the new ontology structure as a child of collective phyllome structure. Annotations for this term are now associated with the new term collective leaf structure (PO:0025022). ~~(Do we need a SF tracker item for this action?)~~	+	*The previously-used term: [https://sourceforge.net/tracker/index.php?func=detail&aid=2993809&group_id=76834&atid=835555 Leaf whorl] (PO:0008034) was made obsolete, because its definition did not match the new ontology structure as a child of collective phyllome structure. Annotations for this term are now associated with the new term collective leaf structure (PO:0025022).

	''All agreed that it was appropriate to obsolete 'leaf whorl'.''		''All agreed that it was appropriate to obsolete 'leaf whorl'.''

@@ Line 103: / Line 103: @@
 ''Ramona showed us how she is linking to the images at [http://www.plantsystematics.org/ PlantSystematics.org].  This is the site where the majority of the images will be kept that are generated at NYBG and Cornell.
-We are working on figuring out the best way to link to these images in the Amigo browser.''
+We are working on figuring out the best way to link to these images in the AmiGO browser.''
-''Update from Alejandra:
+''Update from Alejandra:''
-She has replaced her undergraduates with a technician who is coming twice a week to help with cataloging the images in the slide collections.  They will be labeled with bar codes to facilitate searching. Anticipates making better progress now.''
+''She has replaced her undergraduates with a technician who is coming twice a week to help with cataloging the images in the slide collections.  They will be labeled with bar codes to facilitate searching. Anticipates making better progress now.''
@@ Line 122: / Line 122: @@
 proposed change: fruit is_a 'collective plant structure' and part_of infructescence. (CPS: a proper part of a plant and is composed of two or more organs and any associated portions of plant tissue).
-''PJ (via SourceForge) commented that 'ripe' should not be used here and offered a proposed using 'post-fertilization'.
+''PJ (via SourceForge) commented that 'ripe' should not be used here and offered a proposed def'n using 'post-fertilization'.''
-We came up with a Proposed def'n:
+''We came up with a proposed def'n:
 A collective plant structure that contains a mature gynoecium, together with any other structures that ripen with it and form a unit with it.''
-We will continue these discussions next week.
+We will continue these discussions next week.''

← Older revision		Revision as of 19:06, 28 April 2010
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	Unlike the definition we came up with last week, this definitions does not contain the undefined terms rosette and whorl. It also uses the term 'stem' instead of 'axis', because 'stem' is defined in the PO, and axis is not.		Unlike the definition we came up with last week, this definitions does not contain the undefined terms rosette and whorl. It also uses the term 'stem' instead of 'axis', because 'stem' is defined in the PO, and axis is not.

−	''There was discussion about whether it was appropriate to use the term 'stem' here although all agreed that it was better than axis. Alejandra made the comment that when referring to ~~Gymnosperm needles~~ the ~~term~~ axis ~~would be more appropriate than stem~~. We will make a note to work on the definition of 'stem'- it is on the agenda for May 4th Conf Call. ''	+	''There was discussion about whether it was appropriate to use the term 'stem' here although all agreed that it was better than axis. Alejandra made the comment that when referring to the reproductive structures of the conifers; the cones, "axis" is used to define the central portion of the cones where the sporophylls (micro and mega) are spirally arranged. This is also valid for other "structures" such as the strobili of the lycopods. Those are not considered to be "stems" they are axes''
		+
		+	''We will make a note to work on the definition of 'stem'- it is on the agenda for May 4th Conf Call. ''

@@ Line 27: / Line 27: @@
 'Collective phyllome structure' would replace the original term 'phyllome whorl' ([http://plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0008033&session_id=2766b1271946267/ PO:0008033]) which we have been calling 'whorled phyllome structure.'
-''Note: The original term 'phyllome whorl'(PO:0008033) will be merged into the new term 'collective phyllome structure', which will have a new ID#.  The old name and ID # will be listed as an alternate ID.''
+''Note: The original term 'phyllome whorl'(PO:0008033) will be merged into the new term 'collective phyllome structure', which will have a new ID#.  The old name and ID # will be listed as an alternate (secondary) ID.''
 The proposed new term [http://sourceforge.net/tracker/?func=detail&aid=2982629&group_id=76834&atid=835555/ phyllome aggregation] would be rejected.

← Older revision		Revision as of 17:22, 28 April 2010
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	''Update from Alejandra:		''Update from Alejandra:
−	She has replaced her ~~(unreliable)~~ undergraduates with a technician who is coming twice a week to help with cataloging the images in the slide collections. They will be labeled with bar codes to facilitate searching. Anticipates making better progress now.''	+	She has replaced her undergraduates with a technician who is coming twice a week to help with cataloging the images in the slide collections. They will be labeled with bar codes to facilitate searching. Anticipates making better progress now.''

