Difference between revisions of "Lena Project Notebook"

Revision as of 18:18, 19 November 2013

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

Using XMLPipeDB match to Validate the XML Results from the TallyEngine

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

ID pattern Uniprot: 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.

Export Information

Uniprot:

Version: UniProt release 2013_10 - October 16, 2013

File:UniprotXML Leishmania 05112013 Gabe Lena.xml

GO OBO:

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

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

GOA:

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

Week 14

Week 15

Links

Lena Hunt

Leishmania major

Quality Assurance