Manager 5August2015: Difference between revisions

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**gene_association.goa_ref_cow.gz  
**gene_association.goa_ref_cow.gz  
**gene_association.goa_uniprot_noiea.gz
**gene_association.goa_uniprot_noiea.gz
*Wondering if we could come up with standardized naming for GAFs.  In practice we could perhaps create a decision tree based on content of the file, i.e. single vs. multiple species?  I haven't yet tried to address content, like noiea.  Some possibilities with an attempt at case-sensitivity below; I favor the last version of including the taxon ID and corresponding Genus Species or common name, whichever matches the label associated with the taxon ID.
*Wondering if we could come up with standardized naming for GAFs.  I propose a version including the taxon ID and a name that matches the label associated with the taxon ID:
**gene_association.submittinggroup_Gspecies.gz  where submitting group is all lower case and G = Genus (wouldn't cover all GAFs, though)
***gene_association.genedb_Lmajor.gz
***gene_association.wb_Celegans.gz
**gene_association.submittinggroup_commonname.gz  where common name would be the commonly used name of the highest level of taxonomic classification in the file
***gene_association.goa_cow.gz
***gene_association.wb_platyhelminthes.gz
**gene_association.submittinggroup_taxonid.gz
***gene_association.goa_9913.gz  where 9913 = Bos taurus
***gene_association.wb.6231.gz  where 6231 = Nematoda
**gene_association.submittinggroup_taxonid_gspecies.gz   
**gene_association.submittinggroup_taxonid_gspecies.gz   
**gene_association.submittinggroup_taxonid_commonname.gz   
**gene_association.submittinggroup_taxonid_commonname.gz   
***gene_association.goa_9913_btaurus.gz
***gene_association.goa_9913_btaurus.gz
***gene_association.wb_6239_celegans.gz
***gene_association.wb_6239_celegans.gz
***gene_association.wb.6231_nematoda.gz
***gene_association.wb_6157_platyhelminthes.gz
***gene_association.wb_6157_platyhelminthes.gz
*Other suggestions?
*Other suggestions?
*Does this work for strain-specific files?
*Does this work for strain-specific files?
*What about files like the noieas file that UniProt submits?
==GO user survey==
==GO user survey==
https://www.surveymonkey.com/r/PDMRXBW  
https://www.surveymonkey.com/r/PDMRXBW  

Revision as of 15:18, 3 August 2015


Agenda

GAF Naming Conventions - Standardization? (Kimberly)

  • As mentioned a few weeks ago, WB and WB-ParaSite are preparing to start submitting additional GAFs for other nematode species and for platyhelminthes.
  • We need to decide on appropriate file names for these GAFs.
  • Looking at examples of what is currently submitted by groups that submit multiple files:
    • gene_association.GeneDB_Lmajor.gz
    • gene_association.PAMGO_Atumefaciens.gz
    • gene_association.goa_chicken.gz
    • gene_association.goa_ref_cow.gz
    • gene_association.goa_uniprot_noiea.gz
  • Wondering if we could come up with standardized naming for GAFs. I propose a version including the taxon ID and a name that matches the label associated with the taxon ID:
    • gene_association.submittinggroup_taxonid_gspecies.gz
    • gene_association.submittinggroup_taxonid_commonname.gz
      • gene_association.goa_9913_btaurus.gz
      • gene_association.wb_6239_celegans.gz
      • gene_association.wb.6231_nematoda.gz
      • gene_association.wb_6157_platyhelminthes.gz
  • Other suggestions?
  • Does this work for strain-specific files?
  • What about files like the noieas file that UniProt submits?

GO user survey

https://www.surveymonkey.com/r/PDMRXBW

Symposium day in Washington DC

Planning/schedule/time for side meetings?

Minutes

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