Kevinmcgee Week 9 - Revision history

Kevinmcgee at 19:00, 24 October 2013

2013-10-24T19:00:22Z

Kevinmcgee: uploaded go file

2013-10-24T18:50:15Z

uploaded go file

Kevinmcgee: Added answers

2013-10-24T18:45:50Z

Added answers

Kevinmcgee: Added go obo xml file

2013-10-24T18:13:26Z

Added go obo xml file

Kevinmcgee at 18:06, 24 October 2013

2013-10-24T18:06:52Z

Kevinmcgee: added gdb file

2013-10-24T17:40:57Z

added gdb file

Kevinmcgee: Added work from tuesday

2013-10-24T16:28:23Z

Added work from tuesday

New page

==Export Information==

Version of GenMAPP Builder:2.0b70

Computer on which export was run: Last row of computer in the lab; second computer from the right when facing the front of the classroom.

Postgres Database name: Vibrio cholerae serotype O1_10_22_LM_KM

UniProt XML filename:[[File:Vibrio cholerae serotype O1_10_22_LM_KM.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]):
* Time taken to import: 8.49 minutes

GO OBO-XML filename:[[File:46.V_cholerae_ATCC_39315_10_22_LM_KM.txt]]
*Direct Download from Wiki due to connectivity problems.
* 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:20.02 minutes
* Time taken to process: 14.78 minutes

GOA filename: 46.V_cholerae_ATCC_39315_10_22_LM_KM.txt
* 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: 0.16 minutes

Name of .gdb file: Vc-Std_20131022_LM_KM-gmb2b70.gdb
* Time taken to export .gdb:
* Upload your file and link to it here.

Note: Export started around 11 am; ended at 3:19:06 pm.

← Older revision		Revision as of 19:00, 24 October 2013
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	<!--In this example, this query tells you which IDs are in Riley only:<br>		<!--In this example, this query tells you which IDs are in Riley only:<br>
	select Riley.ID from Riley left outer join Blattner on Riley.ID = Blattner.ID where Blattner.ID is null;-->		select Riley.ID from Riley left outer join Blattner on Riley.ID = Blattner.ID where Blattner.ID is null;-->
		+
		+
		+	[[User:Kevinmcgee\|Kevinmcgee]] ([[User talk:Kevinmcgee\|talk]]) 12:00, 24 October 2013 (PDT)
		+	[[category:Journal Entry]]
		+	[[category: shared]]
		+	*[[Week 9]]
		+	*[[Class Journal Week 9]]

← Older revision		Revision as of 18:45, 24 October 2013
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	[[file:Vc-Std_20131022_LM_KM-gmb2b70.gdb]]		[[file:Vc-Std_20131022_LM_KM-gmb2b70.gdb]]
		+
		+	==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).
		+
		+	[[image:Capture.PNG]]
		+
		+	== 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?
		+
		+	At first the match did not have the same results
		+
		+	[[image:Capture(1).PNG]]
		+
		+	After we added (A\| ) to the command, we were able to get the same results for both the tally engine and the XMLpipe DB Match
		+
		+	[[image:Capture(2).PNG]]
		+
		+	== 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.]]
		+
		+	[[image:Capture3.PNG]]
		+
		+	I was able to get a correct count on and SQL query as well
		+
		+	==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:
		+
		+	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
		+
		+	Note: There was one extra Ordered Locus name in the gdb file than there was in XML pipe DB Match or the Tally Engine.
		+
		+	[[image:Capture4.PNG ]]
		+
		+	Upon further inspection, we have found that this is because one of the Locus names was joined together with a slash mark.
		+
		+	[[image:Capture5.PNG]]
		+
		+	This can be proven by going back into XMLpipeDB Match and accounting for the / in the command. The command shows one significant name with a slash in it
		+
		+	[[image:Capture6.PNG]]
		+
		+	==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?
		+	**There is no date for the Gene ID's present
		+	* 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?
		+	**They all seem to be in the correct form
		+
		+	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:
		+
		+	<!--In this example, this query tells you which IDs are in Riley only:<br>
		+	select Riley.ID from Riley left outer join Blattner on Riley.ID = Blattner.ID where Blattner.ID is null;-->

← Older revision		Revision as of 17:40, 24 October 2013
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	Note: Export started around 11 am; ended at 3:19:06 pm.		Note: Export started around 11 am; ended at 3:19:06 pm.
		+
		+	[[file:Vc-Std_20131022_LM_KM-gmb2b70.gdb]]

@@ Line 17: / Line 17: @@
 * Time taken to process: 14.78 minutes
-GOA filename: 46.V_cholerae_ATCC_39315_10_22_LM_KM.txt
+GOA filename: [[file: 46.V_cholerae_ATCC_39315_10_22_LM_KM.txt]]
 * 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: 0.16 minutes

@@ Line 5: / Line 5: @@
 Computer on which export was run: Last row of computer in the lab; second computer from the right when facing the front of the classroom.
-Postgres Database name: [[File:Vibrio_cholerae_serotype_O1_10_22_LM_KM.xml]]
+Postgres Database name: Vibrio_cholerae_serotype_O1_10_22_LM_KM
 UniProt XML filename:[[File:Vibrio cholerae serotype O1_10_22_LM_KM.xml]]
@@ Line 11: / Line 11: @@
 * Time taken to import: 8.49 minutes
-GO OBO-XML filename:[[File:46.V_cholerae_ATCC_39315_10_22_LM_KM.txt]]
+GO OBO-XML filename:[[File:Go_daily-termdb.obo-10_22-LM-KM.xml.gz]]
 *Direct Download from Wiki due to connectivity problems.
 * 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):