POC Conf. Call 9-8-10 - Revision history

Cooperl: /* Annotations that have no term associated with them */

2010-09-10T00:12:02Z

Annotations that have no term associated with them

Cooperl: /* Status and Update of Progress: PO Release */

2010-09-09T21:07:32Z

Status and Update of Progress: PO Release

Cooperl: /* Status and Update of Progress: PO Release */

2010-09-09T21:07:13Z

Status and Update of Progress: PO Release

Cooperl: /* Responses, as of 8/7/2010: */

2010-09-09T20:09:43Z

Responses, as of 8/7/2010:

Cooperl at 20:00, 9 September 2010

2010-09-09T20:00:49Z

Cooperl at 19:49, 9 September 2010

2010-09-09T19:49:34Z

Cooperl at 17:53, 9 September 2010

2010-09-09T17:53:07Z

Cooperl: /* Feedback on the Beta Release */

2010-09-09T17:26:32Z

Feedback on the Beta Release

Cooperl at 16:47, 9 September 2010

2010-09-09T16:47:09Z

Cooperl at 22:27, 8 September 2010

2010-09-08T22:27:44Z

@@ Line 106: / Line 106: @@
 See comments from CM about replacing the terms:
-On Aug 17, 2010, at 6:51 AM, Walls, Ramona begin_of_the_skype_highlighting     end_of_the_skype_highlighting begin_of_the_skype_highlighting     end_of_the_skype_highlighting wrote:
+On Aug 17, 2010, at 6:51 AM, Walls, Ramona
 > We have put the replacement terms in the obo stanza as "consider" terms for all of these (check on this)

@@ Line 106: / Line 106: @@
 See comments from CM about replacing the terms:
-On Aug 17, 2010, at 6:51 AM, Walls, Ramona begin_of_the_skype_highlighting     end_of_the_skype_highlighting wrote:
+On Aug 17, 2010, at 6:51 AM, Walls, Ramona begin_of_the_skype_highlighting     end_of_the_skype_highlighting begin_of_the_skype_highlighting     end_of_the_skype_highlighting wrote:
 > We have put the replacement terms in the obo stanza as "consider" terms for all of these (check on this)

