Difference between revisions of "Kevinmcgee Week 9"

Revision as of 18:50, 24 October 2013

Export Information

Version of GenMAPP Builder:2.0b70

Computer on which export was run: Last row of computer in the lab; second computer from the right when facing the front of the classroom.

Postgres Database name: Vibrio_cholerae_serotype_O1_10_22_LM_KM

UniProt XML filename:File:Vibrio cholerae serotype O1 10 22 LM KM.xml

• UniProt XML version (The version information can be found at the UniProt News Page):
• Time taken to import: 8.49 minutes

GO OBO-XML filename:File:Go daily-termdb.obo-10 22-LM-KM.xml.gz

• Direct Download from Wiki due to connectivity problems.
• 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):
• Time taken to import:20.02 minutes
• Time taken to process: 14.78 minutes

GOA filename: File:46.V cholerae ATCC 39315 10 22 LM KM.txt

• GOA version (News on this page records past releases; current information can be found in the Last modified field on the FTP site):
• Time taken to import: 0.16 minutes

Name of .gdb file: Vc-Std_20131022_LM_KM-gmb2b70.gdb

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

Note: Export started around 11 am; ended at 3:19:06 pm.

File:Vc-Std 20131022 LM KM-gmb2b70.gdb

TallyEngine

Run the TallyEngine in GenMAPP Builder and record the number of records for UniProt and GO in the XML data and in the PostgreSQL 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?

At first the match did not have the same results

After we added (A| ) to the command, we were able to get the same results for both the tally engine and the XMLpipe DB Match

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

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

I was able to get a correct count on and SQL query as well

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:

Table Rows

Info 1

Systems 30

Relations 18

Other 0

GeneOntologyTree 97982

GeneOntology 5556

UniProt-GOCount 3240

GeneOntologyCount 3239

UniProt-GeneOntology 20464

UniProt 3784

Pfam 2102

RefSeq 3403

PDB 223

InterPro 4349

OrderedLocusNames 3832

EMBL 228

UniProt-EMBL 5452

UniProt-OrderedLocusNames 3832

UniProt-PDB 319

UniProt-InterPro 10393

UniProt-RefSeq 3635

UniProt-Pfam 4648

RefSeq-Pfam 4145

RefSeq-InterPro 9241

RefSeq-PDB 234

RefSeq-OrderedLocusNames 3520

RefSeq-EMBL 3669

OrderedLocusNames-Pfam 4367

OrderedLocusNames-InterPro 9723

OrderedLocusNames-PDB 235

OrderedLocusNames-EMBL 4111

RefSeq-GeneOntology 18931

OrderedLocusNames-GeneOntology 20613

Note: There was one extra Ordered Locus name in the gdb file than there was in XML pipe DB Match or the Tally Engine.

Upon further inspection, we have found that this is because one of the Locus names was joined together with a slash mark.

This can be proven by going back into XMLpipeDB Match and accounting for the / in the command. The command shows one significant name with a slash in it

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?
  • There is no date for the Gene ID's present
• 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?
  • They all seem to be in the correct form

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: