POC Conf. Call 8-18-10 - Revision history

Cooperl: /* Feedback on the Beta Release */

2010-09-23T16:45:00Z

Feedback on the Beta Release

Elserj at 22:48, 30 August 2010

2010-08-30T22:48:18Z

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

2010-08-26T17:38:47Z

Annotations that have no term associated with them

Cooperl: /* Contacting potential Reviewers: */

2010-08-19T18:03:09Z

Contacting potential Reviewers:

Cooperl: /* Contacting potential Reviewers: */

2010-08-19T17:50:17Z

Contacting potential Reviewers:

Cooperl: /* Contacting potential Reviewers: */

2010-08-19T17:49:53Z

Contacting potential Reviewers:

Cooperl: /* Contacting potential Reviewers: */

2010-08-19T17:48:10Z

Contacting potential Reviewers:

Cooperl: /* Contacting potential Reviewers: */

2010-08-19T17:40:54Z

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Cooperl: /* Feedback on the Beta Release */

2010-08-19T17:35:06Z

Feedback on the Beta Release

Cooperl: /* Contacting potential Reviewers: */

2010-08-19T17:02:02Z

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← Older revision		Revision as of 16:45, 23 September 2010
Line 112:		Line 112:
	''Issue is that Chris Sullivan who handles the Mailman server is on vacation, although he is supposedly going to be around today. Laurel will see if he will be able to set this up for us in a timely manner. Otherwise the letters will have to go out with the responses addressed to po-dev.''		''Issue is that Chris Sullivan who handles the Mailman server is on vacation, although he is supposedly going to be around today. Laurel will see if he will be able to set this up for us in a timely manner. Otherwise the letters will have to go out with the responses addressed to po-dev.''

−	Note: after the meeting po-~~disciss~~@plantontology was set up and the members of po-internal were added to it. This is the address that will be used in the letters to the reviewers. Thanks to Chris Sullivan and Justin Elser for helping with this on short notice.	+	Note: after the meeting po-discuss@plantontology was set up and the members of po-internal were added to it. This is the address that will be used in the letters to the reviewers. Thanks to Chris Sullivan and Justin Elser for helping with this on short notice.

@@ Line 1: / Line 1: @@
 '''POC meeting, Webex Conference Call; Date: Aug 18th, 2010 10am (PDT)'''
-In attendance:  Laurel Cooper, Justin Elsner, Justin Preece, Ramona Walls,  Barry Smith.
+In attendance:  Laurel Cooper, Justin Elser, Justin Preece, Ramona Walls,  Barry Smith.
 Absent: Alejandra Gandolfo, Pankaj Jaiswal, Chris Mungal, Dennis Stevenson.

@@ Line 183: / Line 183: @@
 -Laurel compiled a list of the terms that have been obsoleted and how many annotations that are associated with them.
-There were only 11 and only 5 of them are problematic: floral bud, gametophyte, leaf whorl, seedling and sporophyte.  [[File:Obseleted_terms_(LC_8-10-10).pdf‎]]
+There were only 10 and only 5 of them are problematic: floral bud, gametophyte, leaf whorl, seedling and sporophyte.  [[File:Obseleted_terms_(LC_8-10-10).pdf‎]]
 ''In progress....

@@ Line 175: / Line 175: @@
 '''Rich Zobel''', USDA, rich.zobel@ars.usda.gov, root system (PO:0025025), root (PO:0009005); note that he has already submitted suggestions
-'''Austin Mast''', Robert K. Godfrey Herbarium, Florida State University	amast@bio.fsu.edu, cardinal organ part (PO:0025001)
+'''Austin Mast*''', Robert K. Godfrey Herbarium, Florida State University	amast@bio.fsu.edu, cardinal organ part (PO:0025001)
 '''Lukas Mueller and Naama Menda''', Solanum Genomics Network, Need email, tuber (PO:0004543) and all of its part_of and is_a children

@@ Line 134: / Line 134: @@
 ''We will modify the signature box to just include the 3 PIs on the project.''
-*Potential reviewer, institution, email address, suggestions for portions to review
+'''*Potential reviewer, institution, email address, suggestions for portions to review:'''
 '''Sarah Hake*''',	UC Berkeley, The Plant Gene Expression Center, 	hake@berkeley.edu, flower (PO:0009046), collective phyllom structure PO:0025023

