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Linking in to Ensembl

Attaching a file via URL

You can quickly and easily attach any supported file format to Region in Detail using the following URL pattern:

http:/www.ensembl.org/[name_of_species]/Location/View?r=[coordinates];attach=[url_of_your_file]

Note that if your file URL contains semicolons, ampersands (&) or equals signs, these will need to be URL-encoded.

For attaching data to other images or pages, see the advanced customisation tips below.

Linking on a stable ID

If you simply wish to link to a gene, transcript, protein or gene tree page, particularly for automated links, you can do so using the following template:

[site]/id/[stable id]

For example, http://www.ensembl.org/id/ENSG00000139618, or http://grch37.ensembl.org/id/ENSMUST00000103109.

As you can see, you don't need to know the name of the species that the ID belongs to; the website will work that out automatically based on the 3-6 letter prefix.

Note however that you do have to use Ensembl stable IDs; you cannot substitute a gene symbol such as FOXP2, as that is found in many species. To link on a gene symbol, see the standard URL structure section, below.

Find out more about stable IDs.

Valid ID types are:

  • Gene: ENS[species code]G[number]
  • Transcript: ENS[species code]T[number]
  • Protein: ENS[species code]P[number]
  • Gene tree: ENS[species code]GT[number]

More about Ensembl URLs

URLs for Ensembl views take the format:

http://www.ensembl.org/species/section/page?g=gene;t=transcript;r=seq_region:start-end

Location-based views

Any 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:

Feature-based views

Views based on a gene, transcript or variation need the parameter of that type in their URL - a location alone is insufficient:

Advanced link customisation

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:

  • Configuring options for a page
  • Configuring a panel/image (changing the way tracks are rendered)
  • Attaching external data via URL, without using the Control Panel

These are accomplished in a similar, systematic way. Extra parameters are appended to the URL for the relevant page:

context=key=value

Or when setting multiple values:

context=key1=value1,key2=value2,key2=value2

Or when setting multiple different types of parameter:

context1=key1=value1,key2=value2,key2=value2;context2=key3=value3

Global Page Settings

Global page settings are changed using the config key. For example, to turn off the top image on Location > Region in detail:

config=show_top_panel=no

Appending 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=show_top_panel=no

To 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=yes

Configuring Panels

To change configuration for an individual panel add a parameter referring to the panel:

  • Location > Region in detail: contigviewtop and contigviewbottom
  • Location > Region overview: cytoview

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

Track names are systematically named. The following example identifies a track with Ensembl transcripts from the core Ensembl database:

transcript_core_ensembl

Renderers

Renderers depend on the type of track:

  • Transcripts: transcript_label, transcript_nolabel, collapsed_label, collapsed_nolabel or off
  • Alignment features: normal, half_height, stack, unlimited, ungrouped or off

Example - configure a 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=show_top_panel=no

Attaching External Data

To attach 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:

url:source

where source is the location of the external data.

IMPORTANT: You must encode any = & or ; characters in your URL for the attachment to work correctly.

Renderers

Renderers are the same as for alignment tracks (see above), or for wiggle/graph data, either 'off' or 'signal'.

Examples - attach external data

To attach an example data file by URL and display the features with the default renderer:

http://www.ensembl.org/Homo_sapiens/Location/View?g=ENSG00000130544;contigviewbottom=url:http://www.ensembl.org/info/website/upload/sample_files/example.bed

To attach an example data file by URL and display the features in a half_height style:

http://www.ensembl.org/Homo_sapiens/Location/View?g=ENSG00000130544;contigviewbottom=url:http://www.ensembl.org/info/website/upload/sample_files/example.bed=half_height

Note on bedGraph format If attaching a bedGraph file, please add the parameter 'format=bedGraph' to the URL, e.g.

http://www.ensembl.org/Homo_sapiens/Location/View?g=ENSG00000012048;contigviewbottom=url:http://www.abcd.edu/myprojects/data.bed=signal;format=bedGraph