Taur.vil Week 13

Laboratory Journal

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

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

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

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

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_####