Jwoodlee Week 9
Contents
Export Information
Version of GenMAPP Builder: 2.0 Beta
Computer on which export was run: Seaver 120 computer lab, facing the front of the room the computer on the far left in the front row, Windows 7
Postgres Database name: Vcholerae_20151027_gmb3build5
In a windows environment I went to UniProt Complete Proteomes and clicked on download, and then download all, and then selected XML from the drop down menu in the compressed format. To get the next file I navigated to here, to download this text file I clicked on the link, and then hit Ctrl-S to save it. To get the GO OBO-XML file go here, and under Legacy Downloads click on "obo-xml.gz". Now extract the Uniprot XML and the GO OBO-XML.gz files using an unzipping utility such as 7.zip.
Creating the .gdb
Then in order to create the .gdb file, I navigated to Download gmbuilder-3.0.0-build-5.zip. The download should start automatically. I extracted the contents of the .zip file. I launched pgAdmin III and in PostgreSQL 9.4 I right clicked on Databases and selected New Database, I then put in my database name and clicked OK. I clicked on my new database name and clicked the SQL icon in the toolbar. In the SQL query box I clicked the yellow open button and navigated to the folder which had the unzipped GenMAPP builder file. I opened the SQL folder and opened the file gmbuilder.sql. When the code appeared, I clicked the green arrow which executes my query. I then verified that there were 167 tables.
In my folder with my GenMAPP builder file I launched gmbuilder.bat, I selected on the menu File > Configure Database. Under the Database Connections tab the Database Driver defaults to PostgreSQL. I entered information in the following fields: Host or address: localhost Port number: 5432 Database name: <enter the name of the PostgreSQL database you created above> my name is: Vc-Std_20151027_JAW Username: <enter the username of the PostgreSQL database you created above>; in S120, this username is "postgres", so for me I entered postgres Password: <enter the password of the PostgreSQL database you created above>; in S120, ask the instructors for the password, the password is Welcome1 I clicked the OK button.
I went to File > Import UniProt XML... and navigated to the Uniprot XML file that I previously extracted. I went to File > Import GO OBO-XML... and navigated to the GO OBO-XML file that I extracted previously, and clicked the Open button.
Then clicked OK to the message asking to process the GO data. I then went to File > Import GOA File... And I navigated to the GOA file that I downloaded previously and clicked the Import button.
I then selected Select File > Export to GenMAPP Gene Database... Typed my name in the owner field, and selected my species, which in this case is Vibrio cholerae. I clicked next and then hit "save GenMAPP Database file as...", I then made the name I wanted to save it as. I kept all the boxes checked. I then hit the Next button to begin the process. It ened 1 hour and 15 minutes later. More detail about this process is below.
UniProt XML filename (give filename and upload and link to compressed file):File:Uniprot-organism-243277 Jwoodlee.xml.gz
- UniProt XML version (The version information can be found at the UniProt News Page): 10/27/2015 3:10 PM
- UniProt XML download link: here
- Time taken to import: 2.81 minutes
- Note:
GO OBO-XML filename (give filename and upload and link to compressed file): File:Go daily-termdb.obo-xml Jwoodlee.gz
- 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): 10/27/2015 3:16 PM
- GO OBO-XML download link:here
- Time taken to import: 6.97 minutes
- Time taken to process: 4.48 minutes
- Note:
GOA filename (give filename and upload and link to compressed file): File:46.V cholerae ATCC 39315 Jwoodlee.goa.txt
- GOA version (News on this page records past releases; current information can be found in the Last modified field on the FTP site): 13-Oct-2015 07:31 5.0M
- GOA download link:here
- Time taken to import: 0.06 minutes
- Note:
Name of .gdb file (give filename and upload and link to compressed file): File:Vc-Std 20151027 JAW.gdb
- Time taken to export: 1 Hour 15 Minutes
- Start time: 3:54 PM
- End time: 5:09 PM
Note:
TallyEngine
- I Ran the TallyEngine in GenMAPP Builder and recorded the number of records for UniProt and GO in the XML data and in the Postgres databases.
- I chose the menu item Tallies > Run XML and Database Tallies for UniProt and GO... this was the result.
Using XMLPipeDB match to Validate the XML Results from the TallyEngine
Procedure for XMLPipeDB utility here.
