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| | ==[[user:mpetredi|'''Mitchell Petredis''']]== | | ==[[user:mpetredi|'''Mitchell Petredis''']]== |
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| − | ===UniProt XML===
| + | [[[[Team Name]]]] |
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| − | #Go to [[http://www.uniprot.org/taxonomy/complete-proteomes UniProt Complete Proteomes]]
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| − | #Choose a topic from the "Complete proteomes" list
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| − | #*I picked [[http://www.uniprot.org/taxonomy/?query=complete:yes%20ancestor:2 Bacteria]]
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| − | #Pick a specimen from the list of results and click on "Complete proteome set" under its link.
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| − | #*For this exercise, pick [[http://www.uniprot.org/uniprot/?query=organism:243277+keyword:1185 Vibrio cholerae serotype O1 (strain 39315 / El Tor Inaba N16961)]]
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| − | #Once on your specimen page, click on the yellow/orange box in the upper right hand corner called [[http://www.uniprot.org/uniprot/?query=organism%3a243277+keyword%3a1185&format=* Download]] to choose a filetype
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| − | #*Prior to selecting a file type, make sure [[http://www.uniprot.org/uniprot/?query=organism%3a243277+keyword%3a1185&format=*&compress=yes compressed]] results are enabled by clicking on the link.
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| − | #*select [[http://www.uniprot.org/uniprot/?query=organism%3a243277+keyword%3a1185&compress=yes&format=xml XML]]
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| − | #**Extract the .gz file by right-clicking on the file and scrolling to 7-zip/Extract here
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| − | ===GOA===
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| − | #Go to [[http://www.ebi.ac.uk/GOA/downloads UniProt-GOA Downloads]]
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| − | #*Current/previous UniProt-GOA files are located [[ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/ here]]. NOTE: Google Chrome can't find the link, and redirects to [[http://www.ebi.ac.uk/ European Bionformatics Institute]] instead.
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| − | ==Gene Database Information==
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| − | ===Export Information===
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| − | Version of GenMAPP Builder: gmbuilder-2.0b70
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| − | Computer on which export was run:
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| − | Postgres Database name: vc-mpetredi-20131022-gmb2b70
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| − | UniProt XML filename:
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| − | * UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): Vc-uniprot-mpetredi-20131022.xml located in downloads (for now)
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| − | * Time taken to import: 8.72 minutes
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| − | GO OBO-XML filename: go_daily-termdb-mpetredi-20131022.obo.xml
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| − | * 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):
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| − | * Time taken to import:
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| − | * Time taken to process: 14.77 minutes
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| − | GOA filename: 46.V_cholerae_ATCC_39315._mpetredi_20131022.goa
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| − | * ''Direct download from wiki due to network connectivity issue.''
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| − | * 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]):
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| − | * Time taken to import: 0.16 minutes
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| − | Name of .gdb file: Vc-Std_20131022-Mpetredi-gmb2b70.gdb | + | |
| − | * Time taken to export .gdb:
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| − | * Upload your file and link to it here.
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| − | Note: Export started around 11 am; ended at 4:03:36 pm.
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| − | ==TallyEngine==
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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).
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| − | == Using XMLPipeDB match to Validate the XML Results from the TallyEngine==
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| − | [[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#XMLPipeDB_Match | Follow the instructions found on this page to run XMLPipeDB match.]]
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| − | Are your results the same as you got for the TallyEngine? Why or why not?
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| − | == Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==
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| − | [[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL | Follow the instructions on this page to query the PostgreSQL Database.]]
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| − | ==OriginalRowCounts Comparison==
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| − | 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.
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| − | 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].
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| − | Copy the OriginalRowCounts table and paste it here:
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| − | Note:
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| − | ==Visual Inspection==
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| − | Perform visual inspection of individual tables to see if there are any problems.
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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?
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| − | * 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?
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| − | Note:
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| − | ==.gdb Use in GenMAPP==
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| − | Note:
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| − | ===Putting a gene on the MAPP using the GeneFinder window===
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| − | * 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.
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| − | Note:
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| − | ===Creating an Expression Dataset in the Expression Dataset Manager===
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| − | * 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?
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| − | Note:
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| − | ===Coloring a MAPP with expression data===
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| − | Note:
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| − | ===Running MAPPFinder===
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| − | Note:
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| − | == Compare Gene Database to Outside Resource==
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| − | 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.
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| − | Note:
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| − | <!--In this example, this query tells you which IDs are in Riley only:<br>
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| − | select Riley.ID from Riley left outer join Blattner on Riley.ID = Blattner.ID where Blattner.ID is null;-->
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