Laurmagee: Week 9

Export Information

Version of GenMAPP Builder: 2.0b70

Computer on which export was run: last row of computer in the lab; second computer from the right when facing the front of the classroom.

Postgres Database name: Vibrio cholerae serotype O1_10_22_LM_KM

UniProt XML filename:File:Vibrio cholerae serotype O1 10 22 LM KM.xml

• UniProt XML version (The version information can be found at the UniProt News Page): UniProt release 2013_10
• Time taken to import: 8.49 minutes

GO OBO-XML filename:File:Go daily-termdb.obo-10 22-LM-KM.xml.gz

• Direct Download from Wiki due to connectivity problems.
• 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):
• format-version: 1.2
• data-version: 2013-10-22
• Time taken to import:20.02 minutes
• Time taken to process: 14.78 minutes

GOA filename: File:46.V cholerae ATCC 39315 10 22 LM KM.txt

• GOA version (News on this page records past releases; current information can be found in the Last modified field on the FTP site): last updated Oct 14, 2013 8:56 AM
• Time taken to import: 0.16 minutes

Name of .gdb file: File:Vc-Std 20131022 LM KM-gmb2b70.gdb

• Time taken to export .gdb: about 4 hours and 20 minutes

Note: Export started around 11 am; ended at 3:19:06 pm.

TallyEngine

Using XMLPipeDB match to Validate the XML Results from the TallyEngine

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• Are your results the same as you got for the TallyEngine? Why or why not?
  • When running the Command Line, the top picture represents the command java -jar xmlpipedb-match-1.1.1.jar "VC_[0-9][0-9][0-9][0-9]" < uniprot-46.V_cholerae_ATCC_39315.xml. The reason this results in a lower number of matches (2738) is because we are not accounting for the inclusion of possible letter A's in identification. To do this we add (A|) into the pattern portion of our command (ie. java -jar xmlpipedb-match-1.1.1.jar "VC_(A|) [0-9][0-9][0-9][0-9]" < uniprot-46.V_cholerae_ATCC_39315.xml) and we receive the feedback of the second picture. This shows 3831 matches, which is what we expect after seeing our TallyEngine results.

Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine

• Follow the instructions on this page to query the PostgreSQL Database.
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• From the above picture, we see that SQL gives us the same match total of 3831.

OriginalRowCounts Comparison

Within the .gdb file, look at the OriginalRowCounts table to see if the database has the expected tables with the expected number of records. Compare the tables and records with a benchmark .gdb file.

Benchmark .gdb file: (for the Week 9 Assignment, use the "Vc-Std_External_20101022.gdb" as your benchmark, downloadable from here.

Copy the OriginalRowCounts table and paste it here:

Note:

• From the below picture, we see that the 3832 Ordered Locus Names in the above list. This is one off of our previous totals of 3831.
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• To study this further, we question whether there are any locus with two identification numbers back to back. We enter the following query into the command line: java -jar xmlpipedb-match-1.1.1.jar "VC_(A|) [0-9][0-9][0-9][0-9]/VC_(A|) [0-9][0-9][0-9][0-9] " < uniprot-46.V_cholerae_ATCC_39315.xml. We come to find that there is one unique match to this query and this match has the identification of VC_1738/VC_1739.
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• We look closer in our .gdb file and see that it was separated this id into two, because it can't recognize an id stated in such a way. This accounts for the extra locus and we have confirmed again the number of ordered locus names to be 3831.
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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?
  • Not all of the gene ID systems have a date, but the ones included all have a date of 10/22/2013.
• 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?
  • Every System actually has their own specific id assignment, so none of them appear to match up. They all contain a combination of numbers and letters, however UniProt appears to have a very complex organization while RefSeq and OrderedLocusNames are fairly easy to figure out.

.gdb Use in GenMAPP

Note:

Putting a gene on the MAPP using the GeneFinder window

• Try a sample ID from each of the gene ID systems. Open the Backpage and see if all of the cross-referenced IDs that are supposed to be there are there.

Note:

Creating an Expression Dataset in the Expression Dataset Manager

• 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?

Note:

Coloring a MAPP with expression data

Note:

Running MAPPFinder

Note:

Compare Gene Database to Outside Resource

The OrderedLocusNames IDs in the exported Gene Database are derived from the UniProt XML. It is a good idea to check your list of OrderedLocusNames IDs to see how complete it is using the original source of the data (the sequencing organization, the MOD, etc.) Because UniProt is a protein database, it does not reference any non-protein genome features such as genes that code for functional RNAs, centromeres, telomeres, etc.

Note: Laurmagee (talk) 22:55, 24 October 2013 (PDT)