Difference between revisions of "Eyanosch Week 9"

Latest revision as of 05:29, 3 November 2015

Export Information

Version of GenMAPP Builder:

Computer on which export was run: Computer second to the front left of class. (to the right of Jake's class)

Postgres Database name: Vcholerae_20151027_gmb3build5

UniProt XML filename (give filename and upload and link to compressed file): Eyanosch\uniprot-organism%3A243277.xml

• UniProt XML version (The version information can be found at the UniProt News Page):
• UniProt XML download link:
• Time taken to import: 3.08 Minutes
  • Note: I wasn't able to download the GM builder using Chrome FYI, earlier in the process

GO OBO-XML filename (give filename and upload and link to compressed file): go_daily-termdb.obo-xml

• 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):
• GO OBO-XML download link:
• Time taken to import: 7.44 minutes
• Time taken to process: 4.65 minutes
  • Note: Unable to upload the uniprot-organism%3A243277.xml an error appeared "Fatal error: Maximum execution time of 30 seconds exceeded in /apps/xmlpipedb.cs.lmu.edu/biodb/mediawiki-1.25.1-fall2015/includes/libs/XmlTypeCheck.php on line 191"
  • Note: The same was true of go_daily-termdb.obo-xml when I tried to upload it to the wiki

GOA filename (give filename and upload and link to compressed file): 46.V_cholerae_ATCC_39315.goa

• GOA version (News on this page records past releases; current information can be found in the Last modified field on the FTP site):
• GOA download link:
• Time taken to import: 0.07 minutes
  • Note:

Name of .gdb file (give filename and upload and link to compressed file): Vc-Std_20151027_EMY.gdb

• Time taken to export: 1:17:43
  • Start time: 3:54:02
  • End time:5:11:45

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.
  • Choose the menu item Tallies > Run XML and Database Tallies for UniProt and GO...
  • 
  • For more information, see this page.

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

For more information, see this page.

You can also look for counts at the SQL level, using some variation of a select count(*) query. This requires some knowledge of which table received what data. Here’s an initial tip: the gene/name tags in the XML file land in the genenametype table. A query on this table counting values from this table that were marked as ordered locus in the XML file matching the pattern VC_[0-9][0-9][0-9][0-9] would look like this:

select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_[0-9][0-9][0-9][0-9]';

In pgAdmin III, you can issue these queries by clicking on the pencil/SQL icon in the toolbar, typing the query into the SQL Editor tab, then clicking on the green triangular Play button to run.

select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_A?[0-9][0-9][0-9][0-9]';

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

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: File:Vc-Std External 20101022.gdb

New EMY.gbd file: File:Vc-Std 20151027 EMY.gdb

Benchmark:

New gbd:

Note: The row count is different because the 2015 db has more tables, since each row in the rowcount table represents a table. Since more tables were created more information is stored.

Visual Inspection

Perform visual inspection of individual tables to see if there are any problems.

• When looking at the Systems table there is only a date present in EMBL, EnsemblBacteria, GeneID, GeneOntology, InterPro, OrderedLocusNames, Other, PBD, Pfam, RefSeq, and UniProt all dated 10/27/2015

• Uniprot

Some of the entry names are different than the ID names, many are the same with a "_VIBCH" added at the end

• RefSeq

They look like the IDs take the correct form for that type of ID

• OrderedLocusNames

All the IDs seem to take the correct form for that type of ID

.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: