Ensembl .
Data Custom AnnotationDepending on the amount and type of data that you have, Ensembl allows you to display it as features or as user-defined regions in some of its displays (e.g. in KaryoView, ContigView, CytoView, ProtView, or in GeneView). You may also share your data source with others if you wish to do so.
Ensembl KaryoView can be configured to display a series of user-defined data points either along a single chromosome ideogram, such as those displayed on Ensembl MapView, or along an entire karyotype ideogram. Visualising sets of genomic data with discrete positions can be extremely useful to get an overview of your data distribution and to identify any hot or cold spots that might not be immediately obvious.
Generally, KaryoView is linked from MapView pages via the navigation column option "Map your data onto this chromosome", and is available for any species with an assembly mapped to chromosomes. (e.g. Homo sapiens MapView and KaryoView)
The data set is specified as a list of chromosome, start base, end base and feature name values. It can be shown against the chromosomes as a variety of boxes, lines and arrows.
There are a few different ways of attaching your own data to the ContigView, CytoView, ProtView, or GeneView displays. They differ in flexibility, efficiency, and data persistence, i.e. how easy it is to keep the data tracks up to date, how the speed of the loading of an Ensembl display is affected, and for how long the data will be available.
Both ContigView and CytoView are able to attach URL-based data. These displays show features in a genomic context. If you want to attach data to ProtView (proteomic annotations or non-positional annotations on proteins), or GeneView (non-positional annotations on genes) however, you will have to either use user-uploaded data or set up a DAS server (see below for a description of these methods).
For URL-based data, use the pop-up help on URL-based data to get an explanation of how to view genomic features from a file on your own web server. Ensembl reads this file and displays the features as graphical boxes on the ContigView or CytoView displays. As the URL-based data is compatible with the UCSC Custom Track format, the same file can be used for both the UCSC genome browser and the Ensembl genome browser.
URL-based data is only really suitable for a small number of features, as they have to be read by the Ensembl server for each reload of the display, which slows down the responsiveness of the browser. The data is private, but you can share URLs with collaborators, and are as permanent as you make them.
Use the instructions on the the Ensembl help page for DASConfView about how to upload your data into Ensembl.
The Distributed Annotation System (DAS) is a protocol for providing genomic and proteomic annotations over the Internet. A DAS client can connect to several annotation servers simultaneously, allowing users to see and compare annotations from different sources.
DAS is widely used by Ensembl to include external annotations on its ContigView, CytoView, ProtView, and GeneView displays. Ensembl also has its own Ensembl-DAS reference server.
You may also set up and run your own DAS server to display your data in Ensembl. Ensembl ContigView, CytoView, GeneView and ProtView displays can all act as full DAS clients, integrating your data with Ensembl. This data can be much more complex than is possible with the upload data method, and you have far more control over the way you store the data and keep it up to date. This is typically what you would want to do if you would like a more permanent data source attached to Ensembl, or if the data source contains a lot of annotations (e.g. dense annotations for a chromosome or annotations for a whole genome).
© 2008 WTSI / EBI. Ensembl is available to download for public use - please see the code licence for details.
