POC Conf. Call 10-13-10 - Revision history

Cooperl: /* Other Items */

2010-10-15T16:48:17Z

Other Items

Cooperl at 16:40, 15 October 2010

2010-10-15T16:40:29Z

Cooperl: /* POC meeting to be held at NYBG in fall 2010. Date Nov 4-6th */

2010-10-14T18:18:18Z

POC meeting to be held at NYBG in fall 2010. Date Nov 4-6th

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

2010-10-14T00:38:51Z

Status and Update of Progress: PO Release

Rwalls: /* Other Items */

2010-10-14T00:37:21Z

Other Items

Rwalls: /* POC meeting to be held at NYBG in fall 2010. Date Nov 4-6th */

2010-10-14T00:35:19Z

POC meeting to be held at NYBG in fall 2010. Date Nov 4-6th

Rwalls: /* Changes to PSO */

2010-10-14T00:32:38Z

Changes to PSO

Rwalls: /* Housekeeping Items */

2010-10-14T00:30:19Z

Housekeeping Items

Rwalls: /* Priorities for next release */

2010-10-14T00:29:15Z

Priorities for next release

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

2010-10-14T00:19:44Z

Status and Update of Progress: PO Release

@@ Line 249: / Line 249: @@
-The following week, Nov 3rd LC will be traveling to the NYBG meeting- Conf call Friday Nov 5 for those that cannot make it in person?
+The following week, Nov 3rd LC will be traveling to the NYBG meeting-
-Will start at a time convenient for the west coast.  PJ will be in ~ 10am.
+''Conf call Friday Nov 5 for those that cannot make it in person? Will start at a time convenient for the west coast.  PJ will be in ~ 10am.''
 Weds Nov 10th- Barry cannot attend
@@ Line 268: / Line 268: @@
 Weds Dec 29th-ok
-''We will work on setting up a new schedule at the NYBG meeting, PJ cannot do  Weds next term as he is teaching. Alejandra's schedule will probably also be different.''
+''We will work on setting up a new schedule at the NYBG meeting, PJ cannot do Weds next term as he is teaching. Alejandra's schedule will probably also be different.''

@@ Line 3: / Line 3: @@
 In attendance:
-POC members:
+POC members:Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Alejandra Gandolfo, (Cornell University),  Justin Elser (OSU), Justin Preece (OSU), Barry Smith (University at Buffalo, NY), Dennis Stevenson (NYBG),
-Absent:
+Absent: Chris Mungall (Lawrence Berkeley National Lab)

← Older revision		Revision as of 18:18, 14 October 2010
Line 222:		Line 222:

	-Could also invite someone from VirtualPlant (Coruzzi lab). Maybe their bioinformatics person (Manny).''		-Could also invite someone from VirtualPlant (Coruzzi lab). Maybe their bioinformatics person (Manny).''
		+
		+	''Who is going to going to contact them and when should the guests come?''

	==Other Items==		==Other Items==

@@ Line 24: / Line 24: @@
 '''Issues:'''
 *'''Amigo browser''': There are no icons for relations that we added (has_part, derives_from). Show up as question marks.
-What about participates_in?
+What about participates_in? ''We have also created the participates_in and derives_from relations, but they are not currently in use. Will need to create icons for them if we use them in the next release.''
 ''Might be possible to make icons in OboEdit. Justin E. said that if we can figure out how to make the icons, he can probably figure out how to get them on to Amigo. Barry said to contact Chris Mungall to be sure whatever icons we use are consistent with Obo Foundry use.''

@@ Line 237: / Line 237: @@
 Deliverables: Years 2-4: Student workshop at NYBG.
-''We will work on at the NYBG meeting''
+''We will work on at the NYBG meeting. There is someone at the NYBG who can help us with this.''
 '''*Modification of the Conference Call Schedule:'''
@@ Line 264: / Line 264: @@
 Weds Dec 29th-ok
-''We will work on setting up a new schedule at the NYBG meeting, PJ cannot do  Weds next term as he is teaching.''
+''We will work on setting up a new schedule at the NYBG meeting, PJ cannot do  Weds next term as he is teaching. Alejandra's schedule will probably also be different.''
@@ Line 288: / Line 288: @@
 Laurel can set up a Doodle poll??  Who wants to take part?
-''Will not invite him to meeting at NYBG?''
+''Will not invite him to meeting at NYBG''
@@ Line 308: / Line 308: @@
 She started on Friday. Will she take place in POC conference calls? Should we add her to PO mailing lists (dev, internal, discuss)?
-''Will join us when she arrives from Chile''
+''Will join us when she arrives from Chile. Can take part in the meeting at NYBG in November.''
 ==Upcoming meetings 2010-2011:==

