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EMBL-EBI MSD Search and Visualization tools Jawahar Swaminathan http://www.ebi.ac.uk/msd EMBL-EBI 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 http://www.ebi.ac.uk/msd EMBL-EBI biobar A toolbar search application for Mozilla/Netscape or firefox browsers http://www.ebi.ac.uk/msd EMBL-EBI Biobar (http://biobar.mozdev.org) http://www.ebi.ac.uk/msd EMBL-EBI 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. http://www.ebi.ac.uk/msd EMBL-EBI MSDlite A simple form-based query system to search the MSD Databases http://www.ebi.ac.uk/msd EMBL-EBI MSDlite http://www.ebi.ac.uk/msd EMBL-EBI MSDlite http://www.ebi.ac.uk/msd EMBL-EBI The Atlas Pages http://www.ebi.ac.uk/msd EMBL-EBI The Atlas: Ligands http://www.ebi.ac.uk/msd EMBL-EBI The Atlas: Sequence http://www.ebi.ac.uk/msd EMBL-EBI 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 Based on the AstexViewer™ from Astex Technology Limited B-factors and modified under licence by the MSD group http://www.ebi.ac.uk/msd EMBL-EBI 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 http://www.ebi.ac.uk/msd EMBL-EBI 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 http://www.ebi.ac.uk/msd EMBL-EBI 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 http://www.ebi.ac.uk/msd EMBL-EBI MSDpro A flexible graphical search interface for advanced searching http://www.ebi.ac.uk/msd EMBL-EBI http://www.ebi.ac.uk/msd EMBL-EBI http://www.ebi.ac.uk/msd EMBL-EBI 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 http://www.ebi.ac.uk/msd EMBL-EBI 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 http://www.ebi.ac.uk/msd EMBL-EBI Java server http://www.ebi.ac.uk/msd EMBL-EBI Java server architecture Methods DB and external object ontology User interface DB Methods Interface Ontology http://www.ebi.ac.uk/msd EMBL-EBI 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 http://www.ebi.ac.uk/msd EMBL-EBI http://www.ebi.ac.uk/msd/ http://www.ebi.ac.uk/msd