8 Sept 2009 RefGen Phone Conference (Archived): Difference between revisions

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[ACTION ITEM]: Is every group able to import GAF files? Please - everyone report back on this.  
[ACTION ITEM]: Is every group able to import GAF files? Please - everyone report back on this.  
ACTION ITEM: Can everyone answer: Do you have software that allows to import annotation as a GAF file?
ACTION ITEM: Can everyone answer: Do you have software that allows to import annotation as a GAF file?
* GOA:  
* GOA: Yes, we do import external GAF files. GOA provides GAF releases approx. once a month.
* MGI:  
* MGI:  
* RGD:  
* RGD:  

Revision as of 05:31, 7 September 2009

Present

PAINT-based annotations

  • PAINT should be available for all curators to download. We may set up some webex sessions to demo the software.

For now, this is what it looks like for the MSH family:

  • Jim and Daniel have uploaded a GAF file generated by PAINT for the MSH family:

http://gowiki.tamu.edu/wiki/index.php/Category:MSH_family_PANTHER11361

The format is the same as what we use for the annotation jamborees. The names of the columns on this page correspond to the family (PANTHER11361) as all as groups of descendants (foe eg, AN24 is 'ancestor 24')

  • One suggestion would be to distinguish the PAINT-derived ISS from all others.
  • We suggest that curators look at a few families and decide whether they can import the annotation in a semi-automated fashion.

PAINT-generated GAF files

  • The PAINT-generated annotations are written to a GAF file.

[ACTION ITEM]: Is every group able to import GAF files? Please - everyone report back on this. ACTION ITEM: Can everyone answer: Do you have software that allows to import annotation as a GAF file?

  • GOA: Yes, we do import external GAF files. GOA provides GAF releases approx. once a month.
  • MGI:
  • RGD:
  • Flybase:
  • dictyBase:
  • TAIR:
  • Wormbase:
  • AgBase:
  • SGD:
  • Pombe:
  • Ecoli:
  • ZFIN:
  • Those annotations would be treated like InterPro2GO annotations: not systematically manually reviewed bu MOD curators (since they are manually assigned by PAINT curators)

Frequency of updates of GAF files by the MODs

We need up to date annotations to make the best annotations possible to the trees.

ACTION ITEM: Can everyone answer: What is the release schedule of GAF files by the individual MODs

  • GOA:
  • MGI:
  • RGD:
  • Flybase:
  • dictyBase:
  • TAIR:
  • Wormbase:
  • AgBase:
  • SGD:
  • Pombe:
  • Ecoli:
  • ZFIN:


Using UniProt IDs for the gp2protein file

  • Action Item: (carried over from previous call): Emily: will provide a list of mappings to secondary (obsolete) IDSs. Many MODs have issues with that.

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