EMBL-EBI

http://www.ebi.ac.uk/msd

MSD Search and

Visualization tools

Jawahar Swaminathan

EMBL-EBI

http://www.ebi.ac.uk/msd

Issues

The raw database is large and complex:

27,190+ PDB entries

120+ tables in the warehouse, many very large

Cross-referenced against UniProt, PubMed... Need to expose as much of the data as possible, without

making the interface too complex We want to cater for three categories of user:

"Novice" user

Experienced user

Expert user

EMBL-EBI

http://www.ebi.ac.uk/msd

biobar

A toolbar search application for Mozilla/Netscape or firefox

browsers

EMBL-EBI

http://www.ebi.ac.uk/msd

Biobar (http://biobar.mozdev.org)

EMBL-EBI

http://www.ebi.ac.uk/msd

biobar

All major bioinformatics databases covered. Search genomic, proteomic, structural, literature

and functional databases. Links to deposition and analysis tools for

sequence and structural data.

EMBL-EBI

http://www.ebi.ac.uk/msd

MSDlite

A simple form-based query system to search the MSD

Databases

EMBL-EBI

http://www.ebi.ac.uk/msd

MSDlite

EMBL-EBI

http://www.ebi.ac.uk/msd

MSDlite

EMBL-EBI

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The Atlas Pages

EMBL-EBI

http://www.ebi.ac.uk/msd

The Atlas: Ligands

EMBL-EBI

http://www.ebi.ac.uk/msd

The Atlas: Sequence

EMBL-EBI

http://www.ebi.ac.uk/msd

AstexViewer™@MSD-EBI

View structures as wireframe, backbone or ribbons

Built-in sequence viewer Calculate and display

surfaces Various display options:

Ramachandran plotsDistance matrixB-factors

Based on the AstexViewer™ from Astex Technology Limited and modified under licence by the MSD group

EMBL-EBI

http://www.ebi.ac.uk/msd

Strengths: simple, easy to use form allows multiple search fields to be combined relatively fast, despite performing quite complex SQL queries

Weaknesses: not exposing the power of a relational database user can't specify the relationship between search fields:

"name" AND "title" AND "keyword" "name" OR "title" OR "keyword" ( "name" OR "title" ) AND NOT "keyword"

the search form is defined by the authors of the search system, not the author of a query

Simple search interface

EMBL-EBI

http://www.ebi.ac.uk/msd

Describing complex searches

We want to allow the user to entirely control their query Since HTML forms are inherently static, we'll use an

applet to provide a dynamic "form" that will let the user: choose the fields to be searchedspecify the relationships between search fieldschoose the result fields and how results are

presentedperform "complex" sub-queries e.g. SSM, FASTA

EMBL-EBI

http://www.ebi.ac.uk/msd

A graphical database search system

MSDpro uses an applet for constructing queries and a server to execute them

Avoids the need for the user to understand a complex database schema or know SQL

The user describes their query entirely graphically, including logical operations such as AND, OR and NOT

Applet generates an XML description of the user’s query, which is sent to the MSD query server and converted to SQL automatically

EMBL-EBI

http://www.ebi.ac.uk/msd

MSDpro

A flexible graphical search interface for advanced

searching

EMBL-EBI

http://www.ebi.ac.uk/msd

EMBL-EBI

http://www.ebi.ac.uk/msd

EMBL-EBI

http://www.ebi.ac.uk/msd

Automatic SQL query generation

The query server is a Java servlet:accepts a query description as XMLconverts the user’s query description into a

true SQL query, which is then submitted to the search database

Searches can include components that are executed outside of the database, e.g. sequence similarity, determined using FASTA or structural similarity, determined using SSM

EMBL-EBI

http://www.ebi.ac.uk/msd

Search system is generic

The search system is designed to be entirely database-independent

All information about the architecture of the search database is stored in XML dictionaries

Similarly, the search and result fields which the applet presents to the user are controlled by a dictionary

The entire system could move to a completely different database simply by modifying the dictionaries

EMBL-EBI

http://www.ebi.ac.uk/msd

Java server

EMBL-EBI

http://www.ebi.ac.uk/msd

Java server architecture

User interface

Methods

Interface Ontology

DB

DB and external object ontology

Methods

EMBL-EBI

http://www.ebi.ac.uk/msd

Web-services

Some of the new services from MSD are designed as web-services:web-services are network-based services with

published method signaturescan be accessed via the SOAP protocol from

any language with a SOAP library, via httpThe same services used within MSDpro will be

accessible to any SOAP clientThe MSD query engine will also be available as

a web-service, allowing users to submit queries programmatically

EMBL-EBI

http://www.ebi.ac.uk/msd

http://www.ebi.ac.uk/msd/