Managers 28Jan09

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Agenda/chair: Jane
Minutes: Pascale

Present: Jane, Pascale, Michael, Suzi, Judith, David, Chris, Midori, Jen

Apologies:

Action items from January 14

  • Cambridge folks to start looking at venues for September meeting
(very) brief report on progress (Midori)
  • Date: possibly last week of September (after Sept 21); should end before Oct. 6 if we want to use a Cambridge college
  • Midori to check venue availability, then set up a doodle for people's availability

Discussion items

Retiring old format GO files

  • The old format GO files are becoming increasingly hard to maintain as we add new relations etc, and process.ontology is getting so big that cvs is struggling with it. We had a GO help issue with it this week. I suggest we set a date to stop providing it - how about 1st July 2009, which is 6 months, and announce to GO friends? (Jane & Chris).

[ACTION ITEM]: Check with Mike Cherry to see of there is any problem retiring the old files; retire files in 6 months : July 1st 2009 (Jane, Chris)

ontology.edit files not properly or predictably updated

  • Alex says the ontology.edit files are not being updated as they should be.
    • Chris says this is an automated job at Stanford-- will ask Mike Cherry. (Jane) ok, FIXED/DONE

gp2protein files not up to date

  • Val Wood asked last week
  1. Number of protein coding genes (a ball park number as I realise this is difficult for some organisms)
  2. Number of genes with manual GO annotations
  3. Number of publications

Judy suggested that this should come from the gp2protein file, found at http://www.geneontology.org/gp2protein/ However, it seems some files are very old (human, chicken, etc) . People thought the files were up to date. [ACTION ITEM] Chris and Pascale: put clear instructions for submitting data to GO: how are the gp2protein files supposed to be submitted, how often, to whom, etc.

Gene wiki

[ACTION ITEM]: (Michael) will send the email to Jim Hu, and see of he has suggestions for a more coherent action. -- Later: figure out how to link to the gene wiki pages.

[ACTION ITEM]: Midori will answer Andrew and say we are looking at the best way of using this new gene wiki information

Function/process links and regulates links

Work done by David, Tanya and Chris last week (David)

  • QC for F/P links and regulates links
  • ready to implement cross products very soon
  • Process: the file will be available with the links filtered out so that they do not confused users used to the current file
  • Spend quite some time on function terms where the term is defined by the process but there is no function, for example 'caspase regulator activity', while there is no caspase activity. A proposal for this will be presented in March at the GO meeting.
  • GO timeline for releases etc (Chris)


Newsletter moving to RSS feed

  • We're (i.e. newsletter and WPWG) gearing up to unveil a new news feed which Seth has set up for us. It uses the open source software Drupal and will have lots of exciting new features such as RSS feeds and twitter, and will be very easy for people to use. We're currently ironing out the details. (Jane)

Action Items - Summary

[ACTION ITEM]: Check with Mike Cherry to see of there is any problem retiring the old files; retire files in 6 months : July 1st 2009 (Jane, Chris)

[ACTION ITEM] Chris and Pascale: put clear instructions for submitting data to GO: how are the gp2protein files supposed to be submitted, how often, to whom, etc.

[ACTION ITEM]: (Michael) will send the email to Jim Hu, and see of he has suggestions for a more coherent action. -- Later: figure out how to link to the gene wiki pages.

[ACTION ITEM]: Midori will answer Andrew and say we are looking at the best way of using this new gene wiki information (reply to Andrew DONE)


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