A report presented in my BNF 216 (Database Design and Modeling for Bioinformatics) class regarding principles and tips to follow in designing biological databases.
Boost Fertility New Invention Ups Success Rates.pdf
Designing Biological Databases
1. How do you solve a problem like a
biological database?
(BNF 216 - Database Modeling and Design for Bioinformatics)
Arjei Balandra
Software Developer
National Telehealth Center
University of the Philippines – Manila
http://bumblebest.net
2. Database
• A database is a set of data that has a regular
structure and that is organized in such a way
that a computer can easily find the
desired information.
– The Linux Information Project
(http://www.linfo.org/database.html)
3. Biological Database
• Biological databases are libraries of life
sciences information collected from scientific
experiments, published literature, high-
throughput experiment technology, and
computational analyses.
- Wikipedia (en.wikipedia.org/wiki/Biological_database)
7. Why Database?
• Data-intensive techniques such as high-
throughput screening and gene expression
experiments demand methods to correlate
large and diverse datasets.
• Databases integrate information from a
variety of sources allowing faster and more
powerful searches.
9. Good Database Design
• Provides easy access to previous results.
• Supports both expert- and machine-guided
searches for novel correlations in data.
10. Bad Database Design
• Obfuscates the correlations for which the user
is searching
• makes it difficult for biologists to fit their data
into the database or to find previously stored
data resulting to user contempt.
• ‘brittle’
25. • In Biology, one size does not fit all
• Focus on a subset of Biology (ie. Genes,
Proteins)
• In large subsets, do it one at a time
• Inclusive
Keep the database scope manageable
26. LISTEN TO THE PEOPLE WHO HAVE TO
WRITE AND USE THE INTERFACE
Tip #7:
27. • Databases are successful only when people
use it
Users know what they want and need
+ Developers know what they can do
+ Designers know what must be done
---------------------------------------------------------
= Collaborative approach to develop a
successful database
32. References
• The Linux Information Project
(http://www.linfo.org/database.html)
• Nelson, M.R., Reisinger, S.J., Henry, S. (2003).Designing
databases to store biological information. BIOSILICO
Vol. 1, No. 4
• Wikipedia (en.wikipedia.org/wiki/Biological_database)
• Lemer, C., Antezana, E., Couche, F., Fays, F., Santolaria,
X., Janky, R., … Wodak, S. J. (2004). The aMAZE
LightBench: a web interface to a relational database
of cellular processes. Nucleic Acids
Research, 32(Database issue), D443–D448.
doi:10.1093/nar/gkh139