Question

where is mart hsapiens_gene_ensembl ?

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paul28 • 0

@paul28-14860

Last seen 6.2 years ago

how to access hsapiens_gene_ensembl or whatever has replaced it? listDatasets does not show "human" in it on ensembl.org or on uswest.ensembl.org. Worked yesterday.... ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") waits a long long time and come back with a response of no such data set

bioconductor • 2.9k views

ADD COMMENT • link 6.2 years ago paul28 • 0

score 0 · Answer 1 · 2018-01-24

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Mike Smith ★ 6.5k

@mike-smith

Last seen 3 hours ago

EMBL Heidelberg

The main Ensembl site at www.ensembl.org seems to be unresponsive for me at the moment.

You haven't provided the full code you've tried, or the output of sessionInfo() so we can see what versions of R/package you're using, but to make sure you're using one the mirror sites you need to specify the argument ensemblRedirect = FALSE e.g.

ensembl <- useMart(biomart = "ensembl", 
                   dataset = "hsapiens_gene_ensembl",
                   host = "useast.ensembl.org",
                   ensemblRedirect = FALSE)

ADD COMMENT • link 6.2 years ago Mike Smith ★ 6.5k

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Any clues what's causing the malfunction? metazoa.ensemble.org also appears to be failing intermittently and giving strange errors (see below). The code I'm using is the same one as Error in useMart while using a dataset in biomaRt. I've run my script a few times, with failures about 50% of the time.

I.e:Add comment

Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database metazoa_mart_38: DBI connect('database=metazoa_mart_38;host=hh-mysql-eg-mart-web.ebi.ac.uk;port=4599','ensro',...) failed: Lost connection to MySQL server at 'reading authorization packet', system error: 0 at /nfs/public/release/ensweb/live/eg_mart/www_91/metazoa/lib/BioMart/Configuration/DBLocation.pm line 98.

ADD REPLY • link 6.2 years ago dangeles • 0

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I don't know any details, only that the Ensembl team are aware of it (https://twitter.com/ensembl/status/956216658007388162)

ADD REPLY • link 6.2 years ago Mike Smith ★ 6.5k

score 0 · Answer 2 · 2018-01-24

Thank you for the answer. You call worked as used verbatum with no other changes to R or my environment. What worked for me previously but did not work for me today was either

library(biomaRt)
ensembl_us_west <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")

or

library(biomaRt)
ensembl_us_west <- useMart("ensembl", dataset = "hsapiens_gene_ensembl",
host = "uswest.ensembl.org")

Today, these both came back with no such data base, I could use them to get other data bases (e.g. gorilla) but nothing with "Hum" or "Hsap" in the title or description. I will try it using uswest

Thank you again.