Gleis Week 9

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Contents

Export Information

Version of GenMAPP Builder:2.oB70

Computer on which export was run:Back left table, right hand side facing projector

Postgres Database name:vc_Gleis_20131022_gmb2b70

UniProt XML filename: File:VC Uniprot GLeis 10 22.xml

  • UniProt XML version (The version information can be found at the UniProt News Page):
  • Time taken to import:8.65 minutes

GO OBO-XML filename: File:Go daily-termdb.obo-xml GLEIS 20131022.gz

  • 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:19.86 minutes
  • Time taken to process: 14.59 minutes

GOA filename:File:46.V cholerae ATCC 39315 Gleis 10 22.goa

  • 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: 0.17 minutes

Name of .gdb file: File:Vc-Std 20131022-GLeis-gmb2b70.gdb

Note: Export started around 11 am; ended at 3:40:12 pm.

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).

Tally-results-Gleis-20131024.PNG

Using XMLPipeDB match to Validate the XML Results from the TallyEngine

Follow the instructions found on this page to run XMLPipeDB match.

Xmlpipedbmatch Results Gleis.PNG

Are your results the same as you got for the TallyEngine? Why or why not? Yes the results were the same when the code was changed to include the VC and VCA formatting.

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

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

This is a screenshot of the results which correspond with Tally and XMLPipeDB Match SQL-count-GLEIS.PNG

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:Different count for number of ordered locus names (off by one) due to a link of two gene IDs

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?
  • 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:

  • Many gene ID systems lack a proper date
  • All IDs appear correct for their respective ID types

.gdb Use in GenMAPP

Note:Using the newly donwloaded .gdb and the Merrell data, the expression dataset manager caught 5221 errors

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:


Lab Journal

  • Opened Week 9 assignment page
  • Followed instructions to link to Uniprot XML download page: http://www.uniprot.org/uniprot/?query=organism:243277+keyword:1185
  • Downloaded file and named VC_Uniprot_Gleis_10_22.XML
  • Followed instruction to link for obo-xml downloaded
  • Downloaded file and named as go_daily-termdb.obo-xml_Gleis_20131022.gz
  • Extracted files using 7zip
  • Followed Week 9 instructions to Uniprot-GOA download for Vibrio cholerae
  • Downloaded the file and named it:46.V_cholerae_ATCC_39315_Gleis_10_22.goa
  • Recorded version number for data set
  • Updated GenMAPP Builder @ (http://sourceforge.net/projects/xmlpipedb/files/GenMAPP%20Builder/
  • Downloaded and recorded most recent version of Builder
  • Extracted files from download using 7zip
  • Launched PGAdminIII
  • Opened PostgreSQL 9.2
  • Opened Databases
  • Selected New Database
  • Named the database {vc_Gleis_20131022_gmb2b70}
  • Opened new database
  • Opened SQL window by clicking SQL icon
  • Clicked open file icon and opened GenMAPP Builder
  • Opened the file gmbuilder.sql
  • Executed query
  • Closed query window
  • Launch gmbuilder-32bit.bat
  • Selected File > Configure Database
  • Selected Database connections tab
  • Entered the following information in the tab
  • Host: local host
  • Port number: 5432
  • Database name: vc_Gleis_20131022_gmb2b70
  • Username: GLeis
  • Password: Keck
  • Clicked OK to save
  • Selected File from main window > Import Uniprot XML
  • Navigated to XML file and clicked open
  • Recorded time to import
  • Repeated process for Go OBO-XML and GOA files
  • Selected file > Export to GenMAPP Gene Database
  • Typed "Gleis" into owner field in new window
  • Clicked on Vibrio cholera for export species
  • Clicked Next
  • Clicked Save GenMAPP Database file as and modified to fit GenMAPP
  • Saved database
  • Clicked Next and import began.
  • Recorded time to import in the above template
  • Opened https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways
  • Followed directions to check the quality of the Exported gene database
  • The results of the QA are provided in the template above
Retrieved from "https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php?title=Gleis_Week_9&oldid=4202"
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