Managers 28Jan09: Difference between revisions
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* 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). | * 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 | [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) | ||
* Alex says the ontology.edit files are not being updated as they should be. | * Alex says the ontology.edit files are not being updated as they should be. | ||
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Judy suggested that this should come from the gp2protein file, found at http://www.geneontology.org/gp2protein/ | 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. | 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 as to what is supposed to be done: how are the gp2protein files supposed to be submitted, how often, to whom, etc. | |||
*We've been approached by Andrew Su about Gene Wiki (http://dx.doi.org/10.1371/journal.pbio.0060175) and how it might connect with our Community Annotation pages; phone conf proposed. Email forwarded to managers. (Midori) | *We've been approached by Andrew Su about Gene Wiki (http://dx.doi.org/10.1371/journal.pbio.0060175) and how it might connect with our Community Annotation pages; phone conf proposed. Email forwarded to managers. (Midori) | ||
Revision as of 12:27, 28 January 2009
Agenda/chair: Jane
Minutes: Pascale
Present: Jane, Pascale, Michael, Suzi, Judith, David, Chris, Midori
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)
- Midori check availability/ set up a doodle?
Discussion items
- 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)
- 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)
- Val Woods asked last week
- Number of protein coding genes (a ball park number as I realise this is difficult for some organisms)
- Number of genes with manual GO annotations
- 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 as to what is supposed to be done: how are the gp2protein files supposed to be submitted, how often, to whom, etc.
- We've been approached by Andrew Su about Gene Wiki (http://dx.doi.org/10.1371/journal.pbio.0060175) and how it might connect with our Community Annotation pages; phone conf proposed. Email forwarded to managers. (Midori)
- Review of work done by David, Tanya and Chris last week (David)
- GO timeline for releases etc (Chris)
- 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)