POC Conf. Call 8-18-10

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 both the live site and the dev site and on the Jaiswal Lab web page.

• Should also be on the Beta site- when we update it next time* Post updated version of index.html to beta branch

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

B. 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.

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 Ramona contacted??

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

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

• UniProt Posted on their "contact us" page

• BAR Sent to Nicholas Provert and Rohan Patel

Feedback on the Beta Release

A. Feedback Box:

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

• We can customize this with additional fields and boxes for more directed responses

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 feelings about the ontologies. 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?

Update on the 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

-We are working on determining where to reassign the terms and contacting the groups that submitted them

PO:0009003: sporophyte 117:

po_anatomy_gene_arabidopsis_tair.assoc

po_anatomy_gene_oryza_gramene.assoc

po_anatomy_qtl_oryza_gramene.assoc

PO:0000056: floral bud 54:

po_anatomy_gene_arabidopsis_tair.assoc

PO:0009004:gametophyte 1:

po_anatomy_gene_oryza_gramene.assoc

PO:0008034: leaf whorl 15802:

po_anatomy_gene_arabidopsis_tair.assoc

PO:0008037: seedling 16:

po_anatomy_gene_arabidopsis_tair.assoc

• We discussed possibly re-configuring the PO web page so that more information shows up for each annotation, so it is clearer to the users how annotations differ from one another- tabled for later after the release comes out.

We discussed whether or not it would be better for the user groups who made the annotations to decide where to move the terms we are uncertain about. In any case, we will need to prepare a list for them including the terms that were moved automatically (because there was only one replacement term), and our suggestions for terms that could be replaced by multiple terms. They will need to approve any movement of annotations.

2. Notices are being posted on the PO mail lists: po-announce, po-dev, the PO web page and the Jaiswal lab web page that the beta version is available for review.

Done Ramona and Lol will work on an announcement. Dennis will also send this to the BSA for posting in their Plant Sciences Bulletin. Needs to get to BSA by the end of the week.

3. The documentation page will be posted on the POwiki page and the PO webpage with details of the changes made in the new release.

-wiki page has been created. We will load documentation of changes as we go along.

Ramona and Lol will discuss what needs to go on this page, and get it posted.

Contacting user groups:

g

Contacting potential Reviewers:

Next meeting scheduled for: Weds, Aug 25th, 10am