Difference between revisions of "Ajvree Week 13"

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refseq: 3403<br>
 
refseq: 3403<br>
  
−
==Week 13==
+
=='''Week 13'''==
 
'''Tally Engine:'''
 
'''Tally Engine:'''
 
*created new database in pgadmin III
 
*created new database in pgadmin III
Line 27: Line 27:
 
**GOA import took 0.07 min
 
**GOA import took 0.07 min
 
*unzipped go-xml file
 
*unzipped go-xml file
 +
*OBO-XML import time: 19.92 min
 +
*additional gene ontology information was processed, this took 14.96 min
 +
*ran tally, came up with error
 +
*refreshed gmbuilder and tried again successfully
 +
Results:
 +
[[Image:TallyEngineTrial2.PNG]]
 +
 +
  
  
 
'''XMLpipedb Match'''
 
'''XMLpipedb Match'''
 
*downloaded program from sourceforge
 
*downloaded program from sourceforge
 +
*opened cmd program
 +
*cd Downloads file
 +
*moved xmlmatch jar file to download folder
 +
*used match to look for pattern SP_[0-9][0-9][0-9][0-9]
 +
*Total unique matches: 2126
 +
*almost identical to tally engine results of 2127, minus one result
 +
Results:
 +
[[Image:20131107 XMLmatch tATK TIGR4 AJV.PNG]]
 +
 +
 +
 +
'''OriginalRowCounts'''
 +
*Looked at TIGR4 gdb file and benchmard VD file for table similarities/differences
 +
*seemed to have same tables/same information
 +
*took screenshots of both, included here:
 +
TIGR4: [[Image:20131119 ogrowcounts tATK TIGR4 AJV.PNG]]
 +
Benchmark: [[Image:20131119 benchmarkrowcounts tATK TIGR4 AJV.PNG]]
 +
 +
*Note: a few of the rows are missing in the benchmark screenshot- could not fit all of them on screen.
 +
 +
 +
 +
'''SQL'''
 +
*used following query to search for matches:
 +
**select count(*) from genenametype where type = 'ordered locus' and value ~ 'SP_[0-9][0-9][0-9][0-9]';
 +
*Result given was 2126
 +
[[Image:20131119 SQLcountresults tATK TIGR4 AJV.PNG]]
 +
 +
==11/21/13==
 +
 +
'''Tally Engine for Export 3'''
 +
*downloaded Taurus's version of gmbuilder to redo tally engine counting
 +
*used export 3 files instead of previous export 1 files
 +
*connected to avreelan database in pgadminIII, inserted new gmbuilder tables
 +
*opened new version of gmbuilder/tally engine, connected to avreelan database
 +
*XML file import took: 2.02 min
 +
*OBO-XML file import took: 6.25 min
 +
**additional gene ontology data processing took: 4.81 min 
 +
*GOA file import took: 0.04 min
 +
*Results:
 +
**GeneId's now visible, total of 2105 in both xml and database counts
 +
**orderedlocusnames still at same value of 2126 in both xml and database counts
 +
**screenshot: [[Image:20131121 TallyEngineE3 tATK TIGR4 AJV.PNG]]
 +
 +
 +
'''Original Row Counts for Export 3'''
 +
*redid row counts using the export 3 file
 +
*compared with benchmark file
 +
*both files had identical number of tables with same categories in each, although some were out of order.
 +
*Screenshots:
 +
E3 TIGR4: [[Image:20131121 E3rowcounts tATK TIGR4 AJV.PNG]]
 +
Benchmark:[[Image:20131121 benchmarkrowcounts tATK TIGR4 AJV.PNG]]
 +
 +
'''Table Analysis'''
 +
*looked at tables within E3 gdb file to find inconsistencies in data
 +
 +
'''Systems Table'''<br>
 +
[[Image:20131121 E3Systemstable tATK TIGR4 AJV.PNG]]
 +
*There are missing dates for quite a few gene ID systems
 +
 +
'''OrderedLocusNames Table'''
 +
*All ID's took the expected form, SP_####
 +
 +
'''UniProt Table'''
 +
*ID's are scattered. Have a general pattern of beginning with P or Q, following with five characters (mix of numbers and letters)
 +
 +
'''RefSeq Table'''
 +
*all ID's in form NP_######
 +
 +
==Links==
 +
{{Team ATK}}