@@ Line 51: / Line 51: @@
 >>gynoecium: A collective phyllome structure composed of two or more carpels.
-''There was discussion about whether or not the androecium and gynoecium were in fact collective structures, or could include the case where there was only one anther or carpel.  We decided that it was an unusual case and it could be added in a comment.''
+''There was discussion about whether or not the androecium and gynoecium were in fact collective structures, or could include the case where there was only one anther or carpel.  We decided that it was not the typical case and it could be added in a comment.''
 >>calyx: A collective phyllome structure composed of two or more sepals.

@@ Line 127: / Line 127: @@
-Items 6 was tabled for next weeks discussion.
+Item 6 was tabled for next weeks discussion.
 '''6.  Embryo''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2982384&group_id=76834&atid=835555/ embryo])
@@ Line 211: / Line 211: @@
 Alejandra said she talked to the organizers, and we only need to submit 2 or 3 potential speakers. The others can be selected from the abstracts submitted to the meeting. Laurel and Ramona are happy to be organizers and are interested in attending if the funding is available. Pankaj will check with NSF to see if we can use travel funds for an international meeting.
-''Ramona has circulated a proposal to be submitted by Friday April 30th.  There were a few comments about the idea to include a hands on workshop- Ramona will follow up with the organizers about whether or not this is a possibility.  Laurel will confirm whether she or Pankaj will be co-organizer with Ramona.''
+''Ramona has circulated a proposal to be submitted by Friday April 30th.  There were a few comments about the idea to include a hands on workshop- Ramona will follow up with the organizers about whether or not this is a possibility.  Laurel will confirm whether she or Pankaj will be co-organizer with Ramona. Ramona will contact someone from the Genomics of Seed Plants project about being a potential speaker.''

← Older revision		Revision as of 22:06, 27 April 2010
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	'Collective phyllome structure' would replace the original term 'phyllome whorl' ([http://plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0008033&session_id=2766b1271946267/ PO:0008033]) which we have been calling 'whorled phyllome structure.'		'Collective phyllome structure' would replace the original term 'phyllome whorl' ([http://plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0008033&session_id=2766b1271946267/ PO:0008033]) which we have been calling 'whorled phyllome structure.'
		+
		+	''Note: The original term 'phyllome whorl'(PO:0008033) will be merged into the new term 'collective phyllome structure', which will have a new ID#. The old name and ID # will be listed as an alternate ID.''

	The proposed new term [http://sourceforge.net/tracker/?func=detail&aid=2982629&group_id=76834&atid=835555/ phyllome aggregation] would be rejected.		The proposed new term [http://sourceforge.net/tracker/?func=detail&aid=2982629&group_id=76834&atid=835555/ phyllome aggregation] would be rejected.

@@ Line 114: / Line 114: @@
-Does everyone agree that a fruit is a collective plant structure?
+Does everyone agree that a fruit is a collective plant structure? ''All agreed''
 proposed change: fruit is_a 'collective plant structure' and part_of infructescence. (CPS: a proper part of a plant and is composed of two or more organs and any associated portions of plant tissue).
 '''6.  Embryo''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2982384&group_id=76834&atid=835555/ embryo])
@@ Line 149: / Line 156: @@
-Agreed that there should be some group discussion of plant cells before this meeting.Laurel and Ramona will review the Cell Ontology.
+Agreed that there should be some group discussion of plant cells before this meeting. Laurel and Ramona will review the Cell Ontology.
 '''* POC meeting/Annotation workshop to be held in Corvallis on June 29th/30th.'''
@@ Line 159: / Line 167: @@
 Ramona will be in Portland June 26-29, will request that her talk be scheduled for the 27th or 28th.
 Barry will be in France this week and can't attend.
 What about Chris?
@@ Line 179: / Line 188: @@
 We should prepare a brochure to distribute, similar to the one Gramene has.
-'''Annotation workshop with Gramene is scheduled for Saturday July 31, 8am-12pm. more details TBA'''
+'''Annotation workshop with Gramene is scheduled for '''Saturday July 31, 8am-12pm'''. more details TBA'''
@@ Line 199: / Line 208: @@
 Alejandra said she talked to the organizers, and we only need to submit 2 or 3 potential speakers. The others can be selected from the abstracts submitted to the meeting. Laurel and Ramona are happy to be organizers and are interested in attending if the funding is available. Pankaj will check with NSF to see if we can use travel funds for an international meeting.

@@ Line 98: / Line 98: @@
 What do folks think of this as a way to include images in the PO? Is there a way to include images in the obo file?
-Ramona showed us how she is linking to the images at [http://www.plantsystematics.org/ PlantSystematics.org]
+''Ramona showed us how she is linking to the images at [http://www.plantsystematics.org/ PlantSystematics.org].  This is the site where the majority of the images will be kept that are generated at NYBG and Cornell.
 '''Items carried over from last week's agenda:'''