Download A Metric-Space DBMS to Support

The MoBIoS Project
Molecular Biological Information System
Daniel P. Miranker
University of Texas
Rui Mao, Weijia Xu, Wenguo Liu,
Willard Briggs, Smriti Ramakrishnan,
Shu Wang, Francois Barbancon,
Shulin Ni
Bioinformatics Problem:
Must scan entire database, O(n), to find data
matching the most basic of patterns.
–Sequences
–Mass-spectra
– Protein Structure
– Combi-chem Libraries
Compare two genome  O(n2)
Solution:
MoBIoS: A Metric-Space DBMS
– Metric space index enables O(log n) retrieval time
Metric Space is
• a pair, M=(D,d),
where
• D is a set of points
• d is [metric] distance function with the following
properties:
– d(x, y) = d (y, x)
– d(x, y) > 0, d(x, x) = 0
– d(x, y)  d(x, z) + d(z, y)
(symmetry)
(non negativity)
(triangle inequality)
Metric-Space Indexing
C
A B
A
F
E
B
CDEF
D
Materialize Hierarchical Clustering as a
Tree-Based Data Structure
MoBIoS Architecture
(Molecular Biological Information System)
Active Application Efforts
Homology Compartive and
Search Phylo Genomics
– mSQL, simple SQL
extensions enabling fast,
consice bioinformatic
programming.
Other Opportunities
Mass-Spec
De novo Combi-Chem
Protein
Protein
Library
Identification Sequencing Management
MoBIoS SQL (M-SQL)
Query Engine
Mining Engine
MoBIoS Java Interface (MJI)
– Integrated repository
for diverse biologicial
data types.
Metric-Space Based
Storage Manager
DNA Sequences
Peptide Sequences
Mass-Spec. Signatures
Small Molecule & Protein Libraries