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

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(Proposed SOP for uploading GAF files)
 
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[[Category:Reference Genome]][[Category:Archived]]
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==Present==
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* GOA: Emily
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* MGI: Li, Mary, Judy, Harold
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* RGD: Stan
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* Flybase: Susan
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* dictyBase: Pascale, Petra
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* TAIR: Donghui
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* AgBase:
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* SGD: Stacia, Julie
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* pombe
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* Ecoli: Jim
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* Wormbase: Ranjana, Kimberly
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* ZFIN:
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* PPOD: Kara, Mike
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* Berkeley: Suzi, Chris
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==Incorporating new protein family annotations via GAF files==
 
==Incorporating new protein family annotations via GAF files==
# 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:  
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We'd like each group to provide information about how they handle GAF files.  
#* Are there manual and/or automated verifications (redundancies, quality of annotations) before a file from GOA gets integrated in your database?
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The survey is here:  
#* How are existing IEA annotations handled ?
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http://www.surveymonkey.com/s.aspx?sm=zPTWtTxoC_2f6yC8I_2foXmDDg_3d_3d
#* What is the frequency of incorporation ?
 
#* How are the accepted annotations from GOA loaded into the MOD ?
 
#* What appears in their own GAF files they send to the GO site as the annotation source ?
 
  
  
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# Start on the central protein family annotation page here:  http://wiki.geneontology.org/index.php/GAFs_for_trees-based_annotations
 
# Start on the central protein family annotation page here:  http://wiki.geneontology.org/index.php/GAFs_for_trees-based_annotations
 
# View notes/summary on family: http://wiki.geneontology.org/index.php/PANTHER10977
 
# 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.  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:
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# 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:
 
##'''Is the annotation consistent''' with what you know about the gene to date?
 
##'''Is the annotation consistent''' with what you know about the gene to date?
 
##'''Is the inference justified''' by the relationship of the protein to the proteins from which the inference was drawn?
 
##'''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.  
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#*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.  
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#* 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  
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#* Eventually you may simply incorporate them automatically without manual review  
#Provide feedback to the particular PAINT curator, or if all is well, just download the GAF.
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#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.
# Final GAFs will be available from central GO site, but are at Princeton for now
 
## Are the two display options for viewing the annotations just discussed adequate for this review process ?
 
 
# Are there ISS annotations for your species ?
 
# Are there ISS annotations for your species ?
 
## 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  
 
## 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  
 
## If no: then you're done
 
## If no: then you're done
 
# Repeat the above until all questionable annotations have been resolved
 
# Repeat the above until all questionable annotations have been resolved
# Upload the GAF file from the geneontology web site
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# Download the GAF file from the geneontology web site
 
# Load the GAF file into your MOD
 
# Load the GAF file into your MOD
 
# Submit comprehensive GAF file for your species as usual
 
# Submit comprehensive GAF file for your species as usual
  
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==Discussion==
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# Will each family have a different file? Chris says that it would be trivial to concatenate.
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# (Mary D): problem: there are ISS annotations to 'molecular function' (PAINT bug)
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# PAINT needs to also include functionality to look for obsolete terms and secondary IDs
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# Some people would like taxon-specific files; or we could provide a script to parse a specific taxon
 
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Back to [[Conference_Calls]]
 
Back to [[Conference_Calls]]

Latest revision as of 07:21, 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