POC Conf. Call 8-18-10

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)

• Gramene email: gramene@gramene.org

• MaizeGDB Carolyn Lawrence, Mary Schaeffer, Jack Gardiner. No generic contact address

• VirtualPlant Posted to their "contact us" form

• SoyBase Sent to: Rex Nelson and posted to their "contact us" form.

• Genevestigator Sent to:support@genevestigator.com

• SGN Sent to: Lukas Mueller + Naama Menda and posted to their "contact us"

• OryzaBase Sent to: Yukiko Yamazaki and posted on their "contact us" page.

• 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 Shretha

• BRENDA Sent to:project leader Prof. Dr. Dietmar Schomburg

• UniProt Posted on their "contact us" page

• 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.

• 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.

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