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MSD Search and Visualization tools Jawahar Swaminathan. 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...

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MSD Search and

Visualization tools

Jawahar Swaminathan

  • 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



A toolbar search application for Mozilla/Netscape or firefox browsers

  • All major bioinformatics databases covered.
  • Search genomic, proteomic, structural, literature and functional databases.
  • Links to deposition and analysis tools for sequence and structural data.


A simple form-based query system to search the MSD Databases



  • 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

simple search interface
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
describing complex searches
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
a graphical database search system
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


A flexible graphical search interface for advanced searching

automatic sql query generation
Automatic SQL query generation
  • The query server is a Java servlet:
    • accepts a query description as XML
    • converts 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
search system is generic
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

Java server architecture


DB and external object ontology

User interface



Interface Ontology

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