The
Affymetrix Microarray Core Database (AMCDB) stores microarray
data generated on the Affymetrix platform. The AMCDB provides
a institution wide data collection and distribution solution
for the Affymetrix
Microarray Core. The schema is based on the Affymetrix
Analysis Data
Model
(AADM)
with numerous extensions and optimizations to improve overall
efficiency and performance. This schema
provides the capacity to store Affymetrix raw data, libraries,
and investigator analysis data in addition to project
and sample information.
AMCDB
is
a MIAME supportive
database. AMCDB allows for investigators to securely access
and control their own data as
well as allowing investigator to share their
data with other investigators if so desired.
The BBC Development Team developed the production version
of the database two years ago. The web interface for AMCDB
1.0 was launched in December 2002. The web interface allows
investigators to easily manage and view data across projects,
download all files, perform additional data transformations,
generate QA/QC reports and add gene annotation such as
Gene Ontology functions and probe set annotation. AMCDB
is also integrated into the project workflow. Investigators
can submit project and sample applications directly to
the Core via the web interface. The extended data model
and web interface place AMCDB in the top 1% of data management
solutions for microarray cores (non-commercial solution).
For more information about AMCDB, please contact amcdb@ohsu.edu
| Quick Stats: |
as of 12/2003 |
| Number of projects represented in AMCDB: |
156 |
| Number of users: |
147 |
| Number of Chips represented: |
1,585 |
| Number of analysis files represented: |
4,896 |
| Number of tuples (rows) in
AMCDB (excluding system
and non-related tables): |
752,569,063 |
AMCDB Team: Ed Quick (Project Manager), Wayne
Chen, Brian
Tompkins, Vincent Yau, Sean Ressler (now at ITG). Faculty
Advisor: Dr. Shannon McWeeney
The Spotted Microarray Core Database (SMCDB) is currently
under development. Upon completion it will house project
and sample information, the scanned image files, as well
as raw and normalized data. The SMC database schema was
designed using the Microarray Gene Expression Object Model
(MAGE-OM) as a guide to ensure MIAME compliance.
SMCDB Team: Vincent Yau and Wayne
Chen (Development Leads),
Ed Quick. Faculty Advisor: Dr.
Shannon McWeeney. Initial
specifications and modeling were done by Dr.
David Maier (OGI CSE) and former CSE graduate student Leslie Ong.
Projects