Lena Project Notebook

Week 12

Gabriel and I performed an import/export cycle on 11/14/2013.

Export Information

Uniprot: 7.12 minutes

Version: UniProt release 2013_10 - October 16, 2013

File:UniprotXML Leishmania 05112013 Gabe Lena.xml

GO OBO: 6.32 minutes

Version: Monday, ‎November ‎04, ‎2013, ‏‎2:03:38 AM

File:Leishmania 05112013 Gabe Lena.obo-xml.gz

GOA: 4.54 minutes

Version: 14 November, 2013

12-Nov-2013 11:47 3.0M

http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/21780.L_major.goa

File:LeishmaniaGOA 19112013 Lena Gabe.goa

Name of .gdb file

Leishmania_05112013_Lena_Gabe.gdb

File:Leishmania 05112013 Lena Gabe.gdb

Tally Engine

Original Row Counts Comparison

• Uniprot has 8041 which is the same the tallycount.
• There were 0 ordered locus, which is the same as the tallycount.
• There were 8315 hits for RefSeq, which is 2 fewer than was seen in the tallycount.
• There were 8315 hits for GeneID, which is 2 fewer than was seen in the tallycount.

Note:Leishmania major does not have "ordered locus names," instead they are tagged as "ORF."

File Management

• To keep the names of our files consistent, we agreed to name files with 1.) an identifier of what the file contains (such as "Uniprot") 2.) Leishmania 3.) the date in format MMDDYYYY 4.) names of Team members.
• An example of our file titles is: UniprotXML Leishmania 05112013 Gabe Lena.xml
• All files are stored on the main page for Leishmania major for ease of access. On the computer, the files are stored in the Downloads file.

System IDs

OrderedLocusPattern: LmjF##.#### or LmjF_##_#### or LmjF.##.####

Taxon ID: 5664

Week 13

• I updates the export files. The files now have the proper identification information to be found again. The GOA file had to re-downloaded to a more updated version and now has to be imported.
• The reason why no Ordered Locus Names turned up on the tally engine is that Leishmania major's Ordered Locus Names are tagged with ORF instead. Gabe re-coded to account for this.
• Built new database called Leishmania_major_18112013 and ran a new import/export cycle with the updated files.

• My target for this week was to get to know System IDs, and characterize regular expression patterns to detect the IDs. I found ID pattern to be: LmjF##.#### or LmjF_##_#### or LmjF.##.####
• A customized database was built for Leishmania major File:Leishmania major 19112013 Dist.zip

Export Information

Uniprot: 7.42 minutes

Version: UniProt release 2013_10 - October 16, 2013

File:UniprotXML Leishmania 05112013 Gabe Lena.xml

GO OBO: 5.96

Gene Ontology Processing: 4.48 minutes

Version: Monday, ‎November ‎04, ‎2013, ‏‎2:03:38 AM

File:Leishmania 05112013 Gabe Lena.obo-xml.gz

• NOTE:When we went to import this file we got an error message. The file that should be used was called Leishmania_05112013_Gabe_Lena.obo-xml. This file type is not uploadable to the wiki, and so only the zipped version is available. Just remember to use unzipped version for uploads.

GOA: 0.04

Version: 14 November, 2013

12-Nov-2013 11:47 3.0M

http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/21780.L_major.goa

File:LeishmaniaGOA 19112013 Lena Gabe.goa

Name of .gdb file: LeishmaniaGDB_19112013_LenaLGabe/gdb

Leishmania_05112013_Lena_Gabe.gdb

File:Leishmania 05112013 Lena Gabe.gdb

11/21/13: The new database was labeled as generic when we tried to open it before. Today we tried to open a OrderedLocusName in GenMAPP but the gene was not found. The database has to be re-coded and re-exported. I edited the database in eclipse. When we exported to GenMAPP it finally recognized the database. We saved as Media:LeishmaniaGDB 21112013 Lena Gabe.gdb.

Week 14

• Configured Leishmania_major-18112013 in GenMAPP Builder, and ran Tally engine.

Tally Engine

• Finally, the numbers are matching, but the Ordered Locus names are still missing. This may be because Ordered Locus Names are called ORFs for Leishmania major.

XMLpipedb Match

• We XML pipedb Match query to see if we could find the missing terms. "ORF" yielded 40 results; "ordered locus name" yielded 0 results.

• Used Match in the command line. Found 33 matched to lmjf_##_####. Now we have to figure how to get the computer to get either an underscore or period in the name.

Week 15

GenMAPP Expression Dataset Manager

Database: LeishmaniaGDB_26112013_Lena_Gabe.gdb

File: LeishmaniaCompiledStatAnalysis(A).txt

Errors: 14,000 and counting

Started over and cleaned up the gene IDs in the excel report so that the names followed the pattern. Ran Expression Dataset Manager again.

Errors: 1820

Had to tweak the database with new customizations and re-export.

8354 Ordered Locus names in Microsoft Access. All IDS now have two formats LmjF.##.#### and LmjF_##_####.

Reran Expression Dataset Manager and found 1820 errors.

The exceptions file was posted to the Leishmania wiki page

Links

Lena Hunt

Leishmania major

Quality Assurance