Macromolecular Structure Database group

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MSD Search and Visualization tools Jawahar
Swaminathan
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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

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biobar
A toolbar search application for Mozilla/Netscape
or firefox browsers
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Biobar (http//biobar.mozdev.org)
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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.

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MSDlite
A simple form-based query system to search the
MSD Databases
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MSDlite
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MSDlite
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The Atlas Pages
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The Atlas Ligands
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The Atlas Sequence
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AstexViewer_at_MSD-EBI

• View structures as wireframe, backbone or ribbons
• Built-in sequence viewer
• Calculate and display surfaces
• Various display options
• Ramachandran plots
• Distance matrix
• B-factors

Based on the AstexViewer from Astex Technology
Limited and modified under licence by the MSD
group
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Simple search interface

• 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

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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 searched
• specify the relationships between search fields
• choose the result fields and how results are
  presented
• perform "complex" sub-queries e.g. SSM, FASTA

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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 users
  query, which is sent to the MSD query server and
  converted to SQL automatically

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MSDpro
A flexible graphical search interface for
advanced searching
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Automatic SQL query generation

• The query server is a Java servlet
• accepts a query description as XML
• converts the users 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

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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

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Java server
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Java server architecture
Methods
DB and external object ontology
User interface
DB
Methods
Interface Ontology
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Web-services

• Some of the new services from MSD are designed as
  web-services
• web-services are network-based services with
  published method signatures
• can be accessed via the SOAP protocol from any
  language with a SOAP library, via http
• The same services used within MSDpro will be
  accessible to any SOAP client
• The MSD query engine will also be available as a
  web-service, allowing users to submit queries
  programmatically

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http//www.ebi.ac.uk/msd/
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Query generation
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Query generation
SQL gt select ltAgt from ltBgt where ltCgt ltDgt
A selection B DB objects C Query D table
joins E plugin description
B,C,E
A,B
B,D
Fragments of C
B
C - external