TATK E4: TIGR4 Testing Report

1 Export Information
2 TallyEngine
3 Using XMLPipeDB match to Validate the XML Results from the TallyEngine
4 Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine
5 OriginalRowCounts Comparison
6 Visual Inspection
7 .gdb Use in GenMAPP
8 Compare Gene Database to Outside Resource
9 Template

Export Information

Version of GenMAPP Builder: 2.0b73

Database called: tATK_TIGR4_2013NOV25

Computer on which export was run: Tauras' Personal Computer

Postgres Database name: tATK_TIGR4_2013NOV25

UniProt XML filename: 20131118_UniProtXML_tATK_TIGR4_TPV.xml

UniProt XML version: UniProt Release 2013_11; 2013Nov13
Time taken to import: 3.15min

GO OBO-XML filename: Media:20131120_OBOXML_tATK_TPV.gz

GO OBO-XML version: 2013Nov20
Time taken to import: 10.59min
Time taken to process: 9.25min

GOA filename: 20131118_GOA_tATK_TIGR4_TPV.goa

GOA version: 2013Nov12 14:49
Time taken to import: 0.03min

Name of .gdb file: Streptococcus_pneumoniae_TIGR4_20131125.gdb

Time taken to export .gdb: less than 1 hour
- Started at 22:53
- Finished by 23:50
Upload your file and link to it here. Streptococcus_pneumoniae_TIGR4_20131125.gdb

Note: There were no updates to files since last I-E cycle

TallyEngine

Tally Engine run on Tauras' personal computer.
Final Results:
- Ordered Locus XML Count: 2126
- Ordered Locus XML Count: 2126
- All count results found in Tally Engine matched up to expected values.

Ajvree (talk) 09:46, 5 December 2013 (PST)

Using XMLPipeDB match to Validate the XML Results from the TallyEngine

XMLPipeDB match program was downloaded from Sourceforge [[1]]
Moved xmlmatch jar file to Downloads folder on personal computer
Ran cmd program on personal computer
Ran query: cd Downloads file
Searched for pattern: SP_[0-9][0-9][0-9][0-9]
Total unique matches found: 2126
This total matched results found in Tally Engine count

Ajvree (talk) 10:08, 5 December 2013 (PST)

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

Ran pgAdmin III through personal computer to run SQL query
Command used:
- select count(*) from genenametype where type = 'ordered locus' and value ~ 'SP_[0-9][0-9][0-9][0-9]';
Unique matches found: 2126
These results matched those of Tally Engine and XMLPipeDB match, confirming values

Ajvree (talk) 10:19, 5 December 2013 (PST)

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

OriginalRowCounts Comparison

Original Row Counts for Export 4 gdb file contained expected values, including the Ordered Locus Name value of 2126 that was found in Tally Engine, XMLPipeDB match, and SQL.
Tables included in the file were the same in name and count as the benchmark file, although they were in slightly different order.

E4 gdb: Benchmark file:

Ajvree (talk) 10:36, 5 December 2013 (PST)

Visual Inspection

Systems Table

There are numerous missing dates for the gene ID systems.

OrderedLocusNames Table

All ID's took the expected form, SP_####

UniProt Table

Primary ID's are scattered with a general pattern beginning with P, O, or Q, followed by five characters (mix of numbers and letters). All ID's are consistent with this format.
Did supply equivalent 'Related' ID's in expected form SP_####
Further investigation of the UniProt website confirmed Primary ID's were the correct form of ID for this table.

RefSeq Table

'Primary' ID's in form NP_######, unlike expected form SP_####
Did supply equivalent 'Related' ID's in expected form SP_####
further inspection of Primary ID's showed that in actual RefSeq database TIGR4 ID's were listed as SP_#### and not the NP_###### found in the gdb file. ID's in form NP_###### could not be located in the RefSeq database.

Ajvree (talk) 11:40, 8 December 2013 (PST)

.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.