Download Uploading Protein Data

Motif Space
Database Design
Kiranjit Sidhu
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Outline
Schema Design
 Content of Database
 Functionality
 Future Plans

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Sample PDB File

Sample PDB File
 Each
PDB File represented as a text
file (~ 60K Lines)
 Inefficient for pattern matching
 Relational Database required for
most efficient solution
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Structure of Database

DB divided into two major components:
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Protein Data
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Protein Data
Motif (Occurrence) Data
Obtained from PDB Files (Protein Data Bank)
Derived Data
Motif Data
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Obtained from Luke’s FFSM technique
Derived Data
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Schema Design
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Schema Design - Protein
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Schema Design - Motif
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Tools Used
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Obtaining Data
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Perl Scripts
Database:
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SQL Server 2000 and SQL Server 2005
T-SQL (Bulk Import Data)
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Obtaining Data
PDB File
Final DB
Extract
Import
CSV File
Convert and Derive
Temp Tables (T-SQL)
T-SQL Procedures
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Uploading Protein Data

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Input dataset: ~ 70,000 PDB/Chain
Combinations
Entries in tables:

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E.g. Approx. 800 Million Rows in the
proteinchaindistance table
Initial version imported 10 PDB files in 1
day
Current version: under 3 minutes
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Current Functionality

Protein (PDB) data has been completely
uploaded into both:


Production Database (MotifSpace)
Development Database (MotifSpaceDev)
Visualize protein structure using data from
database (data available)
 Data can be obtained from Server using
SOAP or web services.
 Basic Queries such as
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Different PDBs a specific motif occurs in?
Histograms to compute statistics.
Demo
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