Difference between revisions of "POC Conf. Call 8-18-10"

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'''POC meeting, Webex Conference Call; Date: Aug 18th, 2010 10am (PDT)'''
 
'''POC meeting, Webex Conference Call; Date: Aug 18th, 2010 10am (PDT)'''
  
−
In attendance:  
+
In attendance: Laurel Cooper, Justin Elser, Justin Preece, Ramona Walls,  Barry Smith.
  
−
POC members:
+
Absent: Alejandra Gandolfo, Pankaj Jaiswal, Chris Mungal, Dennis Stevenson.
  
−
Absent:  
+
Collaborators: none
  
−
Collaborators:
+
Acceptance of the minutes from the 8-11-10 meeting? All in favor?
 +
''There were no additions, deletions or changes to the minutes of the last meeting.''
  
  
−
Acceptance of the minutes from the 8-11-10 meeting? All in favor?
+
==Status and Update of Progress: PO Release==
−
 
 
  
  
 +
===Beta Browser is Up!- Notices sent out and posted:===
  
 +
[http://beta.plantontology.org:8080/amigo/go  Aug 2010 Beta PO]. 
  
−
==Status and Update of Progress: PO Release==
+
From Ramona:
 +
''I am having a problem with browsing the upper level of the beta browser. When I click on the plus sign to expand the children of plant structure, it works fine, but when I click on the plus sign of next to any of the direct children of plant structure (such as plant organ or collective plant structure), instead of expanding those terms, it collapses plant structure. The only way to expand those terms is to first select one of them, and then click on the plus sign. I have not noticed this problem with any of the lower level terms, but I have not explored intensively. This behavior does not occur in the dev browser or the live browser. I am using Safari.''
  
 +
Anyone else seeing this?  ''We looked at the beta browser and observed the behavior Ramona described.  JE was not sure what would cause it.''
  
−
===.  Beta Browser is Up!- Notices sent out and posted:===
+
Suggestions?? Fixes?
  
−
[http://beta.plantontology.org:8080/amigo/go  Aug 2010 Beta PO].
+
'''A.  Notices posted on "What's New" on the live, dev and the beta sites and on the [http://jaiswallab.cgrb.oregonstate.edu/ Jaiswal Lab web page].'''
  
−
A.  Notices posted on "What's New" on both the live site and the dev site and on the [http://jaiswallab.cgrb.oregonstate.edu/ Jaiswal Lab web page].
+
Note: do we want the contact email to be po-dev@plantontology?  See comments on the Feedback box below:
  
−
*Should also be on the Beta site- when we update it next time*  Post updated version of index.html to beta branch
+
'''B. Announcements sent to: po-dev, po-announce, po-internal.'''
  
−
B. Announcements sent to: po-dev, po-announce, po-internal.
 
  
−
C. Announcement for Plant Sciences Bulletin:
+
'''C. Announcement for Plant Sciences Bulletin:'''
−
Note that this is not for the beta version but the live version due to the timing.
+
Note: that this is not for the '''beta version''' but the '''live version''' due to the timing.
 
Sent to PJ for review 8/12/10
 
Sent to PJ for review 8/12/10
  
−
Dennis will also send this to the BSA for posting on their website.
+
Dennis will also send this to the BSA for posting on their website- but should wait to do this until after the release comes out~ mid September.
 +
 
 +
''Ramona will follow up with Dennis and see what the status of this is.''
  
 
===Announcements sent to user groups===
 
===Announcements sent to user groups===
Line 58: Line 63:
 
*[http://fgp.huck.psu.edu/tribedb/index.pl PlantTribes] Sent to: PI: Claude dePamphilis (Penn State) cwd3@psu.edu
 
*[http://fgp.huck.psu.edu/tribedb/index.pl PlantTribes] Sent to: PI: Claude dePamphilis (Penn State) cwd3@psu.edu
  
−
*[http://www.columbia.edu/cu/traitnet/index.html TraitNet]  Ramona contacted??
+
*[http://www.columbia.edu/cu/traitnet/index.html TraitNet]  Sent to coordinators Farshid Ahrestani (fa2260@columbia.edu) and Dan Bunker (dbunker@njit.edu)
  
