Many users ask us about how to download data from ensembl. Usually, the answer is using BioMart. Comparative genomics data are also available in the standard Mart for your favorite species. For instance to get all the human-mouse orthologs, one can select the human dataset, filter all the genes with no mouse orthologs and choose to output the mouse orthologs for all the resulting genes.
Here is how to get these data in 10 simple steps
1. Go to: http://www.ensembl.org/biomart/martview
2. Choose “Ensembl 52”
3. Choose “Homo sapiens genes (NCBI36)”
4. Click on “Filters” in the left menu
5. Unfold the “MULTI SPECIES COMPARISONS” box, tick the “Homolog filters” option and choose “Orthologous Mouse Genes” from the drop-down menu.
6. Click on “Attributes” in the left menu
7. Click on “Homologs”
8. Unfold the “MOUSE ORTHOLOGS” box and select the data you want to get (most probably the gene ID and maybe the orthology type as well).
9. Click on the “Results” button (top left)
10. Choose your favorite output
Here is the preview of the results:
Other people may prefer to use our Compara Perl API or get the data directly from the Compara DB. These options are also available.
The beginning of this week myself and Paul Flicek were in lovely Rotterdam at the Gen2Phen kick off meeting, an EU project lead by Tony Brookes from Leicester. Like all large European projects, the kick off meeting is a get-to-know everyone, have beers (very good ones in Holland) and get a feel for the project.
For me, the exciting thing was getting closer to the locus specific databases – in the project is Johan den Dunnen (from just down the road in Leiden, Holland) and Andy Devereau (from Manchester) who run locus specific databases and diagnostic databases respectively. Getting this valuable data coordinated with genome data (and the fiddly bit is about sequence coordinates, at least at first) is going to be great thing to do.
There’s lots to do in this area – certainly this is something that effects all the big browsers (UCSC, NCBI, ourselves) and has a had a long history of complex systems and sociological tensions in getting things sorted. But my sense in this small room hidden away in the Erasmus medical centre was that we had good people in the room, committed to finding a good solution whilst understanding the complexity of problem. Next up will be more technical meetings, but it was an excellent start. Don’t expect anything tomorrow, but I think we can expect something end of 2008/2009.
And did I mention the beer was good as well?