Blitvak Week 12 - Revision history

Blitvak: added notes for regular expressions

2015-11-24T03:56:24Z

added notes for regular expressions

2015-11-24T03:48:25Z

added expressions, cleaned ID section

2015-11-24T02:26:38Z

fixed code tag

@@ Line 84: / Line 84: @@
 *Uncommon ID formats included: <letterSet>'''r'''<numberSet> (these correspond to tRNA genes)
 **It was also noticed that a small amount of genes included letters besides '''A''' as the final character in the ordered locus name.
-===Match/PGSQL Expressions for Q/A work===
+==Match/PGSQL Expressions for Q/A work==
 *Match: <code>java -jar xmlpipedb-match-1.1.1.jar "p?BCA[A-Z]?[0-9][0-9][0-9][A-Z]?[0-9]?[A-Z, a-z]?" < filename.xml</code>
 *SQL: <code>select count(*) from genenametype where type = 'ordered locus' and value ~ 'p?BCA[A-Z]?[0-9][0-9][0-9][A-Z]?[0-9]?[A-Z, a-z]?';</code> (needs further testing)
+**Notes: Form was modeled after what was done for xmlpipedb match, however, no entries in that OrderedLocusName ID form were actually present in the tables of the exported J2315 database; will be further tested once a modified version of GenMAPP builder is utilized to export another database.
 ----
 {{Template:GÉNialOMICS}}
 {{Template:blitvak}}

@@ Line 32: / Line 32: @@
 *The GO OBO-XML file was downloaded from the [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology download page]
 *"obo-xml.gz" was selected/clicked under Legacy Downloads
-===Downloading/Updating GenMAPP Builder, Performed on 10/27===
+===Downloading/Updating GenMAPP Builder, Performed on 11/19===
 *The files were downloaded from the [https://github.com/lmu-bioinformatics/xmlpipedb/releases XMLPipeDB releases page on GitHub]
 *[https://github.com/lmu-bioinformatics/xmlpipedb/releases/download/gmbuilder-3.0.0-build-5/gmbuilder-3.0.0-build-5.zip Download link for gmbuilder-3.0.0-build-5 (the version used in this assignment)]
@@ Line 72: / Line 72: @@
 *[[File:UniProt_Data_Table_GEN_BL12_20151119.png]]
 *Gene name ID: BceJ2315_#####
 ===RefSeq===
-*Locus Tag: QU43_RS#####
+*Locus Tag: QU43_RS#####, also found to be in the same form as the OrderedLocusNames within the MOD
 ===GeneID (EntrezGene from NCBI)===
-*GeneID: QU43_RS##### (same as RefSeq)
+*GeneID: WP_#########.1 (same as RefSeq)
 ===GO===
 *GO IDs: GO:#######
@@ Line 82: / Line 84: @@
 *Uncommon ID formats included: <letterSet>'''r'''<numberSet> (these correspond to tRNA genes)
 **It was also noticed that a small amount of genes included letters besides '''A''' as the final character in the ordered locus name.
 ----
 {{Template:GÉNialOMICS}}
 {{Template:blitvak}}

@@ Line 67: / Line 67: @@
 ==Further exploration of the ID systems for ''B. cenocepacia'' J2315==
-*ID formats were explored by conducting searches using the following terms: <code>Burkholderia cenocepacia J2315/code>
+*ID formats were explored by conducting searches using the following terms: <code>Burkholderia cenocepacia J2315</code>
 **The following databases were explored: [http://www.uniprot.org/taxonomy/ UniProt Taxonomy], [http://www.ncbi.nlm.nih.gov/refseq/ NCBI RefSeq], [http://www.ncbi.nlm.nih.gov/gene NCBI Gene], [https://www.ebi.ac.uk/QuickGO/ QuickGO] (strain was found under the taxonomy menu), and the [http://beta.burkholderia.com/ MOD for various burkholderia species]
 ===UniProt===