−
* [http://apps.cimmyt.org/english/wpp/gen_res/index.cfm CIMMYT, Mexico]  [http://www.generationcp.org/ Generation Challenge Program] Sent to: Rosemary Shrestha
+
* [http://apps.cimmyt.org/english/wpp/gen_res/index.cfm CIMMYT, Mexico]  [http://www.generationcp.org/ Generation Challenge Program] Sent to: Rosemary Shretha
  
 
*[http://www.brenda-enzymes.org/ BRENDA] Sent to:project leader  [http://www.brenda-enzymes.org/images/email_dschomburg.png Prof. Dr. Dietmar Schomburg]
 
*[http://www.brenda-enzymes.org/ BRENDA] Sent to:project leader  [http://www.brenda-enzymes.org/images/email_dschomburg.png Prof. Dr. Dietmar Schomburg]
Line 68: Line 73:
 
*[http://www.bar.utoronto.ca/ BAR] Sent to Nicholas Provert and Rohan Patel
 
*[http://www.bar.utoronto.ca/ BAR] Sent to Nicholas Provert and Rohan Patel
  
−
===Feedback on the Beta Release===
+
'''Others:?'''
  
−
'''A.  Feedback Box:'''
+
OBI- Is Helen Parkinson on the mailing list? - not on po-dev
  
−
New link to [http://beta.plantontology.org:8080/db/feedback/send_feedback feedback box] on beta site- emails will go to po-internal
+
Cell Ontology- Already gone to Terry and Alex
  
−
*We can customize this with additional fields and boxes for more directed responses
+
obo-discuss@lists.sourceforge.net (OBO-Foundry)
  
 +
GO Friends list- yes
  
−
'''B.  Response emails'''
+
Trish Whetzel and BioPortal- ''BS also mentioned contacting her as well.  Laurel will send it to her''
  
−
On the notices, we ask the users to respond to po-dev@plantontology. Do we really want people responding to po-dev??
+
===Feedback on the Beta Release===
  
−
That goes out to 68 people, many of who, I suspect would rather not take part in lengthy discussions of user feelings about the ontologies.  Maybe we should set up a new email such as po-feedback that would just go to the internal group?
+
'''A.  Feedback Box:'''
  
−
(Note: We need to define the function of each of the mailing lists: po, po-dev, po-announce, po-internal). I think po-announce, po-internal are fine, but what are the other 2 supposed to be for?
+
New link to [http://beta.plantontology.org:8080/db/feedback/send_feedback feedback box] on beta site- emails will go to '''po-internal'''
  
−
=== Annotations that have no term associated with them===
+
*Laurel and Ramona are working on some changes to customize this with additional fields and boxes for more directed responses
  
−
-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]]
+
Note: It would be better if the feedback box could fill in the relative link automatically from the page.  Is this possible??
 +
"eg: Refer to URL:    http://www.plantontology.org/index.html "
  
 +
''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.''
  
−
'''A.  TAIR'''
 
−
- 8/13/10 message sent to Donghui, Kate and Tanya:
 
−
"The main issues are with the annotations associated with the following PO terms which were obsoleted in the beta version:
 
−
PO:0009003: sporophyte  1  (from: po_anatomy_gene_arabidopsis_tair.assoc)
 
−
PO:0000056: floral bud  54: (from:  po_anatomy_gene_arabidopsis_tair.assoc)
 
−
PO:0008037:  seedling 16  (from po_anatomy_gene_arabidopsis_tair.assoc)
 
−
The first three will need to be looked at to determine where to beat put them.  We have put our recommendations or suggestions on the spreadsheet
 
  
−
PO:0008034: leaf whorl  15,802: (from po_anatomy_gene_arabidopsis_tair.assoc) These ones are pretty straightforward- we recommend to move them all to the new term collective leaf structure PO:0025022
+
'''B. Response emails'''
  
−
Spreadsheet: [[File:TAIR_dangling_annotations_(LC_8-13-10).pdf]]
+
On the notices, we ask the users to respond to po-dev@plantontology. Do we really want people responding to po-dev??
  
  
−
'''B.  Gramene'''
+
That goes out to 68 people, many of who, I suspect would rather not take part in lengthy discussions of user and or reviewers feelings about the ontologies.  Also, should the reviewers responses should go to po-internal not the po-dev list?  But we do not want to publish the po-internal email address.
−
- 8/13/10 message sent to gramene@gramene.org contact email.  Ken replied and said that Pankaj was the best person to look at these.  
 
