Taur.vil Week 13

Laboratory Journal

TIGR4 IMP-EXP C2

Collecting Files

• Signed off on closing Imp-Export cycle 1 due to updated files and unclear documentation
• Created section for I-E2, started with TIGR4
• Downloaded GenMapp Builder 2.0b71
• Found UniProt Complete Proteome [1]
• Downloaded XML file from [2]
• Named XML file: 20131118_UniProtXML_tATK_TIGR4_TPV.xml
  • Uploaded to wiki: Media:20131118_UniProtXML_tATK_TIGR4_TPV.xml
  • Is the 2013Nov13 version
• Went to [3] to download goa file
• Followed link to proteomes directory [4]
• Downloaded the goa file for: 57.S_pneumoniae_TIGR4.goa
  • Version last updated 2013Nov12
  • Downloaded file renamed 20131118_GOA_tATK_TIGR4_TPV.goa
  • Uploaded to wiki: Media:20131118_GOA_tATK_TIGR4_TPV.goa
• Went to [5] to download go-obo file
• Went to beta version and downloaded the obo-xml.gz file
  • Extracted using 7zip
  • Could not find version information, only showed the date it was downloaded in properties
    • Was downloaded 2013Nov18
  • Renamed 20131118_OBOXML_tATK_TPV.obo-xml
  • Uploaded compressed file to wiki: Media:20131118_OBOXML_tATK_TPV.gz

Import-Export Process

• Launched pgAdminIII
• Logged in with password
• Created new database: tATK_TIGR4_2013NOV18
• opened SQL window and opened gmbuilder.sql
  • Executed file
  • Created the 159 tables expected
• Verified 2.0b71 was the most updated version of gmbuilder
• Launched gmbuilder-32bit.bat
  • Connected with database created earlier
• Imported XML file: 20131118_UniProtXML_tATK_TIGR4_TPV.xml
• Imported and processed obo-xml file: 20131118_OBOXML_tATK_TPV.obo-xml
• Imported goa file: 20131118_GOA_tATK_TIGR4_TPV.goa
• Exported as 20131118_E2_tATK_TIGR4.gdb