Difference between revisions of "Dwilliams Week 9 assignment"
From LMU BioDB 2013
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Name of .gdb file: Vc-Std_dwilliams-20131022-gmb2b70.gdb | Name of .gdb file: Vc-Std_dwilliams-20131022-gmb2b70.gdb | ||
* Time taken to export .gdb: 90 minutes and 56 seconds. | * Time taken to export .gdb: 90 minutes and 56 seconds. | ||
| − | * Upload your file and link to it here. [[Media | + | * Upload your file and link to it here. [[Media:Vc-Std dwilliams-20131022-gmb2b70.gdb| Results]] |
Note: Export concluded at 12:10:56 pm | Note: Export concluded at 12:10:56 pm | ||
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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). | ||
| + | |||
| + | [[Image: Screen_Shot_2013-10-24_at_7.01.11_PM.png| Screen Shot]] | ||
== Using XMLPipeDB match to Validate the XML Results from the TallyEngine== | == Using XMLPipeDB match to Validate the XML Results from the TallyEngine== | ||
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Are your results the same as you got for the TallyEngine? Why or why not? | Are your results the same as you got for the TallyEngine? Why or why not? | ||
| + | |||
| + | *No, they are not. At first the total number of unique matches was 2738. This was because the letter A was not accounted for in the VC search. | ||
| + | *After including the A, the total number of unique matches stood at 3831, which did indeed match. | ||
== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine== | == 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.]] | [[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL | Follow the instructions on this page to query the PostgreSQL Database.]] | ||
| + | |||
| + | *Followed SQL queries instructions in order to obtain the required data. | ||
==OriginalRowCounts Comparison== | ==OriginalRowCounts Comparison== | ||
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Copy the OriginalRowCounts table and paste it here: | Copy the OriginalRowCounts table and paste it here: | ||
| + | |||
| + | [[Image:Screen Shot 2013-10-24 at 7.13.32 PM.png| Column 1]] | ||
| + | |||
| + | [[Image:Screen Shot 2013-10-24 at 7.13.54 PM.png| Column 2]] | ||
Note: | Note: | ||
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* Look at the Systems table. Is there a date in the Date field for all gene ID systems present in the database? | * 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? | * 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 field is present for all Genes | ||
| + | #Two of the Gene ID's were originally supposed to be in the same row, however, access put them in two different rows which caused an issue when searching for the gene ID. | ||
Note: | Note: | ||
| Line 62: | Line 75: | ||
==.gdb Use in GenMAPP== | ==.gdb Use in GenMAPP== | ||
| − | Note: | + | Note: This step could not be done due to an error that was explained in class. |
===Putting a gene on the MAPP using the GeneFinder window=== | ===Putting a gene on the MAPP using the GeneFinder window=== | ||
| Line 68: | Line 81: | ||
* 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. | * 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: | + | Note: This step could not be done due to an error that was explained in class. |
===Creating an Expression Dataset in the Expression Dataset Manager=== | ===Creating an Expression Dataset in the Expression Dataset Manager=== | ||
| Line 74: | Line 87: | ||
* 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? | * 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: | + | Note: This step could not be done due to an error that was explained in class. |
===Coloring a MAPP with expression data=== | ===Coloring a MAPP with expression data=== | ||
| − | Note: | + | Note: This step could not be done due to an error that was explained in class. |
===Running MAPPFinder=== | ===Running MAPPFinder=== | ||
| − | Note: | + | Note: This step could not be done due to an error that was explained in class. |
== Compare Gene Database to Outside Resource== | == Compare Gene Database to Outside Resource== | ||
| Line 88: | Line 101: | ||
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. | 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: | + | Note: This step could not be done due to an error that was explained in class. |
<!--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;--> | ||
Latest revision as of 02:20, 25 October 2013
[edit] Export Information
Version of GenMAPP Builder: gmbuilder-2.0b70
Computer on which export was run: bio104
Postgres Database name: vc_dwilliams_20131022-gmb2b70
UniProt XML filename: vc-uniprot-dwilliams-20131022
- UniProt XML version (The version information can be found at the UniProt News Page):
- Time taken to import: 2.77 minutes
GO OBO-XML filename: go_daily-termdb.obo-xml-dwilliams-20131022.gz
- 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:5.94 minutes
- Time taken to process: 4.60 minutes
GOA filename: 46.V_cholerae_ATCC_39315_dwilliams_20131022.goa
- Direct download from wiki due to connectivity problems
- 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_dwilliams-20131022-gmb2b70.gdb
- Time taken to export .gdb: 90 minutes and 56 seconds.
- Upload your file and link to it here. Results
Note: Export concluded at 12:10:56 pm
[edit] 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).
[edit] 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?
- No, they are not. At first the total number of unique matches was 2738. This was because the letter A was not accounted for in the VC search.
- After including the A, the total number of unique matches stood at 3831, which did indeed match.
[edit] Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine
Follow the instructions on this page to query the PostgreSQL Database.
- Followed SQL queries instructions in order to obtain the required data.
[edit] 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:
Note:
[edit] 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?
- The field is present for all Genes
- Two of the Gene ID's were originally supposed to be in the same row, however, access put them in two different rows which caused an issue when searching for the gene ID.
Note:
[edit] .gdb Use in GenMAPP
Note: This step could not be done due to an error that was explained in class.
[edit] 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: This step could not be done due to an error that was explained in class.
[edit] 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: This step could not be done due to an error that was explained in class.
[edit] Coloring a MAPP with expression data
Note: This step could not be done due to an error that was explained in class.
[edit] Running MAPPFinder
Note: This step could not be done due to an error that was explained in class.
[edit] 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: This step could not be done due to an error that was explained in class.
