8 Sept 2009 RefGen Phone Conference (Archived)

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Pascale, Petra, Suzi, Emily, Kara, Donghui, Mike, Jim, Dan, Brenley, Stan, Li, Mary, Ranjana, Stacia

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:


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 (for 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.
  • MGI: We do take in a special GAF from GOC with any of their mouse annotations, and filter them according to redundancy, mapping issues (one to many, etc.), etc. So not all of them are loaded into our database, but we do append any that do not get loaded onto the GAF that we supply. IEAs are not loaded but regenerated by us (since their IEAs are based on spkw2go, ip2go, and ec2go, they are the same.
  • RGD: We import external GAF files.
  • Flybase: no
  • dictyBase: no
  • TAIR: We download the GOA Arabidopsis file from the GO cvs, strip out the IEAs, do a redundancy check with our annotations and append anything that passes those filters to our GAF.
  • Wormbase: We don't have any special software. As of now we are importing the Uniprot worm annotations by just downloading the file from the GOA FTP site and filtering it for redundant annotations (comparing them to ours). We include these in our GAF that we export to the GOC.
  • AgBase:
  • SGD: the GO loading script should be able to load GO annotations in GAF format from any external resource // Mike says that the curation process to uptake those is not yet in place (GO managers 11-04-2009)
  • Pombe: Yes, can also filter so we only take the suggested annotations which are non-redundent with existing manual annotations
  • Ecoli: Yes, with some tweaking.
  • ZFIN: We add non-redundant annotations from the GOA D.rerio GAF to our GAF. This could probably be adapted to also allow loading of a GAF from PAINT. Currently these annotations do not appear online in ZFIN however.
  • 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: GOA provides GAF releases approx. once a month.
  • MGI: We generate a new GAF nightly, always available on our public FTP site. I submit Friday's file to the GOC once a week.
  • RGD: Weekly
  • Flybase: every FlyBase release which is every 4-6 weeks
  • dictyBase: weekly
  • TAIR: Weekly
  • WormBase: Monthly
  • AgBase: part of the GOA release, approx. once a month.
  • SGD: weekly
  • Pombe: Approx every few months, moving to monthly
  • Ecoli: Monthly
  • ZFIN: Weekly with an occasional skipped week here and there (it's a manual cvs commit process)

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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