@@ Line 215: / Line 215: @@
 * Should we invite outside experts, scientists, students and postdocs?  Time to do so is getting short.
--Farshid Ahrestani from TraitNet has been invited, can also invite Dan Bunker (both from NJIT in Newark, so could attend for only a few hours without too much travel)
+-Farshid Ahrestani from TraitNet has been invited, can also invite Dan Bunker from Traitnet (both from NJIT in Newark, so could attend for only a few hours without too much travel)
--Bruce Kirchoff? He would have to travel from South Carolina.  It might be better to just organize a conference call.
+-Bruce Kirchoff? He would have to travel from South Carolina. ''We will organize conference call instead.''
--Folks from the NYBG- review the PGDSO and comment on terms from non-angiosperms.  Suggestions?
+-Folks from the NYBG- review the PGDSO and comment on terms from non-angiosperms.  Suggestions? ''Should probably invite Barbara Ambrose (fern evo-devo)''
 ==Other Items==

← Older revision		Revision as of 00:32, 14 October 2010
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	many of the older items that are on SF are pretty straightforward to deal with, but we will need to either spend one or two meetings talking about them or get a commitment from all curators to look at them and approve them (or not) on SF (see [[Old SF tracker items, fall 2010]])		many of the older items that are on SF are pretty straightforward to deal with, but we will need to either spend one or two meetings talking about them or get a commitment from all curators to look at them and approve them (or not) on SF (see [[Old SF tracker items, fall 2010]])
		+
		+	''We need to make an effort to respond to older items, especially those requested by users. Will try to address these older items through SF and deal with as many of them that way as we can.''

← Older revision		Revision as of 00:30, 14 October 2010
Line 107:		Line 107:
	We will go over the technical aspects in more detail during the Oct. 20th conference call, when Ramona is at Cornell with Ale.		We will go over the technical aspects in more detail during the Oct. 20th conference call, when Ramona is at Cornell with Ale.

−	''JE said after the call that he found out what the problem was and did a manual fix, but the better solution would be to have it one the GO DbX refs. Ask Chris M about?''	+	''JE said after the call that he found out what the problem was and did a manual fix, but the better solution would be to have it one the GO DbX refs. Ask Chris M about this again.''

@@ Line 46: / Line 46: @@
 Any comments or changes?
-From PJ: Top priority for the short term should be addressing the term lack are lacking is_a parents. This will require work on upper level structure for non-material entities.
+''From PJ: Top priority for the short term (mid-December) should be addressing the term that are lacking is_a parents. This will require work on upper level structure for non-material entities. The longer term (mid-February) goal for the next release will involve restructuring of the PGDSO, but we should begin working on that now.''
 '''Prioritizing work that needs to be done:'''
@@ Line 60: / Line 74: @@
 (HP=higher priority, LP=lower priority, MP= medium priority, ?=need to decide priority)
 *'''''(HP)''''' Merging the plant structure and plant developmental stages ontologies-
@@ Line 75: / Line 80: @@
 proposed file name: plant_ontology.obo?  There is already an old merged one on the SVN.
-''Done- plant_ontology.obo''
+''Done- plant_ontology.obo. Don't need to use 'test' suffix any more.''
 *'''''(HP)''''' is_a parents for remaining terms (will require work on upper level structure for non-material entities)
@@ Line 85: / Line 90: @@
 Laurel will ask BS what stage we are in the acceptance process.  is_a completeness is a priority for this.
-BS- Add BFO terms to PSO and PGDSO, filling in the missing parents will help with this process.  The top level parent term "all" is problematic and should have a definition that states :'this is an artefact created by the AmiGO browser.  Inclusion is required"
+BS- Add BFO terms to PSO and PGDSO, filling in the missing parents will help with this process.  The top level parent term "all" is problematic and should have a comment that states :'this is an artefact created by the AmiGO browser.  Inclusion is required. All should be redefined as 'an entity that exists'."
-''Not sure how we do this since it does not show up in OE.  It is present in GO, but does not have a definition there. ''
+''Not sure how we do this since it does not show up in OE.  It is present in GO, but does not have a definition there.  May have to be done in Amigo''
 *'''''(HP)''''' Laurel and Ramona will focus more on adding annotations-
 LC will set up a call with RW and PJ to discuss.  1-2 days per week.  EST libraries, RNA seq datasets.  Lists of candidate papers are being prepared.
-Friday 1:30pm PDT on Skype.  We will discuss the Ilic 2007 paper in Plant Physiology.
+''Friday 1:30pm PDT on Skype.  We will discuss the Ilic 2007 paper in Plant Physiology.''

@@ Line 25: / Line 25: @@
 *'''Amigo browser''': There are no icons for relations that we added (has_part, derives_from). Show up as question marks.
 What about participates_in?
 *The new species annotated by SGN are not reflected in the drop down box on the advanced search page.
@@ Line 33: / Line 35: @@
-''This is another issue with the browser.  Need to request a feature on AmiGO SF tracker for the script to pull in all synonyms based on the NCBI taxon ID and should display common names as well.  ''
+''This is another issue with the browser.  Need to request a feature on AmiGO SF tracker for the script to pull in all synonyms based on the NCBI taxon ID and should display common names as well. Annotation files should just use NCBI id. ''
 ==Priorities for next release==