URLs for Ensembl views take the format:
http://www.ensembl.org/species/section/page?g=gene;t=transcript;r=seq_region:start-endAny combination of the gene, transcript and genomic region may be specified. For example, the following all take the user to the genomic region surrounding the human gene BRCA1:
Views based on a gene, transcript or variation need the parameter of that type in their URL - a location alone is insufficient:
Many of the customisation options available to users of the website in the Control Panel can be manipulated using specially constructed URLs. This allows configuration settings to be shared with colleagues, for example to highlight a particular data track. This includes:
These are accomplished in a similar, systematic way. Extra parameters are appended to the URL for the relevant page:
context=key=valueOr when setting multiple values:
context=key1=value1,key2=value2,key2=value2Or when setting multiple different types of parameter:
context1=key1=value1,key2=value2,key2=value2;context2=key3=value3Global page settings are changed using the config key. For example, to turn off the top image on Location > Region in detail:
config=panel_top=noAppending this to the URL for the Region in detail page, the final URL is:
http://www.ensembl.org/Homo_sapiens/Location/View?r=1:1000-2000;config=panel_top=noTo link directly to the Exon Intron markup panel (Transcript > Exons), to show full introns, only 60bp flanking sequence AND turn the display to be 60bp wide:
http://www.ensembl.org/Homo_sapiens/Transcript/Exons?t=ENST00000309255;config=flanking=60,seq_cols=60,fullseq=yesTo change configuration for an individual panel add a parameter referring to the panel:
Options are again specificed in a comma separated list, where the left hand side of each "=" is the name of the track, and the right hand side is the name of the "renderer" to use - the latter depends on the type of track.
Track names are systematically named. The following example identifies a track with Ensembl transcripts from the core Ensembl database:
transcript_core_ensemblRenderers depend on the type of track:
To collapse the Ensembl genes track down to a single line per gene AND turn off the top panel in Location > Region in detail:
http://www.ensembl.org/Homo_sapiens/Location/View?g=ENSG00000012048;contigviewbottom=transcript_core_ensembl=collapsed_nolabel;config=panel_top=noTo attach DAS or UCSC-style URL data, follow the procedure above for configuring the appropriate panel, using special track names to identify the data source. These special names are of the format:
type:sourceWhere type is either of das or url, and source is the location of the external data.
Renderers depend on the type of track:
To attach an example data file by URL and display the features in an ungrouped style:
http://www.ensembl.org/Homo_sapiens/Location/View?g=ENSG00000012048;contigviewbottom=url:http://www.ensembl.org/info/website/upload/sample_files/example.bed=ungroupedTo attach the Ensembl transcripts DAS source and display the features according to the server's instructions (stylesheet):
http://www.ensembl.org/Mus_musculus/Location/View?g=ENSMUSG00000049878;r=4:120817978-120887689;contigviewbottom=das:http://das.sanger.ac.uk/das/ikmc_products=normalTo attach a DAS source from the DAS registry (in this case human SNPs from ASTD) and force the display of labels:
http://www.ensembl.org/Homo_sapiens/Location/View?g=ENSG00000012048;contigviewbottom=das:http://www.dasregistry.org/das/sources/DS_560=labelsTo attach a text-based DAS source (one which will not be displayed on an image):
http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000139618;r=13:32889611-32973347;t=ENST00000380152;das=http://www.genenames.org/das/HGNC/It is only possible to add a DAS track that is self-configuring. That is, it provides all of the information Ensembl needs to query it automatically via the sources or dsn command. This behaviour is by design. See setting up a DAS server for more details.
Due to a limitation of the website, it is currently only possible to attach a DAS source to a panel (i.e. a track on an image) and not to a page. Thus non-positional (text-based) DAS sources such as those annotating genes cannot be attached in this manner. For more information on the different types of DAS source, see how Ensembl uses DAS.