Latest revision as of 18:56, 21 November 2013

Contents

[edit] Week 12 Information

Export Counting: -open Access, open file (remember to change all to all files) TIGR4 file:
ids used: SP_####
orderedlocusnames count total: 2126 entries
R6 file:
orderedlocusnames count total: 2115 entries
ids used: SPG_####
G54 file:
ids used: SPG_####
orderedlocusnames count total: 2115 entries
After finding identical results for R6 and G54 files, realized that R6 file was actually for the G54 strain. Checked a few times (reopened files multiple times to confirm)
First try on Tally Engine for TIGR4:
XML Count:
orderedlocus: 2127
refseq: 2106
Database Count:
ordered locus: 3831
refseq: 3403

[edit] Week 13

Tally Engine:

  • created new database in pgadmin III
  • in sql, opened gmbuilder.sql
  • ran query, database tables were inserted
  • went in to tally engine and imported files
    • Xml import took 5.41 min
    • GOA import took 0.07 min
  • unzipped go-xml file
  • OBO-XML import time: 19.92 min
  • additional gene ontology information was processed, this took 14.96 min
  • ran tally, came up with error
  • refreshed gmbuilder and tried again successfully

Results: TallyEngineTrial2.PNG



XMLpipedb Match

  • downloaded program from sourceforge
  • opened cmd program
  • cd Downloads file
  • moved xmlmatch jar file to download folder
  • used match to look for pattern SP_[0-9][0-9][0-9][0-9]
  • Total unique matches: 2126
  • almost identical to tally engine results of 2127, minus one result

Results: 20131107 XMLmatch tATK TIGR4 AJV.PNG


OriginalRowCounts

  • Looked at TIGR4 gdb file and benchmard VD file for table similarities/differences
  • seemed to have same tables/same information
  • took screenshots of both, included here:

TIGR4: 20131119 ogrowcounts tATK TIGR4 AJV.PNG Benchmark: 20131119 benchmarkrowcounts tATK TIGR4 AJV.PNG

  • Note: a few of the rows are missing in the benchmark screenshot- could not fit all of them on screen.


SQL

  • used following query to search for matches:
    • select count(*) from genenametype where type = 'ordered locus' and value ~ 'SP_[0-9][0-9][0-9][0-9]';
  • Result given was 2126

20131119 SQLcountresults tATK TIGR4 AJV.PNG

[edit] 11/21/13

Tally Engine for Export 3

  • downloaded Taurus's version of gmbuilder to redo tally engine counting
  • used export 3 files instead of previous export 1 files
  • connected to avreelan database in pgadminIII, inserted new gmbuilder tables
  • opened new version of gmbuilder/tally engine, connected to avreelan database
  • XML file import took: 2.02 min
  • OBO-XML file import took: 6.25 min
    • additional gene ontology data processing took: 4.81 min
  • GOA file import took: 0.04 min
  • Results:
    • GeneId's now visible, total of 2105 in both xml and database counts
    • orderedlocusnames still at same value of 2126 in both xml and database counts
    • screenshot: 20131121 TallyEngineE3 tATK TIGR4 AJV.PNG


Original Row Counts for Export 3

  • redid row counts using the export 3 file
  • compared with benchmark file
  • both files had identical number of tables with same categories in each, although some were out of order.
  • Screenshots:

E3 TIGR4: 20131121 E3rowcounts tATK TIGR4 AJV.PNG Benchmark:20131121 benchmarkrowcounts tATK TIGR4 AJV.PNG

Table Analysis

  • looked at tables within E3 gdb file to find inconsistencies in data

Systems Table
20131121 E3Systemstable tATK TIGR4 AJV.PNG

  • There are missing dates for quite a few gene ID systems

OrderedLocusNames Table

  • All ID's took the expected form, SP_####

UniProt Table

  • ID's are scattered. Have a general pattern of beginning with P or Q, following with five characters (mix of numbers and letters)

RefSeq Table

  • all ID's in form NP_######

[edit] Links

Alina's User Page Kevin's User Page Tauras's User Page
Biological Databases Class Page Gene Database Project Gene Database Project Report Guidelines

Streptococcus pneumoniae

Import Export Cycle 1: tATK Export One: TIGR4 Testing Report
Import Export Cycle 2: tATK E2: TIGR4 Testing Report
Import Export Cycle 3: tATK E3: TIGR4 Testing Report
Import Export Cycle 4: tATK E4: TIGR4 Testing Report
Data Information
Project Roles: Project Manager Coder GenMAPP User Quality Assurance
Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Ajvree_Week_13&oldid=6206"
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