  
−
[[File:Gramene_dangling_annotations_(LC_8-13-10).pdf‎]]
+
'''Maybe we should set up a new email such as po-feedback that would just go to the internal group?'''
 +
BS suggested that it would be better and more consistent with OBO-Foundry practices to have the responses go to a new list called po-discuss@plantontology.org
  
−
===Contacting potential Reviewers:===
+
''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.''
  
−
''We discussed what aspects of the ontology we should ask each reviewer to focus on. See comments in parentheses, in italics.  
+
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.
  
−
We will prepare a general letter to go to all reviewers, with a place where each letter can be customized for the specific reviewer.
 
  
−
Lol and Ramona will send the letters to Dennis, so he can contact the reviewers that he knows personally (those marked with an asterix).''
+
(Note: We need to define the function of each of the mailing lists: po, po-dev, po-announce, po-internal).  I think po-announce, po-internal are fine, but what are the other 2 supposed to be for?
 +
''We all agreed that these need to be reviewed and we need to deal with the spam problem as well.
 +
''
  
 +
===Contacting potential Reviewers:===
  
−
*So the reviewers can access the .obo and OWL files, they should be made available on the download page (http://www.plantontology.org/download/download.html#download).  On all three sites or just on the beta site??**
+
*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.
  
−
Potential reviewers, areas of expertise, and contact information (''suggestions for portions to review in italics''):
+
*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.
  
−
'''Sarah Hake*''' UC Berkeley, The Plant Gene Expression Center (''floral terms, plant tissue or plant cell'')
+
*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). 
 +
On all three sites or just on the beta site??** '' It should be on both Live and the Beta at least.
 +
''
 +
''BS suggested we should add a sentence to the effect that they are responding to a list that is open for others to view.''
  
−
Maize inflorescence development
+
''We will modify the signature box to just include the 3 PIs on the project.''
  
−
“Our laboratory is interested in plant morphology. We are taking a genetic approach to understand the processes that regulate form and function. We are primarily interested in how shoot meristems initiate organs. The knotted1 gene and related knox (knotted1-like homeobox) genes appear to play a critical role in this process. We are studying what regulates knox genes and what genes are regulated by KNOX proteins.”
+
'''*Potential reviewer, institution, email address, suggestions for portions to review:'''
  
−
hake@berkeley.edu
+
'''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 (''whole plant, collective plant structure,  plant tissue'')
+
'''Quentin Cronk*''', Biodiversity Research Center, University of British Columbia, Quentin.cronk@ubc.ca,collective plant structure (PO:0025007)
  
−
“Our lab integrates comparative genomics, molecular developmental biology and evolutionary biology to study plant form. We are interested in the how different morphologies evolve in plants, as well as the functional significance of morphological differences between species.
+
'''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)
−
Our main model organisms for this include the Leguminosae (floral morphology) and black cottonwood, Populus trichocarpa (adaptive evolution of trees).”
 
  
−
Quentin.cronk@ubc.ca
+
'''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
  
−
'''Paula Rudall*''' Head of Micromorphology Section, Royal Botanic Garden, Kew (''overall ontology structure, plant cell, male and female gametophyte'')
+
'''Elena Kramer*''', Harvard University, Organismic and Evolutionary Biology, ekramer@oeb.harvard.edu, plant organ (PO:0009008), flower (PO:0009046)
  
−
plant anatomy expert, monocot systematics
+
'''Neelima Sinha''', UC Davis, nrsinha@ucdavis.edu, plant organ (PO:0009008), especially phyllome (PO:0006001)
  
−
“Use of micromorphology as a source of data in assessments of homology and phylogeny. Focused analytical studies on systematic morphology, anatomy, embryology and palynology in a phylogenetic and developmental-genetic context. A primary focus is to address questions about the evolutionary origin of flowers, including targeted comparative ontogenetic studies on a phylogenetically broad range of angiosperms in which the inflorescence–flower boundary is ambiguous, especially the monocot family Triuridaceae, the eudicot family Euphorbiaceae and the early-divergent angiosperm family Hydatellaceae. A second key research focus is on plant embryology and pollen morphology, including the developmental bases for key innovations in the seed-plant megagametophyte and microgametophyte.  Research portfolio of over 200 research papers and books, including a textbook, Anatomy of Flowering Plants. Collaborative research includes year-out placement students and PhD students, plus a broad international network. Kew’s Micromorphology lab attracts collaborations and research visits from considerable numbers of international researchers.”
+
'''Chelsea Specht*''', UC Berkeley, Plant and Microbial Biology, cdspecht@berkeley.edu, plant organ (PO:0009008), especially plant axis (PO:0025004)
  
