Difference between revisions of "Gene Database Testing Report- cw20151201"

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==Files Asked for in the Gene Database Testing Report==
 
==Files Asked for in the Gene Database Testing Report==
−
For convenience, all of the files explicitly asked for in the "Gene Database Testing Report" section were compressed together in this file: [[]]
+
For convenience, all of the files explicitly asked for in the sections below were compressed together in this file: [[File:Gdtr cw20151201.zip]]
−
(FOCUS ON KEEPING FILE NAMES CONSISTENT DURING UPLOAD)
+
  
 
==Pre-requisites==
 
==Pre-requisites==
Line 18: Line 17:
  
 
*I download the UniProt XML, GOA, and GO OBO-XML files for ''Bordetella Pertussis'' along with the GenMAPP Builder program.
 
*I download the UniProt XML, GOA, and GO OBO-XML files for ''Bordetella Pertussis'' along with the GenMAPP Builder program.
−
**All files were saved to the folder ''Bklein7_CW'' on my computer's ThawSpace.
+
**All files were saved to the folder ''Bklein7_CW\bpertussis_cw20151201'' on my computer's ThawSpace.
 
**Files that required extraction were unzipped using [http://www.7-zip.org/ 7-zip].
 
**Files that required extraction were unzipped using [http://www.7-zip.org/ 7-zip].
 
**Data files that remained in a folder after unzipping were removed from their folders to facilitate organization and command line processing.
 
**Data files that remained in a folder after unzipping were removed from their folders to facilitate organization and command line processing.
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====Downloaded GenMAPP Builder====
 
====Downloaded GenMAPP Builder====
  
−
# I downloaded the vanilla version of ''gmbuilder'' including the ''Bordetella pertussis'' custom class: [[File:Dist cw20151201.zip]].
+
# I downloaded the first custom version of ''gmbuilder'' including the ''Bordetella pertussis'' custom class: [[File:Dist cw20151201.zip]].
 
# I extracted the GenMAPP Builder folder using [http://www.7-zip.org/ 7-zip].
 
# I extracted the GenMAPP Builder folder using [http://www.7-zip.org/ 7-zip].
  
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* I launched ''pgAdmin III'' and connected to the PostgreSQL 9.4 server (localhost:5432).
 
* I launched ''pgAdmin III'' and connected to the PostgreSQL 9.4 server (localhost:5432).
−
** On this server, I created a new database: ''bpertussis_cw20151201_gmb3build5custom''.
+
** On this server, I created a new database: ''bpertussis_cw20151201_gmb3build5''.
 
** I opened the SQL Editor tab to use an XMLPipeDB query to create the tables in the database.
 
** I opened the SQL Editor tab to use an XMLPipeDB query to create the tables in the database.
 
*** I clicked on the Open File icon and selected the file ''gmbuilder.sql''. This imported a series of SQL commands into the editor tab.
 
*** I clicked on the Open File icon and selected the file ''gmbuilder.sql''. This imported a series of SQL commands into the editor tab.
Line 80: Line 79:
 
* I typed my name in the owner field (Brandon Klein).
 
* I typed my name in the owner field (Brandon Klein).
 
* I selected "Bordetella pertussis (strain Tohama I/ATCC BAA-589/NCTC 13251), Taxon ID 257313" as the gene database species and then clicked ''Next''.
 
* I selected "Bordetella pertussis (strain Tohama I/ATCC BAA-589/NCTC 13251), Taxon ID 257313" as the gene database species and then clicked ''Next''.
−
* The database was saved as ''bpertussis-std_cw20151119''.
+
* The database was saved as ''bpertussis-std_cw20151201''.
 
* I checked the boxes for exporting all Molecular Function, Cellular Component, and Biological Process Gene Ontology Terms.
 
* I checked the boxes for exporting all Molecular Function, Cellular Component, and Biological Process Gene Ontology Terms.
 
* Finally, I clicked the "Next" button to begin the export process.
 
