Ensembl Links

Creating URL Links to Ensembl

• On the Ensembl details pages, there are links to the Ensembl Transcript ID and Ensembl Protein ID details pages.

e.g.

 Ensembl Gene Link: ENST00000370314
 Ensembl Protein: ENSP00000359337

where the IDs are the links to Ensembl (http://www.ensembl.org) pages.

• Ensembl is updated every 2 months and the older versions are archived. Check Ensembl [1] for the date of the correct Ensembl release for the track.

• In order to make sure that the URLs constructed for the links are pointing to the correct archive, an ensArchive trackDb setting is added to the assembly level trackDb.ra with the Ensembl release date e.g. for zebrafish danRer5:

 hgwdev> cd ~/kent/src/hg/makeDb/trackDb/zebrafish/danRer5
 hgwdev> vi trackDb.ra

Edit and add a trackDb setting line like this to the ensGene track:

 ensArchive aug2007
 

• A trackDb dataVersion setting line should be added to show the date of the Ensembl Release was used to create the track

 dataVersion August 2007

• Add the release number to the longLabel setting for the track in trackDb.ra for the assembly.

 longLabel Ensembl (Version 46) Gene Predictions (Protein-Coding Genes)

For this track, only protein-coding genes were added so that is reflected in the label.

• NOTE: URLs are constructed by the hgc.c code by the printEnsemblUrl() function that is called by doEnsemblGene().

• IMPORTANT: Make sure that there is an entry in the appropriate make doc with the Ensembl Release number and the release date for that release. An entry should be added even in the track was created using Robert Baertsch's automated Ensembl track build program, hgLoadEnsembl.