DAS, the Distributed Annotation System
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Workshop. Proteomics Bioinformatics. WTAC. 13-17 December 2010.
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DAS, the Distributed Annotation System
- 1. Proteomics Bioinformatics WTAC 13-17 December 2010 Rafael Jimenez rafael@ebi.ac.uk EnCORE presentation DAS Distributed Annotation System
- 2. Table of contents • DAS What is it? Commands and queries Why should I use it? Documentation Clients and servers
- 3. What is it?
- 4. DAS, The Distributed Annotation System The Distributed Annotation System is… – A network of biological data sources – A Service Oriented Architecture (SOA) – RESTful web service – An example of federation • Uniform access to multiple repositories of biological data. • Repositories distributed in different geographical locations. The DAS Protocol is… – An integration platform – A client-server protocol – An agreed standard for web services
- 5. 23.08.18 5 DAS data types Genome sequence Sequence alignments Protein sequence Protein-protein interaction Gel 2D EMAP 3DM Protein structure Protein structure EMAP 3DM Protein-protein interaction Protein structure Gel 2D Mass spectrometry Epigenetics Phenotype Functional genomics Structural genomics Protein sequence Alignment servers Annotation servers Reference servers
- 6. The Distributed Annotation System, 2001 Dowell et al; BMC Bioinformatics. 2001; 2: 7. Published online 2001 October 10. DAS, Architectural Overview illustration
- 7. 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
- 8. Example client behaviour Andy Jenkinson
- 9. Example client behaviour Andy Jenkinson
- 10. Example client behaviour Standardization allows clients to connect to different DAS sources without additional programming Andy Jenkinson
- 12. DAS – Andy Jenkinson 23.08.1812 Query model Structured REST URL – http://server/das/source/command?arguments – servers, data sources, commands, parameters Reference object – e.g. “chromosome X” Reference servers provide sequence – http://server/das/source/sequence?segment=X:1,500 Annotation servers provide features – http://server/das/source/features?segment=X:1,500
- 13. DAS – Andy Jenkinson 23.08.1813 Data model Lightweight XML http://server/das/source/features?segment=X:1,500 <SEGMENT id=“X” start=“1” stop=“500”> <FEATURE id=“…”> <TYPE id=“…” category=“…”>…</TYPE> <METHOD id=“…”>…</METHOD> <START>…</START> <END>…</END> </FEATURE> <FEATURE id=“…”> … </FEATURE> </SEGMENT> http://server/das/source/features?segment=X:1,500 <SEGMENT id=“X” start=“1” stop=“500”> <FEATURE id=“…”> <TYPE id=“…” category=“…”>…</TYPE> <METHOD id=“…”>…</METHOD> <START>…</START> <END>…</END> </FEATURE> <FEATURE id=“…”> … </FEATURE> </SEGMENT>
- 14. DAS Annotation source - Protein Feature Request Non-positional feature Positional feature http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=Q12345
- 15. DAS Reference source - Protein Sequence Request http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/sequence?segment=Q12345
- 16. More DAS Commands • Alignment, Structure and Interaction • More … http://server/das/source/entry_points – entry_points: List of available “chromosomes | contigs | proteins | …” http://server/das/source/types – types – provides a summary of the feature types for a segment. http://server/das/source/stylesheet – stylesheet – gives hints to the DAS client about how to display the feature types. Can be ignored of course. http://server/das/sources – sources – list of available sources in one DAS server. Replaces the original, underspecified dsn command. http://www.biodas.org/wiki/DAS1.6
- 17. Why should I use it?
