Gene Database Testing Report- cw20151203 - Revision history

Bklein7: replaced category with template

2015-12-18T19:21:24Z

replaced category with template

2015-12-09T00:52:35Z

expanded on the visual inspection section

2015-12-09T00:46:17Z

added xmlpipdb match results meaning

← Older revision		Revision as of 19:21, 18 December 2015
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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.		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]]	+	==Team Information & Links==
		+
		+	{{Template:Class Whoopers}}

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 ***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.
-*The "OrderedLocusNames" listing
+**The "OrderedLocusNames" listing properly displayed the implemented changes.
 *UniProt Table
 **This table contained 3258 entries with 6 character IDs.
@@ Line 185: / Line 187: @@
 ***3434 IDs conformed to the pattern "BP####"
 ***1 ID was unique: "BP3167.1"
-***The other 11 IDs showed up as ORF
+***The other 11 IDs were ORFs that conformed to one of the following two patterns: "BP####A" or "BP####B"
 ===.gdb Use in GenMAPP===

@@ Line 133: / Line 133: @@
   cd /d T:\Bklein7_CW\bpertussis_cw20151203
 *I used XMLPipeDB match to identify matches of gene IDs in the UniProt XML file that conformed to the following the patterns: "BP####", "BP####.1", "BP####A", and "BP####B". The command used was as follows:
-  java -jar xmlpipedb-match-1.1.1.jar "BP[0-9][0-9][0-9][0-9](A:B:\.1:)" < "uniprot-proteome%3AUP000002676_cw20151201.xml"
+  java -jar xmlpipedb-match-1.1.1.jar "BP[0-9][0-9][0-9][0-9](A|B|\.1|)" < "uniprot-proteome%3AUP000002676_cw20151201.xml"
 Match Results:
 ===Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine===