Ksherbina Week 9 - Revision history

Ksherbina: Added categories

2013-10-31T00:51:08Z

Added categories

2013-10-25T07:14:56Z

‎Export Information: Added links to files.

2013-10-25T07:12:53Z

‎Export Information: Added link to Uniprot XML file

2013-10-25T07:04:48Z

‎Check the Quality of the Exported Database: Made a modification to last bullet.

2013-10-25T06:51:47Z

‎.gdb Use in GenMAPP: Explained why I could not use GenMAPP with the database created.

2013-10-25T06:43:00Z

‎Visual Inspection: Added results.

2013-10-25T06:37:38Z

‎OriginalRowCounts Comparison: Recorded results

2013-10-25T06:34:25Z

‎Check the Quality of the Exported Database: Added steps on how to use the .gdb file in Excel.

2013-10-25T06:27:47Z

‎Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine: Recorded the results.

2013-10-25T06:24:52Z

‎Check the Quality of the Exported Database: Removed the count generated using the SQL query to put it in another section.

← Older revision		Revision as of 00:51, 31 October 2013
Line 211:		Line 211:
	*Open the .gdb file (Vc-Std_KS_20131022.gdb) that was exported using GenMAPP Builder.		*Open the .gdb file (Vc-Std_KS_20131022.gdb) that was exported using GenMAPP Builder.
	*In the Tables window, double-click on the table named ''OriginalRowCounts'' and look at the row titled ''OrderedLocusNames'' to see how many gene IDs Microsoft Access detected in the file.		*In the Tables window, double-click on the table named ''OriginalRowCounts'' and look at the row titled ''OrderedLocusNames'' to see how many gene IDs Microsoft Access detected in the file.
		+
		+	[[Category:Journal Entry]]
		+	[[Category:Individual Homework]]

@@ Line 17: / Line 17: @@
 * Time taken to import: 4.20 minutes
-GO OBO-XML filename: go_daily-termdb_KS_20131022.obo-xml
+GO OBO-XML filename: [[Media:GOA and GO Files KS 20131013.zip|go_daily-termdb_KS_20131022.obo-xml]]
 * 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: 8.81 minutes
 * Time taken to process: 7.33 minutes
-GOA filename: 46.V_cholerae_ATCC_39315_KS_20131022.goa
+GOA filename: [[Media:GOA and GO Files KS 20131013.zip|46.V_cholerae_ATCC_39315_KS_20131022.goa]]
 * 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]): Latest version released 10/16/2013
 * Time taken to import: 0.10 minutes

@@ Line 13: / Line 13: @@
 Postgres Database name: VC_KS_20131022_gmb2b70
-UniProt XML filename: UniProt_V_cholerae_KSTV_20131022.xml
+UniProt XML filename: [[Media:UniProt V cholerae KSTV 20131022.xml|UniProt V cholerae KSTV 20131022.xml]]
 * UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
 * Time taken to import: 4.20 minutes

@@ Line 210: / Line 210: @@
 *Open Microsoft Access.
 *Open the .gdb file (Vc-Std_KS_20131022.gdb) that was exported using GenMAPP Builder.
-*In the Tables window, double-click on the table named ''OriginalRowCounts''.
+*In the Tables window, double-click on the table named ''OriginalRowCounts'' and look at the row titled ''OrderedLocusNames'' to see how many gene IDs Microsoft Access detected in the file.

@@ Line 109: / Line 109: @@
 ===.gdb Use in GenMAPP===
-Note:
+Note: '''I tried to create an expression dataset using the Merrell et al. data normalized last week and the gene database created this week. As expected, none of the genes in the data matched the genes in the database because the IDs in the latter have underscores while the IDs in the former do not.'''
 ====Putting a gene on the MAPP using the GeneFinder window====

@@ Line 101: / Line 101: @@
 * 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:

← Older revision		Revision as of 06:37, 25 October 2013
Line 58:		Line 58:

	Copy the OriginalRowCounts table and paste it here:		Copy the OriginalRowCounts table and paste it here:
		+
		+	*Table Rows
		+	*EMBL 228
		+	*GeneOntology 5556
		+	*GeneOntologyCount 3239
		+	*GeneOntologyTree 97982
		+	*Info 1
		+	*InterPro 4349
		+	*OrderedLocusNames 3832
		+	*OrderedLocusNames-EMBL 4111
		+	*OrderedLocusNames-GeneOntology 20613
		+	*OrderedLocusNames-InterPro 9723
		+	*OrderedLocusNames-PDB 235
		+	*OrderedLocusNames-Pfam 4367
		+	*Other 0
		+	*PDB 223
		+	*Pfam 2102
		+	*RefSeq 3403
		+	*RefSeq-EMBL 3669
		+	*RefSeq-GeneOntology 18931
		+	*RefSeq-InterPro 9241
		+	*RefSeq-OrderedLocusNames 3520
		+	*RefSeq-PDB 234
		+	*RefSeq-Pfam 4145
		+	*Relations 18
		+	*Systems 30
		+	*UniProt 3784
		+	*UniProt-EMBL 5452
		+	*UniProt-GeneOntology 20464
		+	*UniProt-GOCount 3240
		+	*UniProt-InterPro 10393
		+	*UniProt-OrderedLocusNames 3832
		+	*UniProt-PDB 319
		+	*UniProt-Pfam 4648
		+	*UniProt-RefSeq 3635

	Note:		Note:

← Older revision		Revision as of 06:34, 25 October 2013
Line 171:		Line 171:
	*Count the number of unique gene IDs using the following query:		*Count the number of unique gene IDs using the following query:
	select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_(A\|)[0-9][0-9][0-9][0-9]'		select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_(A\|)[0-9][0-9][0-9][0-9]'
		+	*Open Microsoft Access.
		+	*Open the .gdb file (Vc-Std_KS_20131022.gdb) that was exported using GenMAPP Builder.
		+	*In the Tables window, double-click on the table named ''OriginalRowCounts''.

← Older revision		Revision as of 06:27, 25 October 2013
Line 49:		Line 49:

	[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL \| Follow the instructions on this page to query the PostgreSQL Database.]]		[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL \| Follow the instructions on this page to query the PostgreSQL Database.]]
		+	*'''There were 3831 matches found using an SQL query (the same as with TallyEngine).'''

	===OriginalRowCounts Comparison===		===OriginalRowCounts Comparison===

← Older revision		Revision as of 06:24, 25 October 2013
Line 170:		Line 170:
	*Count the number of unique gene IDs using the following query:		*Count the number of unique gene IDs using the following query:
	select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_(A\|)[0-9][0-9][0-9][0-9]'		select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_(A\|)[0-9][0-9][0-9][0-9]'
−	~~Count = 3831~~