Managing experiment data using Excel and Friends

Managing Experiment Data Using
Excel and Friends: Digging Out
from Under the Avalanche
Yannick Pouliot, PhD
Bioresearch Informationist
Lane Medical Library & Knowledge Management Center
6/1/2006
© 2006 The Board of Trustees of The Leland Stanford Junior University

http://lane.stanford.edu

Course Expectations
Objectives



Demonstrate







Windows vs. Mac
Structure










… good practices
… useful features
… the value of querying via Excel

Examples, use cases
Exercises
Resources

Class evaluation questionnaire:
http://www.surveymk.com/s.asp?u=915602161402

Lane Medical Library &
Knowledge Management Center

2

Contents
Complexity

+
Querying Web sites &
databases using Excel
Excel handy functions

Excel good practices


3

So Why Are We Here?


Lots of data


 Need for better management of these data








Need exceeds Excel
Excel never really meant for data management anyway

Applying common tools to ameliorate the problem
“In IT, there’s no problem that enough money
can’t solve”  not the philosophy here…
Instead: invest yourself and you’ll get a handsome
return 


4

Essential Tip
Clippy: not as dorky as
you might think


How To Help Clippy Give You
Better Answers
 Read a (good) Excel manual cover to cover
Don’t try to understand everything




Just flip pages and let it impress into your brain

Not fun, but it will give you the requisite
vocabulary






Increases your odds of getting the right answer
Gives you an idea of what Excel can do


6

Part I: Essential Excel
Functions


Essential Excel Functions
1.

2.
3.
4.
5.
6.

Conditional Formatting
Named ranges & Input validation
Custom Toolbar
PivotTable
Web Querying
MS Query


8

Excel Functions 1: Conditional
Formatting


Definition: A formatting (e.g., cell shading or
font color) applied automatically by Excel to
cells if a specified condition is true.







Example: applying green cell color to the cell if a
test result exceeds a threshold value
In: Format/Conditional Formatting
See Spreadsheet1.xls/ConditionalExample1 - try

Reference

9

Excel Functions 2: Named Ranges and
Validation




Named ranges are ranges of cells that
are…named!
Named ranges can be used for validating input
data


Important for ensuring data consistency









Essential for queryability

Also useful to avoid repetitive typing by using drop-down
menu
See: Spreadsheet1.xls/InputValidation - try

How to: here
Other references

10

Excel Functions 3: Custom Toolbar





Why? Bring often used functions together for faster
access
DEMO
How to? 50 min online tutorial


Section on custom toolbars here


11

Excel Functions 4: PivotTables


Automatic summarization of data





See: Spreadsheet3.xls/Summary1 - try





Converting same category data into summarized values
Tall/skinny  wide/fat

Underlying data can always be accessed by
clicking on a summary cell

Online demo (5 min)
How to? 30 min online tutorial

12

Excel Functions 5: Web Querying


Why Query the Web Using Excel?


Data in a Web page = first step


Need data stored in tool used for daily work 
Excel


E.g., with a list I can:
 Sort
 Annotate
 Edit


13

Excel Functions 5: Web Querying
Options



Copy/paste Web page into Excel - try
Run Web query from within Excel  more control try

1.
2.





Going one step further: creating a refreshable Web query

Excel Web querying is not perfect…





Still limited to how data are formatted on Web page 
requires editing
Some Web pages don’t work
No arbitrary querying capability (limited by Web interface)

 The answer: direct querying using e.g. SQL

14

BREAK


Part II: Querying
Databases Using Excel


Putting MSQuery to Work


MSQuery, an unknown hero






Free
Facilitates writing a SQL query  graphical
What is SQL?

First, need to find it!


