Difference between revisions of "New Model Implementation Checklist"

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'''Files Needed for Implementing New GO Annotation Model'''
 
'''Files Needed for Implementing New GO Annotation Model'''
  
−
*Updated ?GO_code file - file made, not yet checked in ACeDB
+
*?Analysis
 +
**Needed eight ?Analysis objects in order to properly credit the sources of external GO annotations.
 +
**Status: file created, not yet checked in ACeDB
 +
 
 +
*?Database
 +
**Needed a Database object for Gene Ontology Consortium for GO_REFs
 +
**Status: file created, not yet checked in ACeDB
 +
 
 +
*?GO_code
 
**We needed seven new GO codes to incorporate PAINT and other external annotations.
 
**We needed seven new GO codes to incorporate PAINT and other external annotations.
 +
**Status: file created, not yet checked in ACeDB
 +
 +
*?Strain
 +
**Will use ?Strain objects for dual-taxon annotations (e.g., GO:0050829, defense response to Gram negative bacterium)
 +
**Checked the corresponding column in the GAF.  We have three taxon IDs, all more specific than the current WB taxon ID associated with ?Species objects, since the GO annotations refer to a specific strain of these bacteria.  Each species, and a sample PMID, are listed below:
 +
***taxon:273526 Serratia marcescens subsp. marcescens Db11 (PMID:12176330)
 +
***taxon:652611 Pseudomonas aeruginosa PA14 (PMID:12142542)
 +
***taxon:474186 Enterococcus faecalis OG1RF (PMID:12142542)
 +
**Status: files created, not yet checked in ACeDB
 +
 +
'''GO Annotation File'''
 +
*File created, not yet checked in AceDB
 +
 +
'''WB Models File'''
 +
*models.wrm file created, will need to read into ACeDB
  
−
*New ?Database objects
 
−
**Need a Database object for Gene Ontology Consortium for GO_REFs
 
  
−
*New ?Species objects
+
'''Scripts'''
−
**May need new ?Species objects for dual-taxon annotations (e.g., GO:0050829, defense response to Gram negative bacterium)
+
*How to handle duplicate annotations wrt multiple proteins but one WBGene
−
**Need to check this column in the GAF from GOA and check with Kevin
 

Latest revision as of 19:08, 10 February 2014

Files Needed for Implementing New GO Annotation Model

  • ?Analysis
    • Needed eight ?Analysis objects in order to properly credit the sources of external GO annotations.
    • Status: file created, not yet checked in ACeDB
  • ?Database
    • Needed a Database object for Gene Ontology Consortium for GO_REFs
    • Status: file created, not yet checked in ACeDB
  • ?GO_code
    • We needed seven new GO codes to incorporate PAINT and other external annotations.
    • Status: file created, not yet checked in ACeDB
  • ?Strain
    • Will use ?Strain objects for dual-taxon annotations (e.g., GO:0050829, defense response to Gram negative bacterium)
    • Checked the corresponding column in the GAF. We have three taxon IDs, all more specific than the current WB taxon ID associated with ?Species objects, since the GO annotations refer to a specific strain of these bacteria. Each species, and a sample PMID, are listed below:
      • taxon:273526 Serratia marcescens subsp. marcescens Db11 (PMID:12176330)
      • taxon:652611 Pseudomonas aeruginosa PA14 (PMID:12142542)
      • taxon:474186 Enterococcus faecalis OG1RF (PMID:12142542)
    • Status: files created, not yet checked in ACeDB

GO Annotation File

  • File created, not yet checked in AceDB

WB Models File

  • models.wrm file created, will need to read into ACeDB


Scripts

  • How to handle duplicate annotations wrt multiple proteins but one WBGene
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