Difference between revisions of "TATK E4: TIGR4 Testing Report"

Revision as of 01:13, 8 December 2013

Export Information

Version of GenMAPP Builder: 2.0b71 modified and distributed 2013NOV25 and version not yet updated

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: 20131120_OBOXML_tATK_TPV.obo-xml

• 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: 20131125_E4_tATK_TIGR4.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. Media:20131125_E4_tATK_TIGR4.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

• ID's are scattered. Have a general pattern of beginning with P or Q, following with five characters (mix of numbers and letters)

RefSeq Table

• all ID's in form NP_######
• further inspection of RefSeq ID's showed that in actual RefSeq database TIGR4 ID's were listed as SP_#### and not the NP_##### found in the 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, 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.

Template

Streptococcus pneumoniae

Import Export Cycle 1: tATK Export One: TIGR4 Testing Report

Import Export Cycle 2: tATK E2: TIGR4 Testing Report

Import Export Cycle 3: tATK E3: TIGR4 Testing Report

Import Export Cycle 4: tATK E4: TIGR4 Testing Report

Data Information

• Kmeilak Week 10, Kmeilak Week 11, Kmeilak Week 12, Kmeilak Week 13
• Taur.vil Week 10, Taur.vil Week 11, Taur.vil Week 12, Taur.vil Week 13, Taur.vil Week 14, Taur.vil Week 15
• Ajvree Week 10, Ajvree Week 11, Ajvree Week 12, Ajvree Week 13, Ajvree Week 14, Ajvree Week 15