* Finally, I clicked the "Next" button to begin the export process.
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Postgres Database name: bpertussis_cw20151201_gmb3build5custom
 
Postgres Database name: bpertussis_cw20151201_gmb3build5custom
  
−
UniProt XML filename: [[]]
+
UniProt XML filename: [[File:Uniprot-proteome-UP000002676 cw20151201.zip]]
 
* UniProt XML version (The version information was found at [http://uniprot.org/news the UniProt News Page]): 2015_11
 
* UniProt XML version (The version information was found at [http://uniprot.org/news the UniProt News Page]): 2015_11
 
* UniProt XML download link: [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)]
 
* UniProt XML download link: [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)]
−
* Time taken to import: 2.65 minutes
+
* Time taken to import: 2.59 minutes
−
** Note: The import time was only 0.05 minutes longer than when creating the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb. No interruptions occurred during this process.
+
** Note: The import time was nearly equivalent to that when creating the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (2.60 minute). No interruptions occurred during this process.
  
−
GO OBO-XML filename: [[]]
+
GO OBO-XML filename: [[File:Go daily-termdb cw20151201.zip]]
−
* GO OBO-XML version (The version information was found in the file properties): Last Modified- ‎Thursday, ‎November ‎19, ‎2015, ‏‎2:24:27 AM
+
* GO OBO-XML version (The version information was found in the file properties): Last Modified- ‎‎December ‎01, ‎2015, ‏‎2:21:31 AM
 
* GO OBO-XML download link: [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology legacy download page]
 
* GO OBO-XML download link: [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology legacy download page]
−
* Time taken to import: 7.55 minutes  
+
* Time taken to import: 7.08 minutes  
−
* Time taken to process: 4.43 minutes
+
* Time taken to process: 4.42 minutes
 
** Note: The import and processing times were similar to those for the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (6.99 minutes and 4.48 minutes respectively). No interruptions occurred during these processes.
 
** Note: The import and processing times were similar to those for the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (6.99 minutes and 4.48 minutes respectively). No interruptions occurred during these processes.
  
−
GOA filename: [[File:145.B pertussis ATCC BAA-589 cw20151119.zip]]
+
GOA filename: [[File:145.B pertussis ATCC BAA-589 cw20151201.zip]]
 
* GOA version (found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): Last Modified- 11/10/15 1:39:00 PM
 
* GOA version (found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): Last Modified- 11/10/15 1:39:00 PM
 
* GOA download link: [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/145.B_pertussis_ATCC_BAA-589.goa for ''Bordetella pertussis'' strain Tohama I]
 
* GOA download link: [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/145.B_pertussis_ATCC_BAA-589.goa for ''Bordetella pertussis'' strain Tohama I]
−
* Time taken to import: 0.03 minutes
+
* Time taken to import: 0.04 minutes
−
** Note: The import time was similar to that of the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (0.04 minutes). No interruptions occurred during this process.
+
** Note: The import time was equal to that of the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb. No interruptions occurred during this process.
  
−
Name of .gdb file: [[File:Bpertussis-std cw20151119.zip]]
+
Name of .gdb file: [[File:Bpertussis-std cw20151201.zip]]
 
* Time taken to export:  
 
* Time taken to export:  
−
** Start time: 5:44 PM
+
** Start time: 4:06 PM
−
** End time:  
+
** End time: 5:00 PM
−
** Elapsed time:
+
** Elapsed time: 54 minutes
−
Note: All export windows remained open when I returned to check the export status. No interruptions occurred during the export process.
+
Note: No interruptions occurred during the export process.
  
−
===TallyEngine===
+
===Confirming that Changes to GenMAPP Builder Worked As Expected===
 +
#Systems Table Update
 +
#*In creating the ''Bordetella pertussis'' custom class, changes were implemented to edit the ''OrderedLocusNames'' column in the exported .gdb file. Specifically, the species should be listed as ''Bordetella pertussis'' and a custom GeneDB link should be included in this row.
 +
#*To verify that these changes were working as expected, I opened the file bpertussis-std_cw20151201.gdb in Microsoft Access. Upon opening ''Systems'' table here, all changes were successfully implemented:
 +
#**[[File: Systemstable_cw20151201.png]]
 +
#GenMAPP Gene Backpage Update
 +
#*The ''OrderedLocusNames'' GeneDB link added (as described above) also was designed to have funcitonality in GenMAPP. Sepcifically, gene backpages opened while using this gene database in GenMAPP should redirect users to the GeneDB information page for the specific ''Bordetella pertussis'' gene.
 +
#*I specified bpertussis-std_cw20151201.gdb as the gene database in GenMAPP and put the gene BP3701 on the map. When I clicked on the link to the ID "BP3701" under "OrderedLocusNames" in Gene Finder, I was successfully brought to the corresponding GeneDB information page:
 +
#**[[File:Custombackpage cw20151201.PNG]]
  
