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Advanced Search and Visualization Tools for Biological Databases

Explore complex biological databases with MSD tools, enabling dynamic query control for genomic, proteomic, and structural data. Use graphical interfaces for advanced searches and automatic SQL query generation. Access web services for seamless data retrieval. Stay ahead in bioinformatics research!

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Advanced Search and Visualization Tools for Biological Databases

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  1. MSD Search and Visualization tools Jawahar Swaminathan

  2. 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

  3. biobar A toolbar search application for Mozilla/Netscape or firefox browsers

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

  5. 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.

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

  7. MSDlite

  8. MSDlite

  9. The Atlas Pages

  10. The Atlas: Ligands

  11. The Atlas: Sequence

  12. AstexViewer™@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

  13. 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

  14. 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

  15. 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

  16. MSDpro A flexible graphical search interface for advanced searching

  17. 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

  18. 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

  19. Java server

  20. Java server architecture Methods DB and external object ontology User interface DB Methods Interface Ontology

  21. 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

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

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