Search for “MSQRY32.EXE” using “Search for Files or
Folders”






Search hidden files and folders

On my disk, it is located in C:Program FilesMicrosoft
OfficeOFFICE11
Once you find it, create a shortcut to it and rename it e.g.
MSQuery


move the shortcut to a desired location


17

Example: Network Querying of Ensembl
Database Using MS Query





Remote
Big database, lots of data to return from far away… DB

ult
s



What happens when you use MS Query
DEMO
query
qu
May take some time
e ry

re s



results


18

FYI - Bioinformatics Databases:
Direct
WhoQueryability of Selected Bioinformatics Databases Querying?
Supports Direct
Database

Internet SQL querying?

ArrayExpress

How?

Eventually

Modality

DB Engine

SOAP-based

Ensembl

Yes

http://www.ensembl.org
/info/data/download.ht SQL
ml

Mouse Genome
Database

Yes

ask for account

Yes

http://eutils.ncbi.nlm.nih
.gov/entrez/query/static SOAP-based
/esoap_help.html

SQL Server

Yes

http://www.pharmgkb.or
g/home/projects/webser SOAP-based
vices/

Oracle

NCBI Entrez

PharmGKB

SQL

MySQL

Sybase

Saccharomyces Genome
EventuallyMaybe
Database

Oracle

Stanford Microarray
Database

Oracle


No

19

How to Query Using MSQuery
Steps
1. Make sure you have the requisite driver
2. Create a Data Source Name
3. Write your SQL query
4. Get the results back into Excel!


20

Step1: Getting Drivers
Essential for Querying




A driver is a piece of software that lets your
operating system talk to a database
Each database engine (Oracle, MySQL, etc)
requires its own driver






Generally must be installed by user

Drivers are needed by Data Source Name
tool and querying programs
Require (simple) installation

21

MySQL Driver: Needed to Query
MySQL Databases




Windows: Download MySQL
Connector/ODBC 3.51 here
Must be installed for direct querying using
e.g. Excel


Not necessary if you are using the MySQL Query
Browser


22

Oracle Driver: Needed to Query
Oracle Databases


Installing “client” software will install
driver





Windows: Download 10g Client here
Mac: Download 10g Client here

Must be installed if you are querying
using e.g. Excel


23

Step 2: Creating a Data Source Name




A Data Source Name (DSN) tells programs
on your PC where and how to query a
database
Populating the fields:





Data Source Name: Unique name of your choice
Description: anything
Server: exactly as given by the database provider
Port number: as specified by database provider


Defaults: MySQL: 3306; Oracle: 1521; MS Access: N/A


24

Step 3: Building a Query


DEMO


25

Resources – Excel
Summarizing Numerical Data



Data summarization (text):
http://office.microsoft.com/enus/assistance/HA011864391033.aspx


26

Resources – MS Access
Free Online Training Resources








Using an Access database to store and information (2 min)
http://office.microsoft.com/en-us/assistance/HA011709681033.aspx
Creating a database from Excel (5 min): http://office.microsoft.com/enus/assistance/HA012013211033.aspx
Creating tables in Access (50 min):
http://office.microsoft.com/training/training.aspx?AssetID=RC061183261033
Writing queries (50 min):
http://office.microsoft.com/training/training.aspx?AssetID=RC010776611033


27

Resources - Excel

Accessible from
Lane Library


Available
via Safari

Available
via Safari

28

Resources - Excel

Available from
Lane Library


29

MS Query Resources


Excellent tutorial:
http://office.microsoft.com/training/Training.as
px?AssetID=RP011856321033&CTT=6&Orig
in=RC011856161033


30

Resources – SQL


SQL=Structured Query Language







The Language to Query Relational Databases

Beginning SQL, Wilton P & Colby JW: E
http://jenson.stanford.edu/uhtbin/cgisirsi/5AG
uKeptoD/GREEN/59960102/9#holdings
Oracle SQL*Plus, Gennick, J.
Beginning MySQL: E
http://site.ebrary.com/lib/stanford/Doc?id=101
14227

31

Resources – MS Access

Accessible from
Lane Library


Not in SU catalog; on
order by Lane

1st edition available
from SU; 2nd edition
available via Safari

32

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