−
* I ran the TallyEngine in GenMAPP Builder and specified the following files:
+
==Team Information & Links==
−
**XML- [[File:Uniprot-proteome-UP000002676 cw20151119.zip]]
+
−
**GO- [[File:Go daily-termdb cw20151119.zip]]
+
−
*Results:
+
−
**[[File:TallyEngine cw20151119.png]]
+
−
**All tally results were consistent across both files.
+
−
=== Using XMLPipeDB match to Validate the XML Results from the TallyEngine===
+
−
The following functions were performed using the Windows command line (cmd).
+
−
*I entered my project folder using the following command:
+
−
cd /d T:\Bklein7_CW
+
−
*I used XMLPipeDB match to identify matches of any ordered locus name following the pattern "BP####" in the UniProt XML file. The command sequence used is as follows:\
+
−
java -jar xmlpipedb-match-1.1.1.jar "BP[0-9][0-9][0-9][0-9]" < "uniprot-proteome%3AUP000002676_cw20151119.xml"
+
−
*Match Results:
+
−
**[[File:XMLPipeDBMatch cw20151119.png]]
+
−
**The total number of unique matches listed above, 3438, differs from the Order Locus Names count of 3435 produced by the Tally Engine. Thus, 3 gene IDs present in the original XML file were not imported into ''bpertussis-std_cw20151119.gdb''.
+
  
−
=== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine===
+
{{Template:Class Whoopers}}
−
I ran a SQL query designed to match the pattern BP####:
+
−
 
+
−
select count (*) from genenametype where type = 'ordered locus' and value ~ 'BP[0-9][0-9][0-9][0-9]';
+
−
 
+
−
Results:
+
−
*[[File:SQLQuery cw20151119.png]]
+
−
* The number of unique matches yielded by this SQL query, 3435, matched that produced by the Tally Engine. However, this count was also 3 less than that yielded by the XMLPipeDB Match result reported above. This further indicates that there was an error present in importing all gene IDs from the original XML file.
+
−
 
+
−
===OriginalRowCounts Comparison===
+
−
 
+
−
I opened the gene database file [[File:Bpertussis-std cw20151119.zip]] in  Microsoft Access and assessed the "OriginalRowCounts" table to see if the expected tables were listed with the expected number of records. The contents of this table were compared to the ''OriginalRowCounts'' table of an existing .gdb file created during Week 9.
+
−
+
−
Benchmark .gdb file: ''Vc-Std_20151027_TR''
+
−
 
+
−
"OriginalRowCounts" table from the benchmark and new gdb:
+
−
*[[File:OriginalRowCountsComparison cw20151119.PNG]]
+
−
*All 52 tables present in the 2015 ''Vibrio cholerae'' database were also present in the ''B. pertussis'' database tagged _cw20151119. This confirmed that all expected tables were successfully created.
+
−
*Further, the "OrderedLocusNames" count of 3435 generated by the Tally Engine was confirmed to reflect that actual contents of the database.
+
−
 
+
−
Note: The "OriginalRowCounts" tables were too large to screenshot. To circumvent this problem and facilitate the comparison, I copied the "OriginalRowCounts" tables from both gene databases into an Excel file and zoomed out. The above screenshot was taken from this Excel file. The "OrderedLocusNames" row counts are highlighted in yellow.
+
−
 
+
−
===Visual Inspection===
+
−
I visually inspected individual tables within [[File:Bpertussis-std cw20151119.zip]] using Microsoft Access.
+
−
*Systems Table
+
−
**35 gene ID systems were listed, 11 of which listed the appropriate import date (11/19/2015)
+
−
***All gene ID systems relevant to ''B. pertussis'' were listed. This includes: EMBL, EnsemblBacteria, GeneID, GeneOntology, InterPro, OrderedLocusNames, Pfam, RefSeq, and UniProt.
+
−
***This result corresponded with that of the benchmark .gdb file listed in the "OriginalRowCounts Comparison" section.
+
−
*UniProt Table
+
−
**This table contained 3258 entries with 6 character IDs.
+
−
**All ID's in the UniProt table conform to the following pattern: [[File:UniProt Ascension Number info.PNG]]
+
−
**There are no apparent issues with the 3258 entries. However, it is curious that only 3258 out of 3438 IDs identified through XMLPipeDB Match made it into the database. This suggests the need for gmbuilder coding changes.
+
−
*RefSeq Table
+
−
**This table contained 6627 entries. All IDs began with one of three prefixes: "NP_", "YP_", or "WP_". The meanings of these prefixes can be found in the RefSeq documentation found [http://www.ncbi.nlm.nih.gov/books/NBK50679/ here].
+
−
***"NP_" and "YP_" Prefixes
+
−
****Refer to proteins. There are 3410 "NP_" IDs and 7 "YP_" IDs.
+
−
***"WP_" Prefixes
+
−
****Refer to "autonomous non-redundant proteins that are not yet directly annotated on a genome". There were 3210 IDs with the "WP_" prefixes.
+
−
***Overall, every entry in the ID column was an expected value.
+
−
*OrderedLocusNames Table
+
−
**This table contained 3435 entries (consistent with Tally Engine & SQL counts).
+
−
**The IDs were copied into an Excel document for analysis:
+
−
***3434 IDs conformed to the pattern "BP####"
+
−
***1 ID was unique: "BP3167.1"
+
−
 
+
−
===.gdb Use in GenMAPP===
+
−
 
+
−
<!--Need to add more instructions here.-->
+
−
*By following the instructions in [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols Part 2 of the ''Vibrio cholerae'' Microarray Data Analysis] and looking at Brandon's Week 9 individual journal assignment, I was able to verify that our Gene Database works in GenMAPP.
+
−
*I was able to open the GenMAPP program on the computer, and then I went to Data -> Choose Gene Database -> and selected the cw20151119 gdb file.
+
−
**There were no problems thus far as our database was able to load into the program.
+
−
 
+
−
====Putting a gene on the MAPP using the GeneFinder window====
+
−
 
+
−
*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window. 
+
−
**I clicked on the Drafting Board to place the Gene on the MAPP. 
+
−
**Then I right-clicked on the gene to access the GeneFinder window. 
+
−
**I typed in the gene Id BP3723 into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
+
−
**When the gene was found this is the back page that popped up:
+
−
**[[File:GeneIDbackpage-BP3723orderedlocusname cw20151123.png]]
+
−
**Not all of the expected cross-referenced IDs were present.
+
−
*I decided to try out another orderedlocusname gene id in the GenMAPP system to see if all of the expected cross-referenced IDs were present for a different gene than the first one.
+
−
**In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window. 
+
−
***I clicked on the Drafting Board to place the Gene on the MAPP. 
+
−
***Then I right-clicked on the gene to access the GeneFinder window. 
+
−
***I typed in the gene Id BP2980 into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
+
−
***When the gene was found this is the back page that popped up:
+
−
***[[File:GeneIDbackpage-BP2980orderedlocusname cw20151123.png]]
+
−
***Not all of the expected cross-referenced IDs were present.
+
−
*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window. 
+
−
**I clicked on the Drafting Board to place the Gene on the MAPP. 
+
−
**Then I right-clicked on the gene to access the GeneFinder window. 
+
−
**I typed in the gene Id Q7VUE5 into the Gene ID field and selected "UniProt" for the Gene ID system.
+
−
**When the gene was found this is the back page that popped up:
+
−
**[[File:GeneIDbackpage-Q7VUE5uniprot cw20151123.png]]
+
−
**All of the expected cross-referenced IDs were present.
+
−
*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window. 
+
−
**I clicked on the Drafting Board to place the Gene on the MAPP. 
+
−
**Then I right-clicked on the gene to access the GeneFinder window. 
+
−
**I typed in the gene Id CAE44048 into the Gene ID field and selected "EnsemblBacteria" for the Gene ID system.
+
−
**When the gene was found this is the back page that popped up:
+
−
**[[File:GeneIDbackpage-CAE44048ensemblbacteria cw20151123.png]]
+
−
**All of the expected cross-referenced IDs were present.
+
−
*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window. 
+
−
**I clicked on the Drafting Board to place the Gene on the MAPP. 
+
−
**Then I right-clicked on the gene to access the GeneFinder window. 
+
−
**I typed in the gene Id 2666659 into the Gene ID field and selected "GeneID" for the Gene ID system.
+
−
**When the gene was found this is the back page that popped up:
+
−
**[[File:GeneIDbackpage-2666659geneid cw20151123.png]]
+
−
**All of the expected cross-referenced IDs were present.
+
−
*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window. 
+
−
**I clicked on the Drafting Board to place the Gene on the MAPP. 
+
−
**Then I right-clicked on the gene to access the GeneFinder window. 
+
−
**I typed in the gene Id NP_878949 into the Gene ID field and selected "RefSeq" for the Gene ID system.
+
−
**When the gene was found this is the back page that popped up:
+
−
**[[File:GeneIDbackpage-NP 878949refseq cw20151123.png]]
+
−
**Not of the expected cross-referenced IDs were present.
+
−
*Screenshot of all of the sample ID's on a MAPP:
+
−
*[[File:GenMAPPgenesmapped cw20151123.png]]
+
−
 