- 18. DAS – Andy Jenkinson 23.08.1818 DAS Design Principles Data remains distributed • “live” data • data providers retain responsibility • good for changing data • spreads resources Easy for data providers to implement • simple protocol • lots of data providers
- 19. DAS – Andy Jenkinson 23.08.1819 DAS Design Principles Principally for display • should be responsive (fast) • region-targeted queries • lightweight infrastructure Downsides • Rigid data model • Weak semantics
- 20. Documentation
- 23. Versions of DAS 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 ~250 sources ~380 sources ~650 sources ~ 8 sources DAS 1.01 ~1300 sources DAS 1.53 DAS 2.0 DAS 2.1 DAS 1.53E DAS 1.6DAS 1 DAS/2
- 26. List of DAS Servers 23.08.1826
- 27. DAS Client libraries 23.08.1827 • Bio::Das::Lite (Perl) • Dasobert (Java)
- 28. List of DAS Clients 23.08.1828 • Ensembl uses DAS to pull in genomic, gene and protein annotations. It also provides data via DAS. • Gbrowse is a generic genome browser, and is both a consumer and provider of DAS. • IGB is a desktop application for viewing genomic data. • SPICE is an application for projecting protein annotations onto 3D structures. • Dasty2 is a web-based viewer for protein annotations • Jalview is a multiple alignment editor. • PeppeR is a graphical viewer for 3D electron microscopy data. • DASMI is an integration portal for protein interaction data. • DASher is a Java-based viewer for protein annotations. • EpiC presents structure-function summaries for antibody design. • STRAP is a STRucture-based sequence Alignment Program.
- 29. 23.08.18 29 Protein sequence data Dasty2
- 30. 23.08.18 30 Genome sequence data Ensembl
- 31. 23.08.18 31 Protein structure data Spice-Sisyphus
- 32. 23.08.18 32 Protein-protein interaction data iPfam
- 33. 23.08.18 33 Sequence alignment data Pfam
- 34. 23.08.18 34 EMAP data EMAP: The Edinburgh Mouse Atlas Project Gene expression databases (EMAGE & GXD) DAS reference server EMAP - Ontology DAS annotation servers EMAGE GXD
Hinweis der Redaktion
- An integration platform for biological data a way of bringing together data from different providers federation unifies data sources that are different to each other
- The annotations are stored locally in a database or on file and are served to a DAS client from a DAS server. The real power of DAS comes from the fact that a DAS client can request information from many DAS servers about the same molecule and integrate this information into a single view or analysis.
- The communication between the DAS client and the DAS server is done using standard HTTP requests that return simple XML responses The DAS client pulls annotations from data sources on one or several DAS annotation servers and displays them on sequence obtained from a common reference server that is considered to be the &apos;authority&apos; for the sequence.
- well-formed hierarchical URL, each server has one or more sources, and each source implements one or more commands sequence command provides sequence, and features command provides sequence annotations stylesheet command allows the server to govern how the feature will be rendered by the client. it works by specifying the type and colour of glyph to use for each type of feature. So for instance the COSMIC cancer mutation database DAS server specifies that substitutions should be drawn as crosses, whereas insertions are drawn as triangles.
- live – warehouses allow fast access but data is often not in sync with source database providers are responsible for data, and clients are shielded from database changes rapidly changing data e.g. ENCODE, c.f. warehouses. makes a lot of sense to spread resources given the topology of the network intrinsically simple protocol, and: dumb server – all it has to do is access its adapt the data medium to XML, and existing implementations make that easy clever client –presentation of the data
- fast – user-driven applications have to be fast, as users are only prepared to wait a couple of seconds for content rigid data model means data providers don’t have freedom to put all the data in, but this ensures the system is generic meaning clients get additional data for zero cost weak semantics, though this is being addressed with the ontology
- Graphic representation of the evolution of &quot;Versions of DAS&quot;. It gives a rough idea of when the different specifications were adopted and when DAS/2 started a as independent specification. It also shows an estimation of available DAS sources per year for DAS 1 and DAS/2.
- Integration of biological data of various types and development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing an adapted infrastructure to connect databases, and platforms to enable both generation of new bioinformatics tools and experimental validation of computational predictions. Beyond the use of common standards to format individual datasets, there is a need for sophisticated informatics platforms to enable mining data across various domains, sources, formats and types. The aim of the EnCORE project is to integrate across different disciplines an extensive list of database resources and analysis tools in a computationally accessible and extensible manner, facilitating automated data retrieval and processing with a special focus on systems biology. The EnCORE platform is available as a collection of webservices with a common standard format easy to integrate in Workflow management software such as Taverna. Additionally EnCORE services are also accessible thought EnVISION, a web graphical user interface providing elaborated information such as molecular interaction, biological pathways and computational models of pathways.