−
p.rudall@kew.org
+
'''Rob Martienssen*''', Cold Spring Harbor Laboratory, martiens@cshl.edu, shoot system (PO:0009006), how does our terminology relate to gene annotation
  
−
'''Sarah Mathews*''' Harvard University, Arnold Arboretum (''shoot system, plant organ, plant tissue; how does our terminology relate to gene annotation, especially with respect to gymnosperms'')
+
'''Peter Raven*''', Missouri Botanical Garden peter.raven@mobot.org, upper level structure [direct children of plant structure (PO:0009011)]
  
−
Phytochromes and phylogeny, gymnosperm tree of life
+
'''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
  
−
“Evolution in the plant kingdom is marked by the successive origin of new forms, including the land plants, tracheophytes, seed plants, and flowering plants. The origin of these forms was followed by a period of remarkable innovation, diversification, and extinction, leading to the establishment of the modern land flora. We are interested in the patterns and mechanisms of plant diversification.”
+
'''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
  
−
smathews@oeb.harvard.edu
+
'''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?
  
−
'''Elena Kramer*''' Harvard University, Organismic and Evolutionary Biology (''plant organ, reproductive structures, flower'')
+
'''Rob Last''', Michigan State University, Biochemistry and Molecular Biology, lastr@msu.edu, plant cell (PO:0009002), trichomes (PO:0000282)
  
−
Floral morphology and development
+
'''Robert Stevens''', University of Manchester, Bio and Health Informatics Group, robert.stevens@manchester.ac.uk, entire ontology, upper level structure
  
−
“My lab is very broadly interested in the evolution of floral morphology. We use molecular, morphological, and phylogenetic approaches to study how flowers have changed over the course of evolutionary time. Research projects in the lab cover a diverse set of topics, including gene lineage evolution and the effects of gene duplication, the morphological diversification of floral parts such as petals and fruits, and the evolutionary and ecological significance of pollinator interactions. Within this context, one of our major focus areas is the development of Aquilegia (columbine) as a new system for studying evolutionary and ecological questions.”
+
'''Farshid Ahrestani*''', Columbia University, TraitNet, fa2260@columbia.edu, entire ontology, with reference to whatever structures of interest to Traitnet
  
−
ekramer@oeb.harvard.edu
+
'''Sandy Knapp*''', British Museum, s.knapp@nhm.ac.uk, plant tissue (PO:0009007), overall structure of the ontology
  
−
'''Neelima Sinha''' UC Davis (''plant organ, phyllome'')
+
'''Richard Halse''', Oregon State University,  email:halser@science.oregonstate.edu,
 +
Research area: Taxonomy of the Hydrophyllaceae; ecology and taxonomy of Sidalcea; floristics of Oregon.
  
−
Leaf evolution and development
+
collective plant structure (PO:0025007), cardinal organ part  (PO:0025001)?
  
−
“Sinha Lab at the University of California, Davis focuses on studying fundamental mechanisms of leaf development, using model organisms such as tomato and maize. In order to understand how leaves evolved we are also looking at other organisms like Welwitschia mirabilis, ferns, cycads and basal and derived Angiosperms. Our website will let visitors learn about not only the projects we are working on, but also about the people working on these projects.”
+
'''Rich Zobel''', USDA, rich.zobel@ars.usda.gov, root system (PO:0025025), root (PO:0009005); note that he has already submitted suggestions
  
−
nrsinha@ucdavis.edu
+
'''Austin Mast*''', Robert K. Godfrey Herbarium, Florida State University amast@bio.fsu.edu, cardinal organ part (PO:0025001)
  
−
'''Chelsea Specht*''' UC Berkeley, Plant and Microbial Biology (''reproductive terminology, plant organ, collective plant structure'')
+
'''Lukas Mueller and Naama Menda''', Solanum Genomics Network, Need email, tuber (PO:0004543) and all of its part_of and is_a children
  
−
plant systematics, Zingiberales, plant anatomy expert
+
=== Annotations that have no term associated with them===
  
−
“The Specht Lab focuses on studies in Plant form and function. We use traditional morphological techniques combined with molecular and evolutionary biology to study the natural diversity of plants and to help better understand the forces creating and sustaining this diversity.”
+
-Laurel compiled a list of the terms that have been obsoleted and how many annotations that are associated with them.  
  