@@ Line 136: / Line 136: @@
 *Potential reviewer, institution, email address, suggestions for portions to review
-Sarah Hake*,	UC Berkeley, The Plant Gene Expression Center, 	hake@berkeley.edu, flower (PO:0009046), collective phyllom structure PO:0025023
+'''Sarah Hake*''',	UC Berkeley, The Plant Gene Expression Center, 	hake@berkeley.edu, flower (PO:0009046), collective phyllom structure PO:0025023
-Quentin Cronk*,	Biodiversity Research Center, University of British Columbia, Quentin.cronk@ubc.ca,collective plant structure (PO:0025007)
+'''Quentin Cronk*''',	Biodiversity Research Center, University of British Columbia, Quentin.cronk@ubc.ca,collective plant structure (PO:0025007)
-Paula Rudall*, Head of Micromorphology Section, Royal Botanic Garden, Kew	p.rudall@kew.org	plant cell (PO:0009002), male gametophyte (PO:0020091) and female gametophyte (PO:0020092)
+'''Paula Rudall*''', Head of Micromorphology Section, Royal Botanic Garden, Kew	p.rudall@kew.org	plant cell (PO:0009002), male gametophyte (PO:0020091) and female gametophyte (PO:0020092)
-Sarah Mathews*, Harvard University, Arnold Arboretum, smathews@oeb.harvard.edu, shoot system (PO:0009006), plant tissue (PO:0009007), how does our terminology relate to gene annotation, especially with respect to gymnosperms
+'''Sarah Mathews*''', Harvard University, Arnold Arboretum, smathews@oeb.harvard.edu, shoot system (PO:0009006), plant tissue (PO:0009007), how does our terminology relate to gene annotation, especially with respect to gymnosperms
-Elena Kramer*, Harvard University, Organismic and Evolutionary Biology, ekramer@oeb.harvard.edu, plant organ (PO:0009008), flower (PO:0009046)
+'''Elena Kramer*''', Harvard University, Organismic and Evolutionary Biology, ekramer@oeb.harvard.edu, plant organ (PO:0009008), flower (PO:0009046)
-Neelima Sinha, UC Davis, nrsinha@ucdavis.edu, plant organ (PO:0009008), especially phyllome (PO:0006001)
+'''Neelima Sinha''', UC Davis, nrsinha@ucdavis.edu, plant organ (PO:0009008), especially phyllome (PO:0006001)
-Chelsea Specht*, UC Berkeley, Plant and Microbial Biology, cdspecht@berkeley.edu, plant organ (PO:0009008), especially plant axis (PO:0025004)
+'''Chelsea Specht*''', UC Berkeley, Plant and Microbial Biology, cdspecht@berkeley.edu, plant organ (PO:0009008), especially plant axis (PO:0025004)
-Rob Martienssen*, Cold Spring Harbor Laboratory, martiens@cshl.edu, shoot system (PO:0009006), how does our terminology relate to gene annotation
+'''Rob Martienssen*''', Cold Spring Harbor Laboratory, martiens@cshl.edu, shoot system (PO:0009006), how does our terminology relate to gene annotation
-Peter Raven*, Missouri Botanical Garden	peter.raven@mobot.org, upper level structure [direct children of plant structure (PO:0009011)]
+'''Peter Raven*''', Missouri Botanical Garden	peter.raven@mobot.org, upper level structure [direct children of plant structure (PO:0009011)]
-Gar Rothwell*, Ohio University, Department of Environmental and Plant Biology, rothwell@ohio.edu, plant life cycle phase (PO:0028001); upper level structure [direct children of plant structure (PO:0009011)], especially how it relates to fossil taxa; suggestions for terms that might be missing for fossils
+'''Gar Rothwell*''', Ohio University, Department of Environmental and Plant Biology, rothwell@ohio.edu, plant life cycle phase (PO:0028001); upper level structure [direct children of plant structure (PO:0009011)], especially how it relates to fossil taxa; suggestions for terms that might be missing for fossils
-Peter Linder*, Universität Zürich, Institut für Systematische Botanik, director of botanical garden, peter.linder@systbot.uzh.ch	vascular system, PO:0000034); review the ontology from an ecological perspective
+'''Peter Linder*''', Universität Zürich, Institut für Systematische Botanik, director of botanical garden, peter.linder@systbot.uzh.ch	vascular system, PO:0000034); review the ontology from an ecological perspective
-Chris Hardy*, Millersville University, Herbarium, christopher.hardy@millersville.edu, cardinal organ part (PO:0025001); review ontology from a teaching perspective; how will it appeal to the next generation of plant scientists?
+'''Chris Hardy*''', Millersville University, Herbarium, christopher.hardy@millersville.edu, cardinal organ part (PO:0025001); review ontology from a teaching perspective; how will it appeal to the next generation of plant scientists?
-Rob Last, Michigan State University, Biochemistry and Molecular Biology, lastr@msu.edu, plant cell (PO:0009002), trichomes (PO:0000282)
+'''Rob Last''', Michigan State University, Biochemistry and Molecular Biology, lastr@msu.edu, plant cell (PO:0009002), trichomes (PO:0000282)
-Robert Stevens, University of Manchester, Bio and Health Informatics Group, robert.stevens@manchester.ac.uk, entire ontology, upper level structure
+'''Robert Stevens''', University of Manchester, Bio and Health Informatics Group, robert.stevens@manchester.ac.uk, entire ontology, upper level structure
-Farshid Ahrestani*, Columbia University, TraitNet, fa2260@columbia.edu, entire ontology, with reference to whatever structures of interest to Traitnet
+'''Farshid Ahrestani*''', Columbia University, TraitNet, fa2260@columbia.edu, entire ontology, with reference to whatever structures of interest to Traitnet
-Sandy Knapp*, British Museum, s.knapp@nhm.ac.uk, plant tissue (PO:0009007), overall structure of the ontology
+'''Sandy Knapp*''', British Museum, s.knapp@nhm.ac.uk, plant tissue (PO:0009007), overall structure of the ontology
-Richard Halse, Oregon State University,  email:halser@science.oregonstate.edu,
+'''Richard Halse''', Oregon State University,  email:halser@science.oregonstate.edu,
 Research area: Taxonomy of the Hydrophyllaceae; ecology and taxonomy of Sidalcea; floristics of Oregon.
 collective plant structure (PO:0025007), cardinal organ part  (PO:0025001)?
-Rich Zobel, USDA, rich.zobel@ars.usda.gov, root system (PO:0025025), root (PO:0009005); note that he has already submitted suggestions
+'''Rich Zobel''', USDA, rich.zobel@ars.usda.gov, root system (PO:0025025), root (PO:0009005); note that he has already submitted suggestions
-Austin Mast, Robert K. Godfrey Herbarium, Florida State University	amast@bio.fsu.edu, cardinal organ part (PO:0025001)
+'''Austin Mast''', Robert K. Godfrey Herbarium, Florida State University	amast@bio.fsu.edu, cardinal organ part (PO:0025001)
-Lukas Mueller and Naama Menda, Solanum Genomics Network, Need email, tuber (PO:0004543) and all of its part_of and is_a children
+'''Lukas Mueller and Naama Menda''', Solanum Genomics Network, Need email, tuber (PO:0004543) and all of its part_of and is_a children
 === Annotations that have no term associated with them===