@@ Line 17: / Line 17: @@
 ==Status and Update of Progress: PO Release==
-'''A.  Feedback Box:'''
+'''Feedback Box:'''
 New link to [http://beta.plantontology.org:8080/db/feedback/send_feedback feedback box] on beta site- emails will go to '''po-discuss'''
-*Laurel and Ramona are working on some changes to customize this with additional fields and boxes for more directed responses
+*This could be customized in the future with additional fields and boxes for more directed responses
 Note: It would be better if the feedback box could fill in the relative link automatically from the page.  Is this possible??
@@ Line 29: / Line 28: @@
 ''Apparently this got broken when it was moved to the new spot on the beta browser.  JE is looking at getting it to capture the url of the current page being viewed.''
-''No new news on this to report.''
+''No other news on this to report.''
@@ Line 105: / Line 89: @@
 Tanya"
-Laurel replied and provided more  explanation and invited her to review that section and possibly attend the conference call.
+''Laurel replied and provided more  explanation and invited her to review that section and possibly attend the conference call.  Will follow up with them to get this resolved''
@@ Line 121: / Line 105: @@
 '''*Changes to the annotation files:'''
-- what is the mechanism for making these changes? Are we doing them here or is TAIR/Gramene going to send us new files?
+See comments from CM about replacing the terms:
+On Aug 17, 2010, at 6:51 AM, Walls, Ramona begin_of_the_skype_highlighting     end_of_the_skype_highlighting wrote:
 > We have put the replacement terms in the obo stanza as "consider" terms for all of these (check on this)
@@ Line 133: / Line 115: @@
 - Is there a script for making the changes?  Does this apply to the annotation files or just the OBO files?
 '''*sporphytic phase and gametophytic phase '''
@@ Line 144: / Line 127: @@
 What are other options?
-CM: As an interim strategy you could embed the id in the comments using a standard syntax, then parse the tags out once you merge files.
+''we all agreed that this is  a good idea, but it will have to wait for the next release.''
 '''*floral bud'''
-> > 2. Based on the response from TAIR (see above), we may want to reconsider obsoleting the term floral bud. Perhaps keeping this term for users is more important that getting rid of it to solve an ontological problem (term have multiple parentage).
+> > 2. Based on the response from TAIR (see above), we may want to reconsider obsoleting the term floral bud (or not). Perhaps keeping this term for users is more important that getting rid of it to solve an ontological problem (term have multiple parentage).
-CM: Multiple Inheritance isn't an ontological problem, it's an engineering problem for you, in that manually maintaining MI is tedious and error prone. You should move to towards using the reasoner to infer all these, but in the meantime your asserted links /must/ reflect the biology, which in many cases means asserting MI.
+(from email): CM: Multiple Inheritance isn't an ontological problem, it's an engineering problem for you, in that manually maintaining MI is tedious and error prone. You should move to towards using the reasoner to infer all these, but in the meantime your asserted links /must/ reflect the biology, which in many cases means asserting MI.
 ''Those present at the meeting felt it was preferable to keep the current structure for floral bud. We were concerned about instituting a policy of changing the ontology here and there to fit the convenience of individual users, unless the change is biologically appropriate. Laurel will follow up with TAIR to see if they can work with the new structure for floral bud, and also to find out the status of their annotation files.''
@@ Line 162: / Line 144: @@
 ''Justin P. raised the issue that we should be mindful as to whether or not the utilities we use (like Amigo) will be able to support our future analysis needs (for example, implied relations do not show up in the Amigo browser).''
 '''D.  Resolution:'''
-''We still need to find out (maybe from Justin E. or Pankaj) what the procedure is for updating annotations before the release.''
+''We still need to find out (maybe from Justin E. or Pankaj) what the procedure is for updating annotations before the release.  We do not want to have to hold up our release waiting for their files.''
 ==Feedback on the Beta Release==

@@ Line 246: / Line 246: @@
 ''Also note that we need to add a inflorescence has_part flower (can't use flower part_of inflorescence, because not all flowers are part of an inflorescence).''
 . Collective phyllome structure; PO:0052023 [A collective plant structure that consists of two or more phyllomes originating from the same node or from one or more adjacent nodes with compressed internodes.]
@@ Line 335: / Line 336: @@
 ''Laurel will follow-up with Rich Zobel (Root terms) and Naama Menda (tuber terms), Alejandra will follow up with Gar Rothwell ''
 ===Updates to the PO Web pages===

@@ Line 3: / Line 3: @@
 In attendance:
-POC members:  Laurel Cooper, Alejandra Gandolfo,  Justin Preece begin_of_the_skype_highlighting     end_of_the_skype_highlighting begin_of_the_skype_highlighting     end_of_the_skype_highlighting begin_of_the_skype_highlighting     end_of_the_skype_highlighting, Justin Elser, Ramona Walls, Barry Smith.
+POC members:  Laurel Cooper, Alejandra Gandolfo,  Justin Preece, Justin Elser, Ramona Walls, Barry Smith.
 Absent: Pankaj Jaiswal, Chris Mungal, Dennis Stevenson.

← Older revision		Revision as of 17:26, 9 September 2010
Line 333:		Line 333:

	''Shoot is a synonym of shoot system, and wood is a synonym of secondary xylem. Other terms can be added for the next release. Can fix seed coat part_of portion of plant tissue for this release.''		''Shoot is a synonym of shoot system, and wood is a synonym of secondary xylem. Other terms can be added for the next release. Can fix seed coat part_of portion of plant tissue for this release.''
		+
		+	''Laurel will follow-up with Rich Zobel (Root terms) and Naama Menda (tuber terms), Alejandra will follow up with Gar Rothwell ''
		+
		+

	===Updates to the PO Web pages===		===Updates to the PO Web pages===