−
cdspecht@berkeley.edu
+
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]]
  
−
'''Rob Martienssen*''' Cold Spring Harbor Laboratory (''ow does our terminology relate to gene annotation, collective plant structure, root system, shoot system'')
+
''In progress....
 +
''
  
−
“… a plant geneticist, working on transposons, genome biology, and developmental genetics of maize and the model plant Arabidopsis thaliana…”
+
'''A.  TAIR'''
 +
- 8/13/10 message sent to Donghui, Kate and Tanya:
  
−
martiens@cshl.edu
+
"The main issues are with the annotations associated with the following PO terms which were obsoleted in the beta version:
  
−
'''Peter Raven*''' Missouri Botanical Garden (''whole plant, plant organ, collective plant structure'')
+
PO:0009003: sporophyte  1  (from: po_anatomy_gene_arabidopsis_tair.assoc)
  
−
“General Research Interests: Onagraceae, conservation, sustainable development, plant geography
+
PO:0000056: floral bud  54: (from:  po_anatomy_gene_arabidopsis_tair.assoc)
−
Research Emphases: To summarize the relationships among the species and genera of Onagraceae using the precise definitions and methodologies of phylogenetic systematics. Investigate the biogeography of plants, especially in the tropics and Southern Hemisphere”
 
−
peter.raven@mobot.org
 
  
−
'''Gar Rothwell*''' Ohio University, Department of Environmental and Plant Biology (''overall structure of the ontology, especially how it relates to fossil taxa; any terms were might be missing for fossils?'')
+
PO:0008037:  seedling 16  (from po_anatomy_gene_arabidopsis_tair.assoc)
  
−
Phylogenetic Systematics, 
Evolutionary Developmental Plant Biology, Fossil Plants
+
The first three will need to be looked at to determine where to best put them.  We have put our recommendations or suggestions on the spreadsheet
  
−
“Studies of fossil and living land plants are directed toward a fuller understanding of phylogeny and evolution. These are explored using data from morphological, anatomical, ultrastructural, developmental, and molecular characters. Evaluations of ontogeny, reproductive biology, and organismal interactions are emphasized in interpreting development of the modern flora within the context of evolutionary ecology.”
+
PO:0008034: leaf whorl  15,802: (from po_anatomy_gene_arabidopsis_tair.assoc) These ones are pretty straightforward- we recommend to move them all to the new term collective leaf structure PO:0025022
  
−
rothwell@ohio.edu
+
Spreadsheet: [[File:TAIR_dangling_annotations_(LC_8-13-10).pdf]]
  
−
'''Peter Linder*''' Universität Zürich, Institut für Systematische Botanik, director of botanical garden (''plant tissue, plant organ, vascular system; review the ontology from an ecological perspective'')
 
  
−
plant anatomy expert
+
'''B.  Gramene'''
 +
- 8/13/10 message sent to gramene@gramene.org contact email.  Ken replied and said that Pankaj was the best person to look at these.
  
−
Evolution of the Cape flora,
Systematics of Restionaceae, Diseae (Orchidaceae)
+
[[File:Gramene_dangling_annotations_(LC_8-13-10).pdf‎]]
−
Danthonioideae (Poaceae), Evolution of Wind Pollination
Biogeography in particular phytogeography, of Africa and the Southern Hemisphere generally
 
  
−
peter.linder@systbot.uzh.ch
+
===Documentation page===
 +
Posted on the POwiki [[Summary_of_changes_to_the_Plant_Ontology]] page with link from the PO web page with details of the changes made in the new release.
  
−
'''Chris Hardy*''' Millersville University, Herbarium (''collective plant structure, plant organ; review ontology from a teaching perspective; how will it appeal to the next generation of plant scientists'')
+
I have already had a request from TAIR for an explanation about floral bud, so It would be good to have this on the changes page.
  
−
plant anatomy expert
+
Could everyone please review this for accuracy and completeness?  Thanks a lot
  
−
Plant Systematics & Phylogenetics
+
''Laurel and Ramona are working on updating the participants info on the front page and the documentation pages- Justin will load onto Live and Beta sites once the html files are posted on the svn.''
−
Floral Morphogenesis & Anatomy
 
−
Botanical Illustration
 
  
−
'''Rob Last''' Michigan State University, Biochemistry and Molecular Biology (''plant cell, trichomes'')
+
===No meeting scheduled for: ''' Weds, Aug 25th, 10am===
 +
Laurel will be available to discuss any issues if need be.  We can Skype or Webex if anyone wants to.
  
