Difference between revisions of "Troque Week 12"

Revision as of 23:17, 1 December 2015

Helpful Links

Things to note

• Taxonomy ID: 623
• UP000001006
• File management system: Wiki

Export Information

Version of GenMAPP Builder:

• gmbuilder-3.0.0-build-5

Computer on which export was run:

• Front of the room, 3rd computer from the right.

Postgres Database name:

• Shigella flexneri 20151911

UniProt XML filename (give filename and upload and link to compressed file):

• UniProt XML version (The version information can be found at the UniProt News Page): UniProt release 2015_11
• UniProt XML download link: Click here
• Time taken to import: 4.48 minutes
  • Note:

GO OBO-XML filename (give filename and upload and link to compressed file):

• 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): Version created on 11/19/2015 (at 2:24 AM)
• GO OBO-XML download link: Click here to download.
• Time taken to import: 7.00 minutes
• Time taken to process: 4.99 minutes
  • Note:

GOA filename (give filename and upload and link to compressed file):

• GOA version (News on this page records past releases; current information can be found in the Last modified field on the FTP site): Version released on .
• GOA download link: Click here to download.
• Time taken to import: 0.06 minutes
  • Note:

Name of .gdb file (give filename and upload and link to compressed file): Sf-Std_20151119_OTS.gdb

• Time taken to export: 1 Hours, 32 Minutes, 33 Seconds
  • Start time: 4:06:13 PM PM PDT
  • End time: 5:38:46 PM PDT
  • 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...
  • Choose the UniProt and GO OBO XML files that was uploaded from the previous sections of this assignment.
  • Here is the screenshot of the tally result:

Using XMLPipeDB match to Validate the XML Results from the TallyEngine

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

• In the Thawspace directory, I created a folder called "Shigella_flexneri_BioDB_2015" and created subfolders called "Source" and "Working" to store the source files (i.e., the compressed files) and the working files (i.e., the files I will actually be processing).
• As a result, I had to cd to these directories first before using the command for using Match.
  • In order to change into the ThawSpace0\Shigella_flexneri_BioDB_2015\Working directory, use the following commands on the command prompt window:

T: && cd "Shigella_flexneri_BioDB_2015\Working"

• The command I used once inside the directory I want is:

java -jar xmlpipedb-match-1.1.1/xmlpipedb-match-1.1.1.jar "SF[0-9][0-9][0-9][0-9]" < uniprot-proteome%3AUP000001006.xml

• The results are as follows:

These results did not match up with what the TallyEngine gave (TallyEngine: 7567 vs. Match: 4610)

• As a result, the commands would have to be modified somehow so that the numbers match.

System IDs

• UniProt: A0A0H2[A-Z][A-Z][0-9][0-9], A0A0H2[A-Z][A-Z][A-Z][0-9], A0A0H2[A-Z][0-9][0-9][0-9], or [A-Z][0-9][A-Z][0-9][A-Z][0-9]
  • Examples: A0A0H2USI9, A0A0H2USA4, A0A0H2V010, A5A6A8
• RefSeq: NP_######, WP_#########, YP_#########, YP_######
  • Examples: NP_858405, WP_000002440, YP_001449236, YP_145811 (only one of this)
• GeneID (EntrezGene from NCBI):
• GO: #######
• OrderedLocusNames: CP####, S#### (or S####.1), and SF#### (or SF####.1)

Assignment Links

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• Week 1
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• Week 12
• No Week 13 Assignment
• Week 14
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• Week 1 - This is technically the user page.
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• No Week 13 Assignment
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Shared Journal Entries

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• No Week 13 Assignment
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• Week 15