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News: Ensembl release 84 is out!
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gravatar for Thomas Maurel
20 months ago by
Thomas Maurel700
United Kingdom
Thomas Maurel700 wrote:

We are pleased to announce that the new Ensembl marts for release 84 are now live on www.ensembl.org.

If you are using biomaRt, you can change your host to access our most recent data:

ensembl_mart_84 <- useEnsembl(biomart=“ensembl")

 

  • Ensembl Genes 84
    • Renamed "phase" attribute to "start phase" in the structure and sequence sections
    • Renamed homolog, paralog and ortholog to homologue, paralogue and orthologue
    • Renamed many attributes in the homologues section
    • Added new "associated gene name" attribute for orthologues and paralogues in the homologues section
  • Ensembl Variation 84
    • Retirement of the "population genetics" data
  • Ensembl Regulation 84
    • Retirement of the "regulatory segments" dataset for human
    • Renamed "Has evidence" attribute to "Activity" in the "Regulatory feature" dataset
  • Vega 64

A complete list of the changes in release 84 can be found at http://www.ensembl.org/info/website/news.html

Best Regards,

Thomas 

ADD COMMENTlink modified 19 months ago by arielpaulson20 • written 20 months ago by Thