POC Conf. Call 6-19-12 - Revision history

Cooperl at 21:55, 26 June 2012

2012-06-26T21:55:32Z

Cooperl at 21:53, 26 June 2012

2012-06-26T21:53:55Z

Rwalls at 18:17, 26 June 2012

2012-06-26T18:17:19Z

Rwalls at 18:15, 26 June 2012

2012-06-26T18:15:41Z

Cooperl: /* Upcoming meetings and Presentations 2012: */

2012-06-25T13:24:06Z

Upcoming meetings and Presentations 2012:

Rwalls: /* New located_in relation */

2012-06-22T18:13:33Z

New located_in relation

Rwalls: /* plant ovary (PO:0009072) and similar */

2012-06-22T18:11:30Z

plant ovary (PO:0009072) and similar

Rwalls: /* vascular system */

2012-06-22T18:10:55Z

vascular system

Rwalls: /* Sub-classes of plant structure, for the parts of the various multi-tissue plant structures */

2012-06-22T18:03:44Z

Sub-classes of plant structure, for the parts of the various multi-tissue plant structures

Rwalls: /* Sub-classes of collective plant structure (PO:) */

2012-06-22T17:56:17Z

Sub-classes of collective plant structure (PO:)

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 POC meeting, Webex Conference Call; Date: Tuesday June 19th, 2012 10am PDT/1pm EDT
-In attendance:
+In attendance: ''Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Marie Alejandra Gandolfo (Cornell)''
-POC members:
+Absent: ''Chris Mungall (Lawrence Berkeley National Lab)''

@@ Line 3: / Line 3: @@
 In attendance:
-POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Marie Alejandra Gandolfo (Cornell)
+POC members:
 Collaborators: none
 Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_6-12-12]]?

← Older revision		Revision as of 18:17, 26 June 2012
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	Collaborators: none		Collaborators: none
−
−
−	~~Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=65969132&rKey=9f9f445660d68cfa~~
−
−	~~Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=65969132&rKey=701561c108bc5518~~
−

	Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_6-12-12]]?		Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_6-12-12]]?

@@ Line 3: / Line 3: @@
 In attendance:
-POC members:
+POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Marie Alejandra Gandolfo (Cornell)
 Collaborators: none

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 The focus of the workshop will be on mostly development stages and traits for the crop plants
 =Next meeting scheduled for Tuesday, June 26, 2012 at 10am PDT/1pm EDT=
 See: [[POC_Conf._Call_6-26-12]]

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 Could also add the "inverse located in" relation. For example, we now have seed has_part plant embryo, but this should really be inverse_located_in. This is a terrible name for the relation.
 Need to check with CM about correct xrefs for located_in.
 =[https://sourceforge.net/tracker/index.php?func=detail&aid=3177370&group_id=76834&atid=835555  plant ovary] (PO:0009072) and similar=

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 See more at [[Items_for_future_meetings#ovary_and_the_like]]
+''We will leave this as for now, and deal with it during the next release.''
 =Upcoming meetings and Presentations 2012:=

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 =[https://sourceforge.net/tracker/index.php?func=detail&aid=2903976&group_id=76834&atid=835555 vascular system]=
-'''current def., vascular tissue (PO:0000034):''' A plant structure that includes the totality of the portions of vascular tissue in their specific arrangement in a whole plant or in a constituent part thereof.
+'''current def., vascular system (PO:0000034):''' A plant structure that includes the totality of the portions of vascular tissue in their specific arrangement in a whole plant or in a constituent part thereof.
 We originally decided that vascular system was not a child of portion of vascular tissue, because it can contain portions of other tissue. However, vascular tissue, as it is now defined, can contain portions of other tissues or other cell types. See [http://plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0009015 definition of portion of vascular tissue].
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 comment: A vascular system consist of the totality of the portions of vascular tissue in their specific arrangement in a plant structure.  May include other types of tissues or cells, such as parenchyma (PO:0005421) or fiber cells (PO:0025407).
 =New ''located_in'' relation=

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 Comment: Includes cardinal parts of plant organs (PO:0025001) as well as other multi-tissue plant structures. Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Includes parts with both fiat boundaries, such as leaf base (PO:id), and bona-fide boundaries, such as leaflet (PO:id).
 ===[https://sourceforge.net/tracker/index.php?func=detail&aid=2945268&group_id=76834&atid=835555 cardinal organ part (PO:0025001)]===
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 revised comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.
 '''Re: fiat versus bona-fide boundaries:'''

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 ''okay''
-==Sub-classes of collective plant structure (PO:)==
+==Sub-classes of collective plant structure (PO:0025497)==
 ===[https://sourceforge.net/tracker/?func=detail&aid=2954382&group_id=76834&atid=835555 collective plant organ structure] (PO:0025007)===
 This is currently named '''collective plant structure'''. At the POC meeting on 5-?-12, we discussed renaming it "collective plant organ structure", which is clearer.
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 comment: A collective plant organ structure must have as parts at least two plant organs (PO:0009008) that do not have a part_of relation between them, that is, one must
 be adjacent to the other, rather than one part of the other.  The plant organs in a collective plant structure can be of the same type, such as the corolla (PO:0009059) composed of multiple petals (PO:0009032), or of different types, such as a shoot system (PO:0009006), composed of shoot axes (PO:0025029) and phyllomes (PO:0006001). Other examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for collective plant structures composed of parts of multiple organs, but no complete organs.
 ===[https://sourceforge.net/tracker/index.php?func=detail&aid=3175301&group_id=76834&atid=835555 collective organ part structure] (PO:0025269)===
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 comment stays as is
 ==Sub-classes of plant structure, for the parts of the various multi-tissue plant structures==