+
−
====Expression Dataset and MAPPFinder Analysis====
+
−
*We do not have the expression dataset yet that is to be created by the GenMAPP Builders; they are still working on performing the corrections to the data that has been compiled into an excel spreadsheet.
+
−
*Once the file is complete, we will proceed with the data analysis using the desired programs.
+
−
 
+
−
=== Compare Gene Database to Outside Resource===
+
−
*We will complete this step after progressing further into the project.
+
−
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.
+
−
 
+
−
[[Category: Class Whoopers]]
+

Latest revision as of 19:21, 18 December 2015

Files Asked for in the Gene Database Testing Report

For convenience, all of the files explicitly asked for in the sections below were compressed together in this file: File:Gdtr cw20151201.zip

Pre-requisites

The following set of software was used in the creation and testing of the Bordetella pertussis gene database:

  1. 7-ziptool that for unpacking .gz and .zip files
  2. PostgreSQL on Windows (version 9.4.x)
  3. GenMAPP Builder
  4. Java JDK 1.8 64-bit
  5. GenMAPP 2
  6. XMLPipeDB match utility for counting IDs in XML files
  7. Microsoft Access for reading .mdb files

Gene Database Creation

Downloading Data Source Files and GenMAPP Builder

  • I download the UniProt XML, GOA, and GO OBO-XML files for Bordetella Pertussis along with the GenMAPP Builder program.
    • All files were saved to the folder Bklein7_CW\bpertussis_cw20151201 on my computer's ThawSpace.
    • Files that required extraction were unzipped using 7-zip.
    • Data files that remained in a folder after unzipping were removed from their folders to facilitate organization and command line processing.

UniProt XML

GOA

GO OBO-XML

Downloaded GenMAPP Builder

  1. I downloaded the first custom version of gmbuilder including the Bordetella pertussis custom class: File:Dist cw20151201.zip.
  2. I extracted the GenMAPP Builder folder using 7-zip.

Creating the New Database in PostgreSQL

  • I launched pgAdmin III and connected to the PostgreSQL 9.4 server (localhost:5432).
    • On this server, I created a new database: bpertussis_cw20151201_gmb3build5.
    • I opened the SQL Editor tab to use an XMLPipeDB query to create the tables in the database.
      • I clicked on the Open File icon and selected the file gmbuilder.sql. This imported a series of SQL commands into the editor tab.
      • I clicked on the Execute Query icon to run this command.
      • In viewing the schema for this database, I confirmed that there were 167 tables after running the above command.

Configuring GenMAPP Builder to Connect to the PostgreSQL Database

  • To begin, I launched gmbuilder.bat.
  • I selected the "Configure Database" option and entered the following information into the fields below:
    • Host or address: localhost
    • Port number: 5432
    • Database name: bpertussis_cw20151201_gmb3build5custom
    • Username: postgres
    • Password: Welcome1

Importing Data into the PostgreSQL Database

  • The downloaded data files for Bordetella pertussis were specified and imported into the database by clicking on the following buttons:
    • Selected File > Import UniProt XML...
    • Selected File > Import GO OBO-XML...
    • Clicked OK to the message asking to process the GO data.
    • Selected File > Import GOA...

