==Electronic Lab Notebook==
 
==Electronic Lab Notebook==
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Export of ''Vibrio cholerae'' GenMAPP Gene Database was used following the instructions on the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_9 Week 9] assignment page. The Gene Database Testing Report template we used was found [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Gene_Database_Testing_Report_Sample here].
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Export of ''Vibrio cholerae'' GenMAPP Gene Database was used following the instructions on the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Running_GenMAPP_Builder Running GenMAPP Builder] page. The Gene Database Testing Report template we used was found [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Gene_Database_Testing_Report_Sample here].
    
==Export Information==
 
==Export Information==
   −
Version of GenMAPP Builder:
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First we downloaded UniProt XML, GOA, and GO OBO-XML files. UniProt (protein database) is linked to GO OBO-XML (Gene Ontology) through GOA (Gene Ontology Associations) through XMLPipeDB, subset GenMAPP Builder. GenMAPP Builder takes the data and puts it into PostgreSQL database, where it is converted into a GenMAPP-compatible gene database (GDB). From there, we can then download and analyze microarray data via GenMAPP.
 +
 
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===UniProt XML===
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*Clicked on the UniProt link for ''Vibrio cholerae'' serotype O1 and clicked download all with XML format as a compressed file.
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*Saved <code>uniprot-organism%3A243277.xml.gz</code> in Computer T drive under new folder <code>Kzebrows</code>
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*Clicked on the link to download the proteomes directory
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*Downloaded file and saw that V_cholerae was downloaded 13 Oct 20016 at 07:31
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===GOA===
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*Followed link to Legacy Downloads
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*Download obo-xml.gz to T drive Kzebrows
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*Downloaded gmbuilder-3.0 and extracted in T drive using 7 zip
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==Create New Database in PostgreSQL==
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*Launched PgAdmin III.
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*Double-clicked on PostgreSQL 9.4
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*Selected "Database" and "New Database" and named it "Vcholerae_20151027_gmb3build5". Copied name to clipboard and pressed OK.
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*Ran prepackaged query: open file > Thaw space > gmbuilder-3.0.0-build-5 > sql > gmbuildersql
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**Query returned successfully with no results in 5697 ms
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**Closed query window
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==Configuring GenMAPP Builder to Connect to PostgreSQL Database==
 +
*Launched gmbuilder.bat
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*Select File > Configure Database
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*Entered the following info and clicked OK
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**Host: localhost
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**Port number: 5432
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**Database name: Vcholerae_20151027_gmb3build5
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**Username: postgres
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**password
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*File > Import UniProt XML and found UniProt XML file
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*File > Import GO OBO-XML file
 +
 
 +
==Exporting a GenMAPP Gene Database (.gdb)==
 +
*Selected File > Export to database
 +
*Typed my name into the Owner Field
 +
*Clicked on species ''V. cholerae''
 +
*Created the database by saving under T drive
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*Left the boxes checked for exporting all Molecule Function, Cellular Component, and Gene Ontology terms
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*Clicked next to begin export process
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*Start time: October 27, 2015 at 3:55 pm
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 +
==Gene Database Testing Report==
 +
 
 +
Version of GenMAPP Builder: '''gmbuilder-3.0.0-build-5.zip
    
Computer on which export was run:  
 
Computer on which export was run:  
   −
Postgres Database name:  
+
Postgres Database name: '''Vcholerae_20151027_gmb3build5'''
    
UniProt XML filename (give filename and upload and link to compressed file):
 
UniProt XML filename (give filename and upload and link to compressed file):
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#2 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(227): DiffEngine->diffLocal()
#3 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(721): DiffEngine->diff()
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#5 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(980): MappedDiff->__construct()
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#22 /apps/xmlpipedb/biodb/fall2015/index.php(44): MediaWiki->run()
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