@@ Line 122: / Line 122: @@
 *At the last couple of meetings, we discussed what aspects of the ontology we should ask each reviewer to focus on.
 *Laurel and Ramona prepared and distributed (to po-internal) a general letter to go to all reviewers, which can be customized for the specific reviewer.
 *Laurel and Ramona will send the letters to Dennis, so he can contact the reviewers that he knows personally (those marked with an asterix).  Laurel will contact the rest of the reviewers on the list, copying po-internal.
 *So the reviewers can access the obo, flat files and OWL files, they should be made available on the download page (http://www.plantontology.org/download/download.html#download).

← Older revision		Revision as of 17:35, 19 August 2010
Line 111:		Line 111:

	''Issue is that Chris Sullivan who handles the Mailman server is on vacation, although he is supposedly going to be around today. Laurel will see if he will be able to set this up for us in a timely manner. Otherwise the letters will have to go out with the responses addressed to po-dev.''		''Issue is that Chris Sullivan who handles the Mailman server is on vacation, although he is supposedly going to be around today. Laurel will see if he will be able to set this up for us in a timely manner. Otherwise the letters will have to go out with the responses addressed to po-dev.''
		+
		+	Note: after the meeting po-disciss@plantontology was set up and the members of po-internal were added to it. This is the address that will be used in the letters to the reviewers. Thanks to Chris Sullivan and Justin Elser for helping with this on short notice.