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 previous version is 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, a trackDb setting is added to the assembly level trackDb.ra 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 which Ensembl Release was used to create the track

 dataVersion Ensembl Release 46

• Add the release number to the longLabel setting for the track.

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