Kmeilak Week 9
Export Information
Version of GenMAPP Builder: gmbuilder-2.0b70
Computer on which export was run: bio105 (front row, second from right side of class)
Postgres Database name: vc_kmeilak_20131022-gmb2b70
UniProt XML filename: uniprot-organism%3A243277+keyword%3A1185_KM_10_22_2013.xml
- UniProt XML version (The version information can be found at the UniProt News Page):
- Time taken to import: 2.8 minutes
GO OBO-XML filename: go_daily-termdb_KM_10_22_2013.obo-xml
- 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):
- Time taken to import: 5.91 minutes
- Time taken to process: 4.54 minutes
GOA filename: 46.V_cholerae_ATCC_39315_KM_10_22_2013.goa
- GOA version (News on this page records past releases; current information can be found in the Last modified field on the FTP site):
- Time taken to import: 0.06 minutes
Name of .gdb file: Vc-Std_KM_20131022-gmb2b70.gdb
- Time taken to export .gdb: 109.54 minutes
- Upload your file and link to it here. Media:Vc-Std_KM_20131022-gmb2b70.gdb
Note: Export ended 12:09:54 pm.
TallyEngine
Run the TallyEngine in GenMAPP Builder and record the number of records for UniProt and GO in the XML data and in the PostgreSQL databases (or you can upload and link to a screenshot of the results).
XML Count
- UniProt - 3784
- Ordered Locus - 3831
- RefSeq - 3403
- Geneld - 0
- GO Terms - 39972
Database Count
- UniProt - 3784
- Ordered Locus - 3831
- RefSeq - 3403
- Geneld - 0
- GO Terms - 39972
Using XMLPipeDB match to Validate the XML Results from the TallyEngine
Follow the instructions found on this page to run XMLPipeDB match.
Are your results the same as you got for the TallyEngine? Why or why not?
Initially the results were different (2738 instead of the expected 3831), but when the command was changed to include the possibility of VCA files, the expected result was obtained.
Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine
Follow the instructions on this page to query the PostgreSQL Database.
The PostgreSQL Database was queried using the command found on the above page, and the expected result of 3831 was obtained for the count.
OriginalRowCounts Comparison
Within the .gdb file, look at the OriginalRowCounts table to see if the database has the expected tables with the expected number of records. Compare the tables and records with a benchmark .gdb file.
Benchmark .gdb file: (for the Week 9 Assignment, use the "Vc-Std_External_20101022.gdb" as your benchmark, downloadable from here.
Copy the OriginalRowCounts table and paste it here:
KM gdb
- Table Rows
- Info 1
- Systems 30
- Relations 18
- Other 0
- GeneOntologyTree 97982
- GeneOntology 5556
- UniProt-GOCount 3240
- GeneOntologyCount 3239
- UniProt-GeneOntology 20464
- UniProt 3784
- Pfam 2102
- RefSeq 3403
- PDB 223
- InterPro 4349
- OrderedLocusNames 3832
- EMBL 228
- UniProt-EMBL 5452
- UniProt-OrderedLocusNames 3832
- UniProt-PDB 319
- UniProt-InterPro 10393
- UniProt-RefSeq 3635
- UniProt-Pfam 4648
- RefSeq-Pfam 4145
- RefSeq-InterPro 9241
- RefSeq-PDB 234
- RefSeq-OrderedLocusNames 3520
- RefSeq-EMBL 3669
- OrderedLocusNames-Pfam 4367
- OrderedLocusNames-InterPro 9723
- OrderedLocusNames-PDB 235
- OrderedLocusNames-EMBL 4111
- RefSeq-GeneOntology 18931
- OrderedLocusNames-GeneOntology 20613
Vc_External gdb
- Table Rows
- Info 1
- Systems 30
- Relations 26
- Other 0
- GeneOntologyTree 35314
- GeneOntology 3829
- UniProt-GOCount 2467
- GeneOntologyCount 2466
- UniProt-GeneOntology 13289
- UniProt 3784
- Pfam 1955
- RefSeq 3827
- GeneId 3827
- PDB 157
- InterPro 3942
- OrderedLocusNames 7664
- EMBL 293
- UniProt-EMBL 5742
- UniProt-OrderedLocusNames 7664
- UniProt-PDB 243
- UniProt-InterPro 9565
- UniProt-GeneId 4125
- UniProt-RefSeq 4125
- UniProt-Pfam 4601
- RefSeq-Pfam 4263
- RefSeq-GeneId 3971
- RefSeq-InterPro 8840
- RefSeq-PDB 169
- RefSeq-OrderedLocusNames 7942
- RefSeq-EMBL 4260
- GeneId-Pfam 4263
- GeneId-InterPro 8840
- GeneId-PDB 169
- GeneId-OrderedLocusNames 7942
- GeneId-EMBL 4260
- OrderedLocusNames-Pfam 8538
- OrderedLocusNames-InterPro 17712
- OrderedLocusNames-PDB 338
- OrderedLocusNames-EMBL 8540
- GeneId-GeneOntology 13332
- RefSeq-GeneOntology 13332
- OrderedLocusNames-GeneOntology 26702
Note: The VC_external had more table entries (43) than the KM gdb did (33). The majority of the number counts were different across the two files, with only the following being similar.
- Info
- Systems
- Other
- UniProt
Visual Inspection
Perform visual inspection of individual tables to see if there are any problems.
- Look at the Systems table. Is there a date in the Date field for all gene ID systems present in the database?
- No, there is not a date in the Date field for all gene ID systems present in the database.
- Open the UniProt, RefSeq, and OrderedLocusNames tables. Scroll down through the table. Do all of the IDs look like they take the correct form for that type of ID?
- The ordered locus names and RefSeq tables have included an underscore (_) in between the initial letters and number code. The UniProt IDs look standard.
Note:
.gdb Use in GenMAPP
Note:
Putting a gene on the MAPP using the GeneFinder window
- Try a sample ID from each of the gene ID systems. Open the Backpage and see if all of the cross-referenced IDs that are supposed to be there are there.
Note:
Creating an Expression Dataset in the Expression Dataset Manager
- How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset. Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?
Note:
Coloring a MAPP with expression data
Note:
Running MAPPFinder
Note:
Compare Gene Database to Outside Resource
The OrderedLocusNames IDs in the exported Gene Database are derived from the UniProt XML. It is a good idea to check your list of OrderedLocusNames IDs to see how complete it is using the original source of the data (the sequencing organization, the MOD, etc.) Because UniProt is a protein database, it does not reference any non-protein genome features such as genes that code for functional RNAs, centromeres, telomeres, etc.
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