Difference between revisions of "Ksherbina Week 9"

Revision as of 05:11, 25 October 2013

Export Information

Version of GenMAPP Builder: 2.0b70

Computer on which export was run: Personal computer

Postgres Database name: VC_KS_20131022_gmb2b70

UniProt XML filename: UniProt_V_cholerae_KSTV_20131022.xml

• UniProt XML version (The version information can be found at the UniProt News Page): UniProt release 2013_10
• Time taken to import: 4.20 minutes

GO OBO-XML filename: go_daily-termdb_KS_20131022.obo-xml

• GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the GO Download page has been unzipped):
• Time taken to import: 8.81 minutes
• Time taken to process: 7.33 minutes

GOA filename: 46.V_cholerae_ATCC_39315_KS_20131022.goa

• GOA version (News on this page records past releases; current information can be found in the Last modified field on the FTP site):
• Time taken to import: 0.10 minutes

Name of .gdb file: Vc-Std_KS_20131022.gdb

• Time taken to export .gdb:

• Start Time: 6:50 pm
• End Time: 9:22 pm

• Link to file: Vc-Std KS 20131022.gdb

Note:

Lab Notebook

• Download GenMAPP Builder 2.0b70 from http://sourceforge.net/projects/xmlpipedb/files/GenMAPP%20Builder/

• When the zipped file has downloaded, unzip the folder with 7-zip.

• Download XMLPipeDB Match from http://sourceforge.net/projects/xmlpipedb/files/XMLPipeDB%20Match/

• When the zipped file has downloaded, unzip the folder with 7-zip.

• Download the UniProt XML file for Vibrio cholerae

• Go to the page http://www.uniprot.org/uniprot/?query=organism:243277+keyword:1185
• Click the orange Download link in the upper right-hand corner of the page.
• Download the XML file to the "Downloads" folder on the computer.

• Download the file 46.V_cholerae_ATCC_39315.goa to the "Downloads" folder on the computer.
• Download the GO OBO-XML formatted file from the Gene Ontology download page to the "Downloads" folder on the computer. Click on the link for obo-xml.gz.

• When the zipped file has downloaded, unzip the folder with 7-zip.

Import Data into the PostgreSQL Database

• Launch pgAdmin III.
• Double-click on PostgreSQL 9.2 (localhost:5432) on the upper left hand side of the window. Type in the password to connect.
• Right click on Databases and select New Database...
• Name the new database in the following format and click OK: VC_<your initials>_20131022_gmb2b70 (ex. VC_KS_20131022_gmb2b70).
• Click on your new database name in the treeview on the left.
• Click on the SQL icon in the toolbar at the top of the window.
• Click on the Open File icon in the toolbar (the yellow folder with an arrow).
• Navigate to the folder in which you unzipped GenMAPP Builder.
• Open the sql folder and open the file gmbuilder.sql. You should see SQL code appear in the SQL Editor tab.
• Click the Execute Query icon which looks like a green “Play” triangle button.
• Close the query window.

• To double check that all is OK, click the + sign for the database, then the + sign for Schemas, then finally the + sign for public. Under the Tables section, you should see a count of 159 in parentheses.

Export a GenMAPP Gene Database Using GenMAPP Builder

• Keep pgAdminIII open. Go to the gmbuilder-2.0b70 folder in the Downloads folder and launch gmbuilder-32bit.bat
• Select the menu item File > Configure Database...
• Under the Database Connections tab,

• The Database Driver defaults to PostgreSQL. Enter the following information into the corresponding fields:

• Host or address: localhost
• Port number: 5432
• Database name: VC_KS_20131022_gmb2b70
• Username: postgres
• Password: <enter the password of the PostgreSQL database you created above>

• Click the OK button.
• Select File > Import UniProt XML...

• Navigate to the UniProt XML file that you extracted previously and click the Open button.

• Select File > Import GO OBO-XML...

• Navigate to the GO OBO-XML file that you extracted previously. Click the Open button.
• Click OK to the message asking you to process the GO data.

• Select File > Import GOA...

• Navigate to the GOA file that you downloaded previously and click the Import button.

• Use XMLPipeDB Match to count the number of unique gene ideas in the V. cholerae Uniprot XML file.

java -jar xmlpipedb-match-1.1.1.jar "VC_[0-9][0-9][0-9][0-9]" < UniProt_V_cholerae_KSTV_20131022

2738 unique matches were found.

java -jar xmlpipedb-match-1.1.1.jar "VC_(A|)[0-9][0-9][0-9][0-9]" < UniProt_V_cholerae_KSTV_20131022

3831 unique matches were found.

• Count the number of unique gene IDs using an SQL query:

select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_(A|)[0-9][0-9][0-9][0-9]'

Count = 3831