Ensembl Links: Difference between revisions
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* NOTE: URLs are constructed by the hgc.c code by the printEnsemblUrl() function that is called by doEnsemblGene(). | * NOTE: URLs are constructed by the hgc.c code by the printEnsemblUrl() function that is called by doEnsemblGene(). | ||
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Revision as of 01:37, 19 November 2007
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 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().