Exporting a GenMAPP Gene Database (.gdb)

  • I selected File > Export to GenMAPP Gene Database... to begin the export process.
  • I typed my name in the owner field (Brandon Klein).
  • I selected "Bordetella pertussis (strain Tohama I/ATCC BAA-589/NCTC 13251), Taxon ID 257313" as the gene database species and then clicked Next.
  • The database was saved as bpertussis-std_cw20151201.
  • I checked the boxes for exporting all Molecular Function, Cellular Component, and Biological Process Gene Ontology Terms.
  • Finally, I clicked the "Next" button to begin the export process.

Gene Database Testing Report

Export Information

Version of GenMAPP Builder: Version 3.0.0 Build 5

Computer on which export was run: Seaver 120- Last computer on the right in the row farthest from the front of the room

Postgres Database name: bpertussis_cw20151201_gmb3build5custom

UniProt XML filename: File:Uniprot-proteome-UP000002676 cw20151201.zip

GO OBO-XML filename: File:Go daily-termdb cw20151201.zip

  • GO OBO-XML version (The version information was found in the file properties): Last Modified- ‎‎December ‎01, ‎2015, ‏‎2:21:31 AM
  • GO OBO-XML download link: Gene Ontology legacy download page
  • Time taken to import: 7.08 minutes
  • Time taken to process: 4.42 minutes
    • Note: The import and processing times were similar to those for the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (6.99 minutes and 4.48 minutes respectively). No interruptions occurred during these processes.

GOA filename: File:145.B pertussis ATCC BAA-589 cw20151201.zip

  • GOA version (found in the Last modified field on the FTP site): Last Modified- 11/10/15 1:39:00 PM
  • GOA download link: for Bordetella pertussis strain Tohama I
  • Time taken to import: 0.04 minutes
    • Note: The import time was equal to that of the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb. No interruptions occurred during this process.

Name of .gdb file: File:Bpertussis-std cw20151201.zip

  • Time taken to export:
    • Start time: 4:06 PM
    • End time: 5:00 PM
    • Elapsed time: 54 minutes

Note: No interruptions occurred during the export process.

Confirming that Changes to GenMAPP Builder Worked As Expected

  1. Systems Table Update
    • In creating the Bordetella pertussis custom class, changes were implemented to edit the OrderedLocusNames column in the exported .gdb file. Specifically, the species should be listed as Bordetella pertussis and a custom GeneDB link should be included in this row.
    • To verify that these changes were working as expected, I opened the file bpertussis-std_cw20151201.gdb in Microsoft Access. Upon opening Systems table here, all changes were successfully implemented:
      • Systemstable cw20151201.png
  2. GenMAPP Gene Backpage Update
    • The OrderedLocusNames GeneDB link added (as described above) also was designed to have funcitonality in GenMAPP. Sepcifically, gene backpages opened while using this gene database in GenMAPP should redirect users to the GeneDB information page for the specific Bordetella pertussis gene.
    • I specified bpertussis-std_cw20151201.gdb as the gene database in GenMAPP and put the gene BP3701 on the map. When I clicked on the link to the ID "BP3701" under "OrderedLocusNames" in Gene Finder, I was successfully brought to the corresponding GeneDB information page:
      • Custombackpage cw20151201.PNG

Team Information & Links

GenMAPP Analysis of Bordetella pertussis Microarray Data

Gene Database Project Links
Overview Deliverables Reference Format Guilds Project Manager GenMAPP User Quality Assurance Coder
Teams Heavy Metal HaterZ The Class Whoopers GÉNialOMICS Oregon Trail Survivors

Journal Entries

Class Whoopers Individual Journal Entries
Brandon Klein Week 11 Week 12 Week 14 Week 15
Lena Olufson Week 11 Week 12 Week 14 Week 15
Mahrad Saeedi Week 11 Week 12 Week 14 Week 15
Team Entries Week 11 Week 12 Week 14 Week 15

Group Members

Team Weekly Assignments

  • Week 10 Creation of page and combined annotated bibliography (midnight 11/10)
  • Week 11 (midnight 11/17)
  • Week 12 (midnight 11/24)
  • Week 14 (midnight 12/8)
  • Week 15 (midnight 12/15)
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