DAS: Distributed Annotation System

The Wellcome Trust Sanger Institute provides support for the Distributed Annotation Systems via a range of different projects, websites and applications. This information resource provides an overview of these.

New large scale techniques in biology are producing a rapidly growing amount of public available data. Centralized database resources are confronted with the task how to scale their storage facilities, how to manage frequent updates and how to exchange the data with the community.

The Distributed Annotation System (DAS) addresses these issues. It is frequently being used to openly exchange biological annotations between distributed sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients.

DAS is a client-server system in which a client like Ensembl integrates information from multiple servers. It allows a single machine to gather up genome annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers.

DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities.

[Genome Research Limited]

New to DAS?

The manual explains how to install and run the software and what most parts of the program do.

How does it work?

DAS provides a convention how to encode a DNA or protein sequence and its annotated features into simple XML documents that are exchanged over the Internet. Protein sequences or regions on a chromosome are considered to be the reference objects. DAS servers that provide this sequence information are called reference servers. Only few such servers are available. In contrast to this a large number of annotation servers provide the actual annotation data that is available for the reference objects.

The registration server collects the location of all DAS servers. A DAS client, like Ensembl, can retrieve this listing. It then contacts a reference server to obtain the sequence and all the available annotation servers, in order to provide an integrated view of the results.

For full details on the specification please see the DAS specification. To adopt DAS also for structural and multiple alignment data we have extended the original DAS specification with new commands. The documentation for these can be found at http://www.dasregistry.org/help_capabilities.jsp

How can I find out which data is already available via DAS?

We are providing a DAS registration server at http://www.dasregistry.org It keeps track which DAS servers have been published worldwide. Currently it contains more than 200 DAS sources coming from 15 countries.

Show me some examples

We provide support for DAS through different web sites and software applications. In an ideal case and to keep things simple, you will not see that the data comes via DAS at all!

  • Show protein structures mapped to predicted Ensembl proteins - Ensembl
  • The ZF-MODELS project provide various Zebrafish data via DAS - ZF-MODELs Tilling data
  • A few SPICE screenshots - how to map SNPs onto protein structures SPICE

How can I set up my own DAS server?

It is very easy to set up your own DAS server. We provide DAS server implementations in both Perl and Java. Ready made plugins are available that allow quick setup from popular file formats like e.g. GFF files. If you want to point a DAS server to your own local database, all you have to do is to write a simple plugin to convert your data structures into the one's used by the servers.

Publications

Recent publications related to DAS:

  • ProServer: a simple, extensible Perl DAS server.

    Finn RD, Stalker JW, Jackson DK, Kulesha E, Clements J and Pettett R

    Bioinformatics (Oxford, England) 2007;23;12;1568-70

    PUBMED: 17237073; PMC: 2989875; DOI: 10.1093/bioinformatics/btl650

  • Integrating sequence and structural biology with DAS.

    Prlić A, Down TA, Kulesha E, Finn RD, Kähäri A and Hubbard TJ

    BMC bioinformatics 2007;8;333

    PUBMED: 17850653; PMC: 2031907; DOI: 10.1186/1471-2105-8-333

  • Ensembl 2006.

    Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Gräf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kähäri A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C and Hubbard TJ

    Nucleic acids research 2006;34;Database issue;D556-61

    PUBMED: 16381931; PMC: 1347495; DOI: 10.1093/nar/gkj133

  • Adding some SPICE to DAS.

    Prlić A, Down TA and Hubbard TJ

    Bioinformatics (Oxford, England) 2005;21 Suppl 2;ii40-1

    PUBMED: 16204122; PMC: 2656757; DOI: 10.1093/bioinformatics/bti1106

Where can I get help?

several projects that provide DAS support have their own DAS help pages:

Contact

* quick link - http://q.sanger.ac.uk/i5w11nym