Difference between revisions of "Troque Week 12"

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{{Template:Troque}}
 
{{Template:Troque}}
 +
{{Template:Oregon Trail Survivors}}
  
 +
== 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 [http://uniprot.org/news the UniProt News Page]): '''UniProt release 2015_11'''
 +
* UniProt XML download link: '''[http://www.uniprot.org/uniprot/?query=proteome:UP000001006 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 [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): '''Version created on 11/19/2015 (at 2:24 AM)'''
 +
* GO OBO-XML download link: '''[http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz 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 [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): '''Version released on .'''
 +
* GOA download link: '''[http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/103.S_flexneri_301.goa 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): '''[[Media:Sf-Std 20151119 OTS.gdb | 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:
 +
<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 +
[[Image:TallyEngine results OTS 112115.jpg]]
 +
</div>
 +
 +
== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==
 +
[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways | 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:
 +
<div class="center">
 +
[[Image:Match results OTS 112115.jpg]]
 +
</div>
 +
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####.#), and SF#### (or SF####.#)
  
 
{{Template:Troque_Journal}}
 
{{Template:Troque_Journal}}

Latest revision as of 05:55, 8 December 2015

User Page        Bio Databases Main Page       


Helpful Links

Team Links
Files Team Members Week 11 Assignment Week 12 Assignment Week 14 Assignment Week 15 Assignment
OTS Deliverables Trixie Week 11 Week 12 Week 14 Week 15
Jake Week 11 Week 12 Week 14 Week 15
Gene Database Testing Report Erich Week 11 Week 12 Week 14 Week 15
Kristin Week 11 Week 12 Week 14 Week 15
Gene Database Project Links
Overview Deliverables Reference Format Guilds Project Manager GenMAPP User Quality Assurance Coder
Teams Heavy Metal HaterZ The Class Whoopers GÉNialOMICS Oregon Trail Survivors

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:

TallyEngine results OTS 112115.jpg

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:

Match results OTS 112115.jpg

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####.#), and SF#### (or SF####.#)

Assignment Links

Weekly Assignments

Individual Journal Entries

Shared Journal Entries

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