POC Conf. Call 8-18-10

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

In attendance:

POC members:

Absent:

Collaborators:


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:

Aug 2010 Beta PO.

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.

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)
  • CIMMYT, Mexico Generation Challenge Program Sent to: Rosemary Shrestha 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
  • 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- ?

Trish Whetzel

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 made 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 "


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??

Lol: Upload list of po-dev recipients: File:Pov dev mailing list.pdf

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, the reviewers responses should go to po-internal not the po-dev list.

Maybe we should set up a new email such as po-feedback that would just go to the internal group?

(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?

Contacting potential Reviewers:

At the last couple of meetings, we discussed what aspects of the ontology we should ask each reviewer to focus on.

See comments in parentheses, below, in italics.

  • 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??**


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 cel (PO:0009002)l, 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 toTraitnet

Sandy Knapp* British Museum s.knapp@nhm.ac.uk plant tissue (PO:0009007), overall structure of the ontology

Richard Halse Oregon State University Need email 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 11 and only 5 of them are problematic: floral bud, gametophyte, leaf whorl, seedling and sporophyte. File:Obseleted terms (LC 8-10-10).pdf


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

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 9th), Laurel Aug 27th-Sept 8th.

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