DAS. Technical introduction to the Distributed Annotation System.
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Primer for Predocs . 17-19 January 2011.
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DAS. Technical introduction to the Distributed Annotation System.
- 1. Primer for Predocs 17-19 January 2011 Rafael Jimenez rafael@ebi.ac.uk EnCORE presentation DAS Technical introduction to the Distributed Annotation System
- 2. Table of contents • DAS Commands and queries Design principles Documentation Clients and servers
- 4. DAS – Andy Jenkinson 23.08.184 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
- 5. DAS – Andy Jenkinson 23.08.185 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>
- 6. DAS Annotation source - Protein Feature Request Non-positional feature Positional feature http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=Q12345
- 7. DAS Reference source - Protein Sequence Request http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/sequence?segment=Q12345
- 8. 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
- 10. DAS – Andy Jenkinson 23.08.1810 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
- 11. Documentation
- 14. 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
- 17. List of DAS Servers 23.08.1817
- 18. DAS Client libraries 23.08.1818 • Bio::Das::Lite (Perl) • Dasobert (Java) • jsDAS (Javascript)
- 19. List of DAS Clients 23.08.1819 • 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.
- 20. 23.08.18 20 Protein sequence data Dasty2
- 21. 23.08.18 21 Genome sequence data Ensembl
- 22. 23.08.18 22 Protein structure data Spice-Sisyphus
- 23. 23.08.18 23 Protein-protein interaction data iPfam
- 24. 23.08.18 24 Sequence alignment data Pfam
- 25. 23.08.18 25 EMAP data EMAP: The Edinburgh Mouse Atlas Project Gene expression databases (EMAGE & GXD) DAS reference server EMAP - Ontology DAS annotation servers EMAGE GXD
Editor's Notes
- 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
- 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.