This is a test version of Biostars. For the public version, visit https://www.biostars.org.
News: is Biomart dead ? "We have frozen BioMart but it remains accessible via our archive servers."

is Biomart dead ?

FYI: https://support.bioconductor.org/p/9163690/

Hi, Jorge from Ensembl here. Thanks for the query and sorry for the error. We have frozen BioMart but it remains accessible via our archive servers. the query above should work if you change the host to our latest archive which supports BioMart - host="https://e116.ensembl.org". (...) The Ensembl useast and asia mirrors are retired, and will no longer work. As we moved a few weeks ago, we are still looking into our links and redirects. I can tell some things are not working as expected, so we'll look into those as soon as we can. As for the future, we are developing a new tool that serves data from our new site.

The upstream Biomart service was discontinued by Ensembl.

ensembl
• 225 views • link
updated by Istvan Albert Istvan Albert • written by Pierre Lindenbaum Pierre Lindenbaum

On a different note: Does anyone know why the requirement to preselect at least one genome is now mandatory for doing any searches? Why can't a term be searched against entire Ensembl site, as used to be the case forever.

• 0 views • link
written by GenoMax GenoMax

Perhaps an implementation flaw, their indexing does not work across genomes

• 0 views • link
written by Istvan Albert Istvan Albert

1 answer

There is some hope that BioMart (or a new replacement referred to above) may appear in future (as noted on the main Ensembl page pop-up).

We’re actively developing this site to expand tools, features, and species coverage. If you rely on features not yet available here, previous Ensembl versions remain accessible via our archives for the long term.

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this