Difference between revisions of "Jkuroda Week 9"

Revision as of 22:57, 29 October 2015

Export Information

Version of GenMAPP Builder: 3 build 5

Computer on which export was run: HP Compaq 8300 Elite SFF FC

Postgres Database name: Vibrio Cholerae_10-27-15_GMB3-build-5

UniProt XML filename: uniprot-organism%3A243277

• UniProt XML version: UniProt release 2015_10 - October 14, 2015
• UniProt XML download link
• Time taken to import: 3.14 minutes
  • Note: n/a

GO OBO-XML filename: go daily-termdb.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):
• GO OBO-XML download link
• Time taken to import: 7.46 minutes
• Time taken to process: 4.34 minutes
  • Note: n/a

GOA filename: 46.V_cholerae_ATCC_39315.goa

• GOA version (News on this page records past releases; current information can be found in the Last modified field on the FTP site): October 14, 2015 - GOA Proteome Sets 124
• GOA download link
• Time taken to import: 0.07 minutes
  • Note: n/a

Name of .gdb file: Vc-Std_20151027_JK.gdb

• Time taken to export: 1 hour and 15 minutes
  • Start time: 3:55pm
  • End time: 5:10pm
  • Note: n/a

TallyEngine

• Run the TallyEngine in GenMAPP Builder and record the number of records for UniProt and GO in the XML data and in the Postgres databases.
  • Choose the menu item Tallies > Run XML and Database Tallies for UniProt and GO...
  • Take a screenshot of the results. Upload the image to the wiki and display it on this page.
  • For more information, see this page.

Using XMLPipeDB match to Validate the XML Results from the TallyEngine

Follow the instructions found on this page to run XMLPipeDB match.

Are your results the same as you got for the TallyEngine? Why or why not?

• Initially, we got 3831 IDs for both XML and Postgres DB from TallyEngine but got 2738 IDs by using XMLPipeDB match. However, we realized that we were not accounting for the IDs that had the prefix of "VC_A" so we changed the command to reflect that:

java -jar xmlpipedb-match-1.1.1.jar "VC_A?[0-9][0-9][0-9][0-9]" < uniprot-organism%3A243277.xml

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

For more information, see this page.

You can also look for counts at the SQL level, using some variation of a select count(*) query. This requires some knowledge of which table received what data. Here’s an initial tip: the gene/name tags in the XML file land in the genenametype table. A query on this table counting values from this table that were marked as ordered locus in the XML file matching the pattern VC_A?[0-9][0-9][0-9][0-9] would look like this:

select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_A?[0-9][0-9][0-9][0-9]';

In pgAdmin III, you can issue these queries by clicking on the pencil/SQL icon in the toolbar, typing the query into the SQL Editor tab, then clicking on the green triangular Play button to run.

Are your results the same as reported by the TallyEngine? Why or why not?

• Once again, we first got 2737 IDs by using SQL, which differed from the 3831 IDs from TallyEngine. But this was a result of the same mistake we made with XMLPipeDB Match. Once we accounted for the "VC_A" prefix, we got 3831 IDs.

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:

Copy the OriginalRowCounts table from the benchmark and new gdb and paste them here:

Original Row Counts Table

Note: n/a

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?
• 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?

Note:

.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:

Josh Kuroda's page

Individual Journal Entries

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