−
Plant genomics, Trichomes project
+
On Vacation:  Pankaj (till Sept 3rd) but may still take part by skype, Ramona (till sept 7th), Laurel Aug 27th-Sept 8th.
−
 
 
−
“Our group uses genetic, genomic and biochemical approaches to understand the regulation of biosynthetic pathways of importance to flowering plants and the animals that depend on plants for sustenance.”
 
−
 
 
−
lastr@msu.edu
 
−
 
 
−
'''Robert Stevens''' University of Manchester, Bio and Health Informatics Group (''entire ontology, upper level structure'')
 
−
 
 
−
Ontology expert- needs OWL format
 
−
 
 
−
robert.stevens@manchester.ac.uk
 
−
 
 
−
 
 
−
'''Farshid Ahrestani''' Columbia University, TraitNet (''shoot system, plant organ, or entire ontology with reference to the particular structures his group is interested in'')  
 
−
 
 
−
Bioinformatics, Semantic web applications using PO. Post-doc in Shahid Naeem's lab.
 
−
 
 
−
 
 
−
'''Sandy Knapp*''' British Musem
 
−
 
 
−
Systematics, solanaceae
 
−
 
 
−
s.knapp@nhm.ac.uk
 
−
 
 
−
 
 
−
Also to consider: 
 
−
 
 
−
'''Richard Halse''', Oregon State
 
−
 
 
−
 
 
−
'''Rich Zobel''' <Rich.zobel@ars.usda.gov> (''Roots'')
 
−
 
 
−
 
 
−
'''Austin Mast''' Robert K. Godfrey Herbarium, Florida State University
 
−
 
 
−
Using PO to code USDA key for legumes. Involved with Morphbank.
 
−
 
 
−
amast@bio.fsu.edu
 
−
 
 
−
===Documentation page===
 
−
Posted on the POwiki [[Summary_of_changes_to_the_Plant_Ontology]] page with link from the PO web page with details of the changes made in the new release.
 
−
 
 
−
Could everyone please review this for accuracy and completeness?  Thanks a lot
 
  
−
===Next meeting scheduled for: ''' Weds, Aug 25th, 10am===
+
===Next meeting scheduled for: ''' Weds, Sept 8th, 10am===

Latest revision as of 16:45, 23 September 2010

POC meeting, Webex Conference Call; Date: Aug 18th, 2010 10am (PDT)

In attendance: Laurel Cooper, Justin Elser, Justin Preece, Ramona Walls, Barry Smith.

Absent: Alejandra Gandolfo, Pankaj Jaiswal, Chris Mungal, Dennis Stevenson.

Collaborators: none

Acceptance of the minutes from the 8-11-10 meeting? All in favor? There were no additions, deletions or changes to the minutes of the last meeting.


Status and Update of Progress: PO Release

Beta Browser is Up!- Notices sent out and posted:

Aug 2010 Beta PO.

From Ramona: I am having a problem with browsing the upper level of the beta browser. When I click on the plus sign to expand the children of plant structure, it works fine, but when I click on the plus sign of next to any of the direct children of plant structure (such as plant organ or collective plant structure), instead of expanding those terms, it collapses plant structure. The only way to expand those terms is to first select one of them, and then click on the plus sign. I have not noticed this problem with any of the lower level terms, but I have not explored intensively. This behavior does not occur in the dev browser or the live browser. I am using Safari.

Anyone else seeing this? We looked at the beta browser and observed the behavior Ramona described. JE was not sure what would cause it.

Suggestions?? Fixes?

A. Notices posted on "What's New" on the live, dev and the beta sites and on the Jaiswal Lab web page.

Note: do we want the contact email to be po-dev@plantontology? See comments on the Feedback box below:

B. Announcements sent to: po-dev, po-announce, po-internal.


C. Announcement for Plant Sciences Bulletin: Note: that this is not for the beta version but the live version due to the timing. Sent to PJ for review 8/12/10

Dennis will also send this to the BSA for posting on their website- but should wait to do this until after the release comes out~ mid September.

Ramona will follow up with Dennis and see what the status of this is.

Announcements sent to user groups

  • TAIR email: curator@arabidopsis.org
  • NASC sent to: email: bioinfo@arabidopsis.info

(not really clear who to send it to here)

  • MaizeGDB Carolyn Lawrence, Mary Schaeffer, Jack Gardiner. No generic contact address
  • PlantTribes Sent to: PI: Claude dePamphilis (Penn State) cwd3@psu.edu
  • TraitNet Sent to coordinators Farshid Ahrestani (fa2260@columbia.edu) and Dan Bunker (dbunker@njit.edu)
  • BAR Sent to Nicholas Provert and Rohan Patel

Others:?

OBI- Is Helen Parkinson on the mailing list? - not on po-dev

Cell Ontology- Already gone to Terry and Alex

obo-discuss@lists.sourceforge.net (OBO-Foundry)

GO Friends list- yes

Trish Whetzel and BioPortal- BS also mentioned contacting her as well. Laurel will send it to her

Feedback on the Beta Release

A. Feedback Box:

New link to feedback box on beta site- emails will go to po-internal

  • Laurel and Ramona are working on some changes to customize this 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?? "eg: Refer to URL: http://www.plantontology.org/index.html "

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.


B. Response emails

On the notices, we ask the users to respond to po-dev@plantontology. Do we really want people responding to po-dev??


That goes out to 68 people, many of who, I suspect would rather not take part in lengthy discussions of user and or reviewers feelings about the ontologies. Also, should the reviewers responses should go to po-internal not the po-dev list? But we do not want to publish the po-internal email address.

Maybe we should set up a new email such as po-feedback that would just go to the internal group? BS suggested that it would be better and more consistent with OBO-Foundry practices to have the responses go to a new list called po-discuss@plantontology.org

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-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.


(Note: We need to define the function of each of the mailing lists: po, po-dev, po-announce, po-internal). I think po-announce, po-internal are fine, but what are the other 2 supposed to be for? We all agreed that these need to be reviewed and we need to deal with the spam problem as well.

Contacting potential Reviewers:

  • 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.

On all three sites or just on the beta site??** It should be on both Live and the Beta at least. BS suggested we should add a sentence to the effect that they are responding to a list that is open for others to view.

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:

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)

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

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)

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

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

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?

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

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

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

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

Annotations that have no term associated with them

-Laurel compiled a list of the terms that have been obsoleted and how many annotations that are associated with them.

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....

A. TAIR - 8/13/10 message sent to Donghui, Kate and Tanya:

"The main issues are with the annotations associated with the following PO terms which were obsoleted in the beta version:

PO:0009003: sporophyte 1 (from: po_anatomy_gene_arabidopsis_tair.assoc)

PO:0000056: floral bud 54: (from: po_anatomy_gene_arabidopsis_tair.assoc)

PO:0008037: seedling 16 (from po_anatomy_gene_arabidopsis_tair.assoc)

The first three will need to be looked at to determine where to best put them. We have put our recommendations or suggestions on the spreadsheet

PO:0008034: leaf whorl 15,802: (from po_anatomy_gene_arabidopsis_tair.assoc) These ones are pretty straightforward- we recommend to move them all to the new term collective leaf structure PO:0025022

Spreadsheet: File:TAIR dangling annotations (LC 8-13-10).pdf


B. Gramene - 8/13/10 message sent to gramene@gramene.org contact email. Ken replied and said that Pankaj was the best person to look at these.

File:Gramene dangling annotations (LC 8-13-10).pdf

Documentation page

Posted on the POwiki Summary_of_changes_to_the_Plant_Ontology page with link from the PO web page with details of the changes made in the new release.

I have already had a request from TAIR for an explanation about floral bud, so It would be good to have this on the changes page.

Could everyone please review this for accuracy and completeness? Thanks a lot

Laurel and Ramona are working on updating the participants info on the front page and the documentation pages- Justin will load onto Live and Beta sites once the html files are posted on the svn.

No meeting scheduled for: Weds, Aug 25th, 10am

Laurel will be available to discuss any issues if need be. We can Skype or Webex if anyone wants to.

On Vacation: Pankaj (till Sept 3rd) but may still take part by skype, Ramona (till sept 7th), Laurel Aug 27th-Sept 8th.

Next meeting scheduled for: Weds, Sept 8th, 10am
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