TATK Export One: TIGR4 Testing Report
Export Information
Version of GenMAPP Builder: 2.0b71
Computer on which export was run: lab computer, front left
Postgres Database name: tATK_20131107
UniProt XML filename: 20131107_UniProtXML_tATK_TIGR4_AJV.xml
- UniProt XML version: 2013_10 (has since been updated)
- Time taken to import: 1.62min
GO OBO-XML filename: 20131107_GO-OBO_tATK_KM.obo-xml
- GO OBO-XML version: was last updated 2013OCT10
- Time taken to import: 5.46min
- Time taken to process: 4.09min
GOA filename: 20131107_UniProtXML_tATK_TIG4_AJV.goa
- GOA version (News on this page records past releases; current information can be found in the Last modified field on the FTP site): 2013NOV12 (will have to update)
- Time taken to import: 0.03min
Name of .gdb file: 20131107_GenMappExport_tATK_TIGR4_TPV.gdb
- Time taken to export .gdb: Unknown, left overnight in the lab
- Upload your file and link to it here. 20131107_GenMappExport_tATK_TIGR4_TPV.gdb
Note:
TallyEngine
TIGR4 Results:
(using gmbuilder70 version)
- GeneID's were not shown to a glitch in this version of gmbuilder, but will be redone using Tauras's newer version.
Ajvree (talk) 14:21, 20 November 2013 (PST)
Using XMLPipeDB match to Validate the XML Results from the TallyEngine
XML Match Results:
- The final count on XML match was 1 less than that of the Tally Engine results (2127 matches). XML match found all of the unique results, whereas the tally engine must have counted a repeated match into the total.
Ajvree (talk) 14:21, 20 November 2013 (PST)
Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine
- Query used in SQL:
- select count(*) from genenametype where type = 'ordered locus' and value ~ 'SP_[0-9][0-9][0-9][0-9]';
- Results were identical to that of XML match: 2126
Ajvree (talk) 14:44, 20 November 2013 (PST)
Follow the instructions on this page to query the PostgreSQL Database.
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:
TIGR4: 
Benchmark: 
Note: a few of the rows are missing in the benchmark screenshot- could not fit all of them on screen.
Ajvree (talk) 14:36, 20 November 2013 (PST)
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:
