Class: Advanced SQL Querying of Bioinformatics Databases

Description
Have you ever found yourself limited by the interface of your favorite Web-accessible genomics database? Well, powerful relational databases of "omics" data are available on the Internet, queryable directly using SQL.

Content
This class is intended for biomedical researchers with a modicum of prior experience with SQL who are interested in understanding examples of biologically meaningful SQL queries, and how these can be put to work in their research. Most examples will focus on Ensembl databases from the European Bioinformatics Institute.

Prior to class, registrants will be asked to provide examples of queries they would like to see addressed in the class, from which a subset will be selected.

When/Where/Sign-up
Wednesday, March 5, 10 am - 1 pm, in Alway Room M114.

Instructor Lane Librarian

Class materials

•  Slides (final version)
•  Querying with MS Excel (ExampleExcelQueryingEnsembl1.xls + queries)
• Class videorecording

Resources

• Example queries to be reviewed in class: Identifying candidate genes using the BioWarehouse: a case study, Pouliot, Y, Lee, T.J., Wagner, V.; Karp, P.D. (2005), ICSEng 2005, 18th International Conference on Systems Engineering, pp. 332-340, 16-18 Aug. 2005
•  Access Data analysis Cookbook, (2007). Excellent collection of data analysis recipes that using MS Access. Applicable to other relational databases with minor modifications.
• Query browser: WinSQL, (Windows only). Good, reasonably economical query browser that can query multiple vendors of relational databases.
• Query browser: MySQL Query Browser, (Win, Mac, Linux). Good, free query browser for MySQL only.
• Paper: Lee TJ, Pouliot Y, Wagner V, Gupta P, Stringer-Calvert DW, Tenenbaum JD, and Karp PD. (2006) BioWarehouse: a bioinformatics database warehouse toolkit , BMC Bioinformatics 7:170.
• Cheat Sheet: Setting up Internet SQL querying on windows.
• Quick reference card: A life-saver when you are programming and need to quickly refresh your mind. Here's an excellent source: Visibone's MySQL Cheat Sheets.

pafrench, September 18, 2009