Gene Database Testing Report Sample

Export Information

Version of GenMAPP Builder:

Computer on which export was run:

Postgres Database name:

UniProt XML filename:

• UniProt XML version (The version information can be found at Integr8):
• Time taken to import:

GO OBO-XML filename:

• GO OBO-XML version (The version information can be found at the GO Download page):
• Time taken to import:
• Time taken to process:

GOA filename:

• GOA version (News on this page records past releases, this page has current info):
• Time taken to import:

Name of .gdb file:

• Time taken to export .gdb:
• Upload your file and link to it here.

Note:

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 (or you can upload and link to a screenshot of the results).

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?

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

Follow the instructions on this page to query the PostgrSQL Database.

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

OriginalRowCounts Comparison in Microsoft Access

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 Vibrio cholerae use Vc-Std_External_20101022.gdb).

Copy the OriginalRowCounts table and paste it here:

Note:

Visual Inspection of Tables in .gdb

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, GeneId, 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

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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?

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Coloring a MAPP with expression data

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Running MAPPFinder

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