Standardization and integration of molecular biology information with DAS
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This document discusses molecular biology database systems and data integration using the Distributed Annotation System (DAS). It provides examples of how DAS allows different data types like genome sequences, protein sequences, protein structures, and gene expression data to be integrated and accessed uniformly through a common protocol. It also highlights some DAS client applications that have been developed, including ones that integrate multiple data types or visualize genome annotations at the karyotype level.
Standardization and integration of molecular biology information with DAS
- 1. Rafael Jimenez [email protected] 30th March 2009 MRC, London Standardization and integration of molecular biology information with DAS
- 2. Molecular biology database systems A AA A DB A AA A GUI DB GUI DB GUI DB GUI DB GUI A AA A DB GUI DB DB DB SP SP SP SP Centralized database In-house databases Federated databases A Annotator Database Graphical User InterfaceGUI User Standard protocolSP
- 3. Molecular biology database systems A AA A DB A AA A GUI DB GUI DB GUI DB GUI DB GUI A AA A DB GUI DB DB DB SP SP SP SP Centralized database In-house databases Federated databases A Annotator Database Graphical User InterfaceGUI User Standard protocolSP
- 4. Molecular biology database systems A AA A DB A AA A GUI DB GUI DB GUI DB GUI DB GUI A AA A DB GUI DB DB DB SP SP SP SP Centralized database In-house databases Federated databases A Annotator Database Graphical User InterfaceGUI User Standard protocolSP
- 5. Data integration • Complete genomes provide the framework to pull all biological data together such that each piece says something about biology as a whole • Biology is too complex for any organisation to have a monopoly of ideas or data • The more organisations provide data or analysis separately, the harder it becomes for anyone to make use of the results Tim Hubbard
- 6. Scientificimpact Too little bioinformatics Too many databases Too diverse interfaces Utility of bioinformatics Tim Hubbard
- 7. Split data and representation • Databases responsible for curating data and serving it as primitive datatypes defined by open standards (high cost) • Different front ends or components of front ends compete for users (development of each low cost). Tim Hubbard
- 8. Distributed Annotation System (DAS) • A network of biological data sources • Uniform access to multiple repositories of biological data. • Repositories distributed in different geographical locations. • Different biological data types: Genome, Protein sequence, Protein structure, … • The DAS Protocol is… • An integration platform • A client-server protocol • An agreed standard for web services • More ... http://biodas.org
- 9. Service broker Service consumer Service provider Service Contract ... ... Interact PublishFind Service Oriented Architecture DAS implementation DAS ... ... ... DAS Registry DAS Clients Annotation sources Reference source Alignment sources Alignment sources Alignment sources Annotation sources Annotation sources DAS Clients DAS Clients Protocol
- 12. Example client behaviour Standardization allows clients to connect to different DAS sources without additional programming
- 13. DAS client examples Standardization of biological data types
- 19. EMAP data EMAP: The Edinburgh Mouse Atlas Project Gene expression databases (EMAGE & GXD) DAS reference server EMAP - Ontology DAS annotation servers EMAGE GXD
- 20. DAS client examples Integration of different data types
- 21. Protein sequence and protein structure data Dasty2
- 22. Genome sequence, protein sequence and 3D structure data Spice
- 23. EMAP data and Protein data
- 24. Data types integration in DAS Genome sequence Protein sequence 3DM Protein structures EMAP Gel 2D Mass spectrometry Protein-Protein interaction Protein alignments Sequence alignments DAS alignment server DAS alignment server DAS alignment server DAS alignment server DAS alignment server DAS alignment server DAS alignment server DAS alignment server DAS alignment server DAS alignment server
- 25. KaryoDAS DAS client to visualize genome annotations at the karyotype level
- 26. Visualization of genome data in combination with experimental data and genome analysis helps to formulate testable hypothesis. Eukaryotic Genome browsers specialized to represent annotations on ... Specific chromosomes Genome regions in one chromosome Detailed views on genome regions Eukaryotic genome analysis requires visualization in a higher representation level ... Full genomic context -> Karyotype Introducction
- 27. Karyotype DAS client DAS web browser to visualize Eukaryotic genome data at the level of karyotype, chromosome and cytoband. Still a prototype! For more detail views in a lower representation level it interacts with the Ensembl web browser. Karyotype Chromosome Genome region Detailed view Karyotype DAS viewer Ensembl
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- 29. 1 Karyotype Chromosome Genome region Qualitative Quantitative (score) +/- sources by view
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- 40. Thank you! Thanks for its support to … Bioinfomatics department