10 NOV 2009 RefGen Phone Conference (Archived): Difference between revisions

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==Uploading GAF files==
[[Category:Reference Genome]][[Category:Archived]]
# How are you handling externally submitted GAF files right now? Primarily, these are the GAF files from GOA. What is the existing process ? For example:  
==Present==
#* Are there manual and/or automated verifications (redundancies, quality of annotations) before a file from GOA gets integrated in your database?
* GOA: Emily
#* How are existing IEA annotations handled ?
* MGI: Li, Mary, Judy, Harold
#* What is the frequency of incorporation ?
* RGD: Stan
#* How are the accepted annotations from GOA loaded into the MOD ?
* Flybase: Susan
#* What appears in their own GAF files they send to the GO site as the annotation source ?
* dictyBase: Pascale, Petra
# Steps to the review process (monthly to start): Princeton HTML link here (when it exists this afternoon) that has all the links below
* TAIR: Donghui
* AgBase:  
* SGD: Stacia, Julie
* pombe
* Ecoli: Jim
* Wormbase: Ranjana, Kimberly
* ZFIN:
* PPOD: Kara, Mike
* Berkeley: Suzi, Chris


#* View notes/summary on family: http://wiki.geneontology.org/index.php/PANTHER10977
==Incorporating new protein family annotations via GAF files==
We'd like each group to provide information about how they handle GAF files.
The survey is here:  
http://www.surveymonkey.com/s.aspx?sm=zPTWtTxoC_2f6yC8I_2foXmDDg_3d_3d


#* Review the annotations visually: link to DAG (coming this afternoon)


#*Feedback to PAINT curators, or just download the GAF (from GO site soon, from Princeton temporarily)
==Proposed SOP for incorporating GAF files==
 
Steps to the review process (monthly to start)
 
# Start on the central protein family annotation page here:  http://wiki.geneontology.org/index.php/GAFs_for_trees-based_annotations
## Final GAFs will be available from central GO site, but are at Princeton for now
# View notes/summary on family: http://wiki.geneontology.org/index.php/PANTHER10977
 
# Review the annotations: from the above page, we will have summaries, visual representations of the annotations, and tables to peruse.  In addition to the display options shown now, we are working on an additional view that will show the original experimental annotations, in addition to just the new ones.  While reviewing these proposed annotations is up to the MOD, if you do review them, we especially encourage you to answer the following for each PAINT ISS:
##* Review of the reference genome GAFs will necessarily be different than GOA. Unlike GOA, which provides a mix of IEA and literature based annotations, these will all be ISS.  
##'''Is the annotation consistent''' with what you know about the gene to date?
##* The primary issue is whether you know of any evidence that might contradict the ISS that has been made based on protein family.  
##'''Is the inference justified''' by the relationship of the protein to the proteins from which the inference was drawn?
##* Are the two display options for viewing the annotations just discussed adequate for this review process ?
#*Review of the reference genome GAFs will necessarily be different than GOA. Unlike GOA, which provides a mix of IEA and literature based annotations, these will all be ISS.  
##* Eventually you may simply incorporate them automatically without manual review  
#* The primary issue is whether you know of any evidence that might contradict the ISS that has been made based on protein family.  
## Are there ISS annotations for your species ?
#* Eventually you may simply incorporate them automatically without manual review  
##* If yes: then if you see mistakes or have questions contact the ref. genome curator who made the inference for corrections. Note the reason for the correction in the annotation guidelines for the future  
#Provide feedback to the particular PAINT curator, or if all is well, just download the GAF.  Final GAFs will be available from central GO site.
##* If no: then you're done
# Are there ISS annotations for your species ?
## Repeat the above until all questionable annotations have been resolved
## If yes: then if you see mistakes or have questions contact the ref. genome curator who made the inference for corrections. Note the reason for the correction in the annotation guidelines for the future  
## Upload the GAF file from the geneontology web site
## If no: then you're done
## Load the GAF file into your MOD
# Repeat the above until all questionable annotations have been resolved
## Submit comprehensive GAF file for your species as usual
# Download the GAF file from the geneontology web site
# Load the GAF file into your MOD
# Submit comprehensive GAF file for your species as usual


==Discussion==
# Will each family have a different file? Chris says that it would be trivial to concatenate.
# (Mary D): problem: there are ISS annotations to 'molecular function' (PAINT bug)
# PAINT needs to also include functionality to look for obsolete terms and secondary IDs
# Some people would like taxon-specific files; or we could provide a script to parse a specific taxon
----
----


Back to [[Conference_Calls]]
Back to [[Conference_Calls]]

Latest revision as of 11:21, 16 January 2018

Present

  • GOA: Emily
  • MGI: Li, Mary, Judy, Harold
  • RGD: Stan
  • Flybase: Susan
  • dictyBase: Pascale, Petra
  • TAIR: Donghui
  • AgBase:
  • SGD: Stacia, Julie
  • pombe
  • Ecoli: Jim
  • Wormbase: Ranjana, Kimberly
  • ZFIN:
  • PPOD: Kara, Mike
  • Berkeley: Suzi, Chris

Incorporating new protein family annotations via GAF files

We'd like each group to provide information about how they handle GAF files. The survey is here: http://www.surveymonkey.com/s.aspx?sm=zPTWtTxoC_2f6yC8I_2foXmDDg_3d_3d


Proposed SOP for incorporating GAF files

Steps to the review process (monthly to start):

  1. Start on the central protein family annotation page here: http://wiki.geneontology.org/index.php/GAFs_for_trees-based_annotations
  2. View notes/summary on family: http://wiki.geneontology.org/index.php/PANTHER10977
  3. Review the annotations: from the above page, we will have summaries, visual representations of the annotations, and tables to peruse. In addition to the display options shown now, we are working on an additional view that will show the original experimental annotations, in addition to just the new ones. While reviewing these proposed annotations is up to the MOD, if you do review them, we especially encourage you to answer the following for each PAINT ISS:
    1. Is the annotation consistent with what you know about the gene to date?
    2. Is the inference justified by the relationship of the protein to the proteins from which the inference was drawn?
    • Review of the reference genome GAFs will necessarily be different than GOA. Unlike GOA, which provides a mix of IEA and literature based annotations, these will all be ISS.
    • The primary issue is whether you know of any evidence that might contradict the ISS that has been made based on protein family.
    • Eventually you may simply incorporate them automatically without manual review
  4. Provide feedback to the particular PAINT curator, or if all is well, just download the GAF. Final GAFs will be available from central GO site.
  5. Are there ISS annotations for your species ?
    1. If yes: then if you see mistakes or have questions contact the ref. genome curator who made the inference for corrections. Note the reason for the correction in the annotation guidelines for the future
    2. If no: then you're done
  6. Repeat the above until all questionable annotations have been resolved
  7. Download the GAF file from the geneontology web site
  8. Load the GAF file into your MOD
  9. Submit comprehensive GAF file for your species as usual

Discussion

  1. Will each family have a different file? Chris says that it would be trivial to concatenate.
  2. (Mary D): problem: there are ISS annotations to 'molecular function' (PAINT bug)
  3. PAINT needs to also include functionality to look for obsolete terms and secondary IDs
  4. Some people would like taxon-specific files; or we could provide a script to parse a specific taxon

Back to Conference_Calls