Difference between revisions of "Ksherbina Week 9"
From LMU BioDB 2013
(→Lab Notebook: Added sub-sections.) |
(→Export a GenMAPP Gene Database Using GenMAPP Builder: Included more steps to export a database) |
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*Select File > Import GOA... | *Select File > Import GOA... | ||
:*Navigate to the GOA file that you downloaded previously and click the Import button. | :*Navigate to the GOA file that you downloaded previously and click the Import button. | ||
| + | *Select File > Export to GenMAPP Gene Database... | ||
| + | :*Type a name in the Owner field (ex. LMU_Fall2013_BIOL367_KS). | ||
| + | :*GenMAPP Builder scans your PostgreSQL database to see what species are available. Click on the species that you would like to export, then click Next to continue. | ||
| + | :*Click on the ''Save GenMAPP Database File As...'' button. Make sure that the ''Downloads'' folder appears. Modify the default file name to include your initials and then click on Save. | ||
| + | *Click the Next button. This starts the import process. | ||
*Use XMLPipeDB Match to count the number of unique gene ideas in the V. cholerae Uniprot XML file. | *Use XMLPipeDB Match to count the number of unique gene ideas in the V. cholerae Uniprot XML file. | ||
Revision as of 05:20, 25 October 2013
| Assignment Description | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 13 | Week 15 |
| Class Journal | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | |||||
| Individual Journal | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 |
| Other | Week 5: Database Wiki |
| Final Project | Team H(oo)KD Project Page | Journal Club Presentation | Project Individual Journal |
Contents |
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.
- Select File > Export to GenMAPP Gene Database...
- Type a name in the Owner field (ex. LMU_Fall2013_BIOL367_KS).
- GenMAPP Builder scans your PostgreSQL database to see what species are available. Click on the species that you would like to export, then click Next to continue.
- Click on the Save GenMAPP Database File As... button. Make sure that the Downloads folder appears. Modify the default file name to include your initials and then click on Save.
- Click the Next button. This starts the import process.
- 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
