DAS writeback server implementation

DAS Description

The main idea of DAS (Distrubuted Annotation System) is to bring together annotations from different genome annotation sources, see http://www.biodas.org/wiki/Main_Page for more details. The annotation data can be shared between institutions through the standard DAS exchange protocol and according to defined DAS XML specification.

With increasing speed of large-scale genome sequencing, the information systems providing facilities to store, analyze and display genomic data have become an important issue. Data sharing is an other question that arises from the fact that biological annotations are provided not by centralized database, but by different scientific organizations around the world.

Ensembl http://www.ensembl.org/index.html is one of the largest genomic data storages. Currently the number of genomes available from Ensembl is 33, which increased rapidly from 15 genomes in year 2006. The other large collections of genomes are UCSC http://genome.ucsc.edu/ and NCBI http://www.ncbi.nlm.nih.gov/ genome browsers. The mission of Ensembl is to make all its data and software source code available to all users.

An other well-known open-source genome browser is GBrowse http://www.gmod.org/wiki/index.php/GBrowse.

DAS extensions

DAS writeback

Implemented in this project DAS writeback functionality allows to enhance the original DAS read-only concept by providing the possibility to add, edit and store the annotations through the web-interface. Although some annotation servers already supported writeback to their local sources, it was not commonly used.

This project develops implementations for the DAS writeback specification http://biodas.org/documents/das2/das2_writeback.html. It is implemented in Java (IDE Eclipse) usind XML web-protocol.

The standard writeback document is used to POST it to a defined URL to add, modify or delete features. The server responses to a writeback and inserts modifications into database.

This feature will be used by everybody wishing to contribute the biological annotations. It will be publicly available as for example Ensembl genome browser.

Implementation

The writeback is based on the concept of client-server architecture and basically consists of three layers : database, user interface and a functional logic between the first two.

User interface

Consists of several JSP pages. see more

Functional logic

Servlets and java classes. see more

Database

MySQL, Ensembl like database. see more

Open ID sign-in

An important feature of the writeback implementation is an OpenID user-login.

OpenID is a free and decentralized single sign-on system https://www.myopenid.com/. It enables simple and reliable user-login.

The writeback document

The writeback document is in XML format with content-type "application/x-das-writeback+xml". All of the DAS writeback elements are in the standard DAS2 namespace http://biodas.org/documents/das2. This namespace is reserved and authors of DAS extensions may not create new XML elements in it.

Here is an example of a writeback document modifying a single feature:

<WRITEBACK>
   <MESSAGE>Changed the feature cTel54X</MESSAGE>
   <UPDATES>
       <UPDATE uri="cTel54X" />
   </UPDATES>
   <FEATURE  featureid="cTel54X" featuretype="exon" method="experiment">
       <LOC segment="ENSG00000139618" range="0:0:+" />
       <PROPERTY phase="." />
       <PROPERTY score="1.135" />
       <PROPERTY link="http://" />
       <PROPERTY groups="similarity2" />
       <PROPERTY system="101" />
       <PROPERTY system_uri="CS_DS82" />
       <PROPERTY commit_msg="Changed the feature cTel54X" />
       <PROPERTY user="http://user.myopenid.com/" />
   </FEATURE>
</WRITEBACK>

see description

This code of this project may be freely distributed and modified under the terms of the GNU Lesser General Public Licence http://www.gnu.org/copyleft/lesser.html