Difference between revisions of "Taur.vil Week 13"
From LMU BioDB 2013
(TIGR4 E2) |
(→Laboratory Journal) |
||
| Line 38: | Line 38: | ||
*Imported goa file: 20131118_GOA_tATK_TIGR4_TPV.goa | *Imported goa file: 20131118_GOA_tATK_TIGR4_TPV.goa | ||
*Exported as 20131118_E2_tATK_TIGR4.gdb | *Exported as 20131118_E2_tATK_TIGR4.gdb | ||
| + | |||
| + | ==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. | ||
Revision as of 18:31, 19 November 2013
Contents |
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
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.
