AgBase Meeting Minutes 2008

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10th January 2008

Participants: Fiona McCarthy, Jennifer Deegan

New AgBase Staff

Fiona now has 2 full time GO curators, called Teresia and Divia.
They were previously grad students at Fiona's institute and have attended the GO annotation training camp at Stanford.
They are working to annotate GO chicken/cow and are working on the chicken reference genome effort.

Avian Meeting

Fiona is arranging a training camp in May for avian species:
Conference 19-20 May
Annotation Training 21st-22nd May

The Avian GO Workshop will be held in conjunction with the “Delivering Value from Avian Genomics” conference. Both events will be held at Mississippi State University, with the conference May 19-20 and the workshop scheduled for May 21-22. We expect that the workshop will finish around 11-11:30 so that people have time to catch flights.

Possible Topics to cover

  • Perhaps get prioritisation list of genes from the users?
  • teach basic GO?
  • teach tools?
  • gprofiler is online annotation tool with agricultural species in it, perhaps teach this?
  • It is regularly updated.
  • About 70% of microarray tools do not do agricultural species so are not as good.
  • She is thinking that she could give examples of what GO is used for.
  • Give simple tools introduction.
  • Get gene priority list.

Question: What do the people know about GO and want from it?

Fiona: The expected workshop audience will be a mixture of PIs and graduate students, working mainly with array data. For the conference we are targeting researchers working with chicken, song bird, quail, turkey, condor and other avian species so it likely the workshop will include researchers working in non-chicken avian species.

My concern is that in the 11/2 day span it is unlikely that we will be able to achieve tangible outcomes if we use the ‘jamboree’ format that is focused on experts making GO annotations. Instead I would like to take this opportunity to teach the researches more about GO and how they can use it to analyze their data. The challenge is that I expect the audience to be a mixture of researchers who are quite familiar with using GO and researchers who have never used it before. Moreover I expect that the audience will be a mixture of PIs (who need to know enough about the GO to know how it would benefit their research) and graduate students/post-docs (who are at the coal face and have to actually do the analysis).

PIs always say: "I have my array data and I need it analysed."
Sometime later: Grad student shows up at the door needing training.


Fiona feels she needs to convince PIs but then teach grad student the mechanism and she's not sure whether this meeting will attract PIs or grad students.

Fiona would appreciate any feedback about how to best organize the workshop to meet each of these needs.

If a lot of people want to learn how to use GO for microarray analysis then perhaps she could invite tool developers along to help with the teaching?

The people expected to attend are:

  • usda representative
  • some commercial people
  • some non-chicken avian species
  • songbird people (zebra finch)
  • turkey
  • us army core of engineers are keen on quail - researchers
  • dinosaur guy

We discussed how to proceed with planning. Fiona is going to have a number of meetings with Rama and Harold. Jen also will attend as required.
Regular reports will be sent to keep Judy up to date with progress. It is envisaged that these will be included as part of the outreach report and that important questions requiring feedback from Judy will go via Jennifer to the Managers phone call, which takes place fortnightly on Wednesday afternoons.