Linking in to Ensembl…

Due to the changes in the web interface there have been a number of changes to the URLs for pages. In most cases the web code catches these changes but there are a number of requests which due to the nature of the site have changed:

  • Configuring the way a page is rendered;
  • Changing the way tracks are rendered;
  • Adding DAS sources via a web-address and not via the web interface;
  • Attach UCSC style external resources.

These are now all attached in a similar – systematic way:

  • To change global page settings: add a paramter config=key=value{,key=val}
    e.g.
    to turn off the top image on Location > Region in detail

    http://www.ensembl.org/Homo_sapiens/Location/View?r=1:1000-2000;config=view_top=off

    e.g. to link directly to the Exon Intron markup panel (Transcript > Exons) and to show full introns and 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

  • To change configuration for an individual panel add a parameter refering to the panel (this will be documented shortly on the website) e.g. For Location > Region in detail the two panels are contigviewtopcontigviewbottom, for Location > Region overview it is cytoview. This is again 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. Additionally the left hand side can be used to integrate external data: Notes:
    • Track names are now systematically named so will have changed from the values you may have been used to using – again we will shortly publish a list of these, but examples are: transcript_core_ensembl – the ensembl genes from the ensembl database.
    • Renderers depend on the type of track, but e.g. for transcripts you have the option of “transcript_label”, “transcript_nolabel”, “collapsed_label” and “collapsed_nolabel”, for alignment features (and also url attached data at the moment) “normal”, “half_height”, “stack”, “unlimited” and “ungrouped”, for DAS tracks “labels” (show labels if configured by the source) or “nolabels” – hide labels.
    • At the moment two special parameters can be used:
      das:http://www.mydas.source/das/my_data=render
      – which attaches a DAS source to the session and selects the renderer
      url:http://www.myweb.server/my_data.format=render

    For example:

    http://www.ensembl.org/Homo_sapiens/Location/View?g=ENSG00000012048;config=panel_top=off;contigviewbottom=das:http://www.ensembl.org/das/Homo_sapiens.NCBI36.transcript=nolabels,transcript_core_ensembl=collapsed_nolabel

    Turns on a das source (in this case the Ensembl transcripts) and collapses the standard ensembl track down to a single line per Gene AND also turns off the top panel!

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