TV test - Revision history

Taur.vil: /* TallyEngine */ verified and inserted photo

2013-10-24T16:56:46Z

‎TallyEngine: verified and inserted photo

Taur.vil: /* Export Information */ upload export file

2013-10-24T16:36:53Z

‎Export Information: upload export file

Taur.vil: /* Export Information */ added final time

2013-10-24T08:31:48Z

‎Export Information: added final time

Taur.vil: /* Export Information */

2013-10-23T03:45:55Z

‎Export Information

Taur.vil: /* Export Information */ uniprot import on own comp

2013-10-23T02:20:40Z

‎Export Information: uniprot import on own comp

Taur.vil: /* Export Information */

2013-10-22T17:21:20Z

‎Export Information

Taur.vil: /* Export Information */ added database name

2013-10-22T17:07:46Z

‎Export Information: added database name

Taur.vil: /* Export Information */ added links and notes

2013-10-22T17:06:03Z

‎Export Information: added links and notes

Taur.vil: adding file names

2013-10-22T16:56:06Z

adding file names

Taur.vil: Pasting testing report sample

2013-10-22T16:41:36Z

Pasting testing report sample

New page

==Export Information==

Version of GenMAPP Builder:

Computer on which export was run:

Postgres Database name:

UniProt XML filename:
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]):
* Time taken to import:

GO OBO-XML filename:
* 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):
* Time taken to import:
* Time taken to process:

GOA filename:
* 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]):
* Time taken to import:

Name of .gdb file:
* Time taken to export .gdb:
* Upload your file and link to it here.

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 PostgreSQL databases (or you can upload and link to a screenshot of the results).

== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#XMLPipeDB_Match | 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?

== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==

[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL | Follow the instructions on this page to query the PostgreSQL Database.]]

==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 [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download here].

Copy the OriginalRowCounts table and paste it here:

Note:

==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?
* 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?

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.

Note:

← Older revision		Revision as of 16:56, 24 October 2013
Line 31:		Line 31:

	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).		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).
		+
		+	Tally verified: [[Image:Tally_ENgine_output.PNG]]

	== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==		== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

@@ Line 24: / Line 24: @@
 : started at 20:15, finished by 23:30
-* Upload your file and link to it here.
+* Upload your file and link to it here. [[Media:Vc-Std 20131022 TVKS gmb2b70.gdb|gdb export file]]
 Note:

@@ Line 21: / Line 21: @@
 Name of .gdb file:
-* Time taken to export .gdb:
+* Time taken to export .gdb:~3 hours
-: started at 20:15
+: started at 20:15, finished by 23:30
 * Upload your file and link to it here.

@@ Line 9: / Line 9: @@
 UniProt XML filename: VC_2013_10_22_TVKS.xml
 * UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]):
-* Time taken to import: 8.31 minutes
+* Time taken to import: 8.31 minutes (0.15 on own computer)
 GO OBO-XML filename: go_daily-termdb_TVKS_2013_10_22.obo-xml

@@ Line 9: / Line 9: @@
 UniProt XML filename: VC_2013_10_22_TVKS.xml
 * UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]):
-* Time taken to import:
+* Time taken to import: 8.31 minutes
 GO OBO-XML filename: go_daily-termdb_TVKS_2013_10_22.obo-xml

@@ Line 5: / Line 5: @@
 Computer on which export was run:BIOL 206, back right
-Postgres Database name:
+Postgres Database name: VC_TVKS_2013_10_22_gmb2b70
 UniProt XML filename: VC_2013_10_22_TVKS.xml

@@ Line 1: / Line 1: @@
 ==Export Information==
-Version of GenMAPP Builder:
+Version of GenMAPP Builder: 2.0b70
-Computer on which export was run:
+Computer on which export was run:BIOL 206, back right
 Postgres Database name: