Difference between revisions of "Taur.vil Week 13"

Latest revision as of 18:35, 21 November 2013

[edit] Laboratory Journal

[edit] TIGR4 IMP-EXP C2

[edit] 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

[edit] 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

[edit] TIGR4 IMP-EXP C3

[edit] Collecting files

• Verified that goa and XML files had not been updated
• Downloaded Nov. 20, 2013 obo-xml file from [6]
• created new database in pgAdminIII called tATK_TIGR4_2013NOV20
• Executed gmbuilder.sql (the new version, see bellow) in SQL
  • Verified success by the 159 tables created

[edit] Import-Export Cycle

• Opened new version of gmbuilder-32bit.bat
• Connected to database created earlier
• Imported UniProt XML file: 20131118_UniProtXML_tATK_TIGR4_TPV.xml
• Imported the obo-xml file: 20131120_OBOXML_tATK_TPV.obo-xml
• Imported the goa file: 20131118_GOA_tATK_TIGR4_TPV.goa
• Exported to 20131120_E3_tATK_TIGR4.gdb

[edit] gmbuilder coding in class

• Checked out gmbuilder in eclipse, labeled it tATK_gmbuilder3
• Edited StrptococcusPenumoniaeTIGR4UniProtSpeciesProfile.java in the src folder to include the appropriate species id of 170189 and gene identifier of http://www.streppneumoniae.com/gene_detail_output.asp?id=2741&name=~
• Copied over dist folder (what Dondi called the baby gmbuilder) onto my flash drive
• Will use for additional export cycle.

• Discovered we had linked to the wrong database
• Went back into eclipse and linked files to http://bacteria.ensembl.org/streptococcus_pneumoniae_tigr4/Gene/Summary?g=~
• Added VC-like code to adjust gene IDs to match microarray data, XML, and database
• Copied over dist_Experiment20131121 to flash drive
• Will use for I-E C4

[edit] Microarray Data

• Verified that all gene IDs matched for different column
• Deleted Gene IDs except for the first column
• In the microarray data:
  • SP#### is used for TIGR4
  • SPN#### is used for G54
  • spr#### is used for R6
  • Various other formats exist for controls
• Gene names for TIGR4 database are as SP_####

[edit] Future Steps

Export, check for custom link, load microarray data

[edit] Template

Streptococcus pneumoniae

Import Export Cycle 1: tATK Export One: TIGR4 Testing Report

Import Export Cycle 2: tATK E2: TIGR4 Testing Report

Import Export Cycle 3: tATK E3: TIGR4 Testing Report

Import Export Cycle 4: tATK E4: TIGR4 Testing Report

Data Information

• Kmeilak Week 10, Kmeilak Week 11, Kmeilak Week 12, Kmeilak Week 13
• Taur.vil Week 10, Taur.vil Week 11, Taur.vil Week 12, Taur.vil Week 13, Taur.vil Week 14, Taur.vil Week 15
• Ajvree Week 10, Ajvree Week 11, Ajvree Week 12, Ajvree Week 13, Ajvree Week 14, Ajvree Week 15