POC Conf. Call 12-20-11

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POC meeting, Webex Conference Call; Date: Tuesday Dec 20th, 2011 10am (PST)

In attendance:

POC members:

Absent:


Collaborators: none


Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_12-13-11?

Back to POC Meetings Minutes

PSDSO Revisions: Whole plant development stages

Continued from last week

Trichome terms

Need to address outstanding issues and wrap this up.

Status of New Annotation Files for data release in Dec:

This content below needs updating: Copied from 9-27-11 meeting

Physcomitrella Annotations

LC has been working with DL and SR to get the Physcomitrella annotations added

Gramene Annotations

During the last release cycle, LC worked with the Gramene collaborators to get their files updated. They were also going through a realase as well. Have not received any new annotations, even though they said they should be coming from Gramene in the next 1-2 weeks

Grape and Strawberry

  • LC working on grape file, see sample

What links do we need to use for these and how do we get AmiGO to recognize them?

See notes above

Potato Annotations

LC has been in contact with the group who published the potato genome paper and they are interested in collaborating with us to assign ontology terms to the annotations.

From Dr. Richard Finker (Wageningen, The Netherlands):

"We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."

This will go in the next release, do they have expression data- RNA Seq?

Comments from PJ about Annotation Guidelines

Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info. Maybe co-author it with SR

-This will also be helpful when applying for new grants

-it would be helpful to have a detailed guide on our wiki for collaborators

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