|
|
| | [[File:XmlpipedbmatchoutputBK1029.png]] | | [[File:XmlpipedbmatchoutputBK1029.png]] |
| | [[File:XmlpipedbmatchoutputBK1029 Updated.png]] | | [[File:XmlpipedbmatchoutputBK1029 Updated.png]] |
| | + | ==Importing Data into the PostgreSQL Database== |
| | + | |
| | + | * Select File > Import UniProt XML... |
| | + | ** Navigate to the UniProt XML file that you extracted previously and click the Open button. |
| | + | ** This should take about 5-10 minutes, but may take longer depending on the size of the file, processor speed, and available memory of the machine. When the process has completed, record the elapsed time from the message window that appears. |
| | + | ***Import Time: 2.92 minutes |
| | + | * Select File > Import GO OBO-XML... |
| | + | ** Navigate to the GO OBO-XML file that you extracted previously. Click the Open button. |
| | + | ** This should take about 5-10 minutes, but may take longer depending on the size of the file, processor speed, and available memory of the machine. When the process has completed, record the elapsed time from the message window that appears. |
| | + | ***Import Time: 6.88 minutes |
| | + | * Click OK to the message asking you to process the GO data. |
| | + | ** This should take about 5-10 minutes, but may take longer depending on the size of the file, processor speed, and available memory of the machine. When the process has completed, record the elapsed time from the message window that appears. |
| | + | ***Processing Time: 4.49 minutes |
| | + | * Select File > Import GOA... |
| | + | ** Navigate to the GOA file that you downloaded previously and click the Import button. This process should only take a minute or so. |
| | + | ***Import Time: 0.06 minutes |
| | + | ==Exporting a GenMAPP Gene Database (.gdb)== |
| | + | |
| | + | * Select File > Export to GenMAPP Gene Database... |
| | + | * Type a name in the Owner field (or else it won't let you export). |
| | + | ** When doing the individual exercise for the [[Week 9]] assignment, use your own name. When doing this for your team project, use your team's name. |
| | + | * 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. |
| | + | * Create GenMAPP Database: click on the "Save GenMAPP Database File As..." button. |
| | + | ** In the Save dialog box that appears, navigate to the "T:" drive, and then modify the default file name by appending your initials. Click the "Save" button |
| | + | * Leave the boxes checked for exporting all Molecular Function, Cellular Component, and Biological Process Gene Ontology Terms. |
| | + | * Click the "Next" button to begin teh export process. |
| | + | ** Record the starting and ending times from the black console window. This will take 1-2 hours for a typical bacterial genome, depending on the size of the database, the processor speed, and available memory. Large eukaryotic genomes (like ''Arabidopsis thaliana'') or genomes with many GO annotations (like ''Saccharomyces cerevisiae'') can take much longer, in the range of 12-24 hours. |
| | + | **NOTE: the progress bar is not accurate. |
| | + | ***Start Time: 4:44 PM (restarted export after class) |
| | + | ***End Time: 6:11 PM |
| | + | ***Elapsed Time: 1 hour, 27 minutes |
| | ==Gene Database Testing Report== | | ==Gene Database Testing Report== |
| − | ===Export Informatio=n== | + | ===Export Information=== |
| | | | |
| | Version of GenMAPP Builder: | | Version of GenMAPP Builder: |
|
|
| | * UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): | | * UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): |
| | * UniProt XML download link: | | * UniProt XML download link: |
| − | * Time taken to import: | + | * Time taken to import: 2.92 minutes |
| | ** Note: | | ** Note: |
| | | | |
|
|
| | * GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): | | * GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): |
| | * GO OBO-XML download link: | | * GO OBO-XML download link: |
| − | * Time taken to import: | + | * Time taken to import: 6.88 minutes |
| − | * Time taken to process: | + | * Time taken to process: 4.49 minutes |
| | ** Note: | | ** Note: |
| | | | |
|
|
| | * GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): | | * GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): |
| | * GOA download link: | | * GOA download link: |
| − | * Time taken to import: | + | * Time taken to import: 0.06 minutes |
| | ** Note: | | ** Note: |
| | | | |
| | Name of .gdb file (give filename and upload and link to compressed file): | | Name of .gdb file (give filename and upload and link to compressed file): |
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#0 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(544): DiffEngine->diag()
#1 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(344): DiffEngine->compareSeq()
#2 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(227): DiffEngine->diffLocal()
#3 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(721): DiffEngine->diff()
#4 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(859): Diff->__construct()
#5 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(980): MappedDiff->__construct()
#6 /apps/xmlpipedb/biodb/fall2015/includes/diff/TableDiffFormatter.php(194): WordLevelDiff->__construct()
#7 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(140): TableDiffFormatter->changed()
#8 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(82): DiffFormatter->block()
#9 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(888): DiffFormatter->format()
#10 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(802): DifferenceEngine->generateTextDiffBody()
#11 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(733): DifferenceEngine->generateContentDiffBody()
#12 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(662): DifferenceEngine->getDiffBody()
#13 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(632): DifferenceEngine->getDiff()
#14 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(453): DifferenceEngine->showDiff()
#15 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(795): DifferenceEngine->showDiffPage()
#16 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(506): Article->showDiffPage()
#17 /apps/xmlpipedb/biodb/fall2015/includes/actions/ViewAction.php(44): Article->view()
#18 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(395): ViewAction->show()
#19 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(273): MediaWiki->performAction()
#20 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(566): MediaWiki->performRequest()
#21 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(414): MediaWiki->main()
#22 /apps/xmlpipedb/biodb/fall2015/index.php(44): MediaWiki->run()
#23 {main}