After downloading the application from the XMLPipeDB SourceForge site I moved the .zip into my T drive and extracted it there. I then moved the .jar file into the same directory as my XML file. Then I opened cmd and moved to that directory. I then typed the following command: java -jar xmlpipedb-match-1.1.1.jar "VC_A?[0-9][0-9][0-9][0-9]" < uniprot-organism%3A243277.xml The question mark is included to account for the difference in naming convention. A gene could have the pattern "VC_A[0-9][0-9][0-9][0-9]" or "VC_[0-9][0-9][0-9][0-9]".
Are your results the same as you got for the TallyEngine? Why or why not? Yes they are because I made sure to account for the two different ways a gene could be named. In class we at first got the wrong answer but that was quickly remedied once we figured out this fact.
Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine
For procedure see this page.
In PostgreSQL I ran the following command in the query tool.
select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_A?[0-9][0-9][0-9][0-9]';
Are your results the same as reported by the TallyEngine? Why or why not? Yes they are because I again made sure to account for the two ways to name the genes. The same regular expression can be used in the xmlpipedb utility and SQL.
OriginalRowCounts Comparison
Within the .gdb file, I looked at the OriginalRowCounts table to see if the database had the expected tables with the expected number of records. Then compared the tables and records with the benchmark .gdb file.
Benchmark .gdb file: File:Vc-Std External 20101022.gdb
OriginalRowCounts table from the benchmark and new gdb screenshots:
Both files opened to OriginalRowCounts in Access. As you can see the numbers are off from each other, this is most likely due to the fact that the 2010 benchmark .gdb doesn't have the most updated information. The new database that we created has a higher row count which is probably because new information was added in the last five years.
Visual Inspection
Perform visual inspection of individual tables to see if there are any problems.
- Look at the Systems table. Is there a date in the Date field for all gene ID systems present in the database?
- There is not a date for every row in the database.
- Open the UniProt, RefSeq, and OrderedLocusNames tables. Scroll down through the table. Do all of the IDs look like they take the correct form for that type of ID?
- For each table it appears that there is a common naming convention that is shared across both versions, our 2015 and the 2010 benchmark. The tables on my database share this convention and don't seem to falter away from it.
.gdb Use in GenMAPP
Part 2 of the Vibrio cholerae Microarray Data Analysis
Putting a gene on the MAPP using the GeneFinder window
- In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window. Then clicked on the Drafting Board to place the Gene on the MAPP. Then, right-clicked on the gene to access the GeneFinder window. I pasted the ID VC_2537 into the Gene ID field selected OrderedLocusNames and clicked the Search button. The ID was found, and I clicked the OK button to return to the Drafting Board window.
- Open the Backpage by left-clicking on the gene box on the Drafting Board to see if all of the cross-referenced IDs that are supposed to be there are there.
I then opened the back page by left-clicking on the gene box:
All the cross-referenced IDs that are supposed to be there are there.
Note:
Creating an Expression Dataset in the Expression Dataset Manager, Coloring a MAPP with expression data, and Running MAPPFinder
I selected the Data menu from the main Drafting Board window and chose Expression Dataset Manager from the drop-down list. From the Expression Datasets menu, I selected the tab-delimited text file from Week 8. The Expression Dataset Manager converted the data and generated a .EX. 121 errors recorded, same as last week. Opening the .EX in excel I determined that I had 121 errors of the same type. The error was: "Gene not found in OrderedLocusNames or any related system."
I made two color sets. I selected the "Avg_LogFC_all" to be used as the Gene Value from the drop down list. Using the formulas [Avg_LogFC_All] > 0.25 AND [Pvalue] < 0.05 and [Avg_LogFC_All] < -0.25 AND [Pvalue] < 0.05, I set the criteria. The former was increased and the latter was decreased. I then saved the expression dataset by selecting save from the expression dataset menu, and ran MappFinder the same as Week 8.
- How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset. Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?
- 5221 IDs were imported, with 121 Exceptions, the error codes were the same as last week: "Gene not found in OrderedLocusNames or any related system." VC2209 was one of the gene IDs that threw an exception. This gene is not in the OrderedLocusNames in the .gdb we created, this is reason to believe that they were not originally present in the Uniprot XML file.
BIOL 367, Fall 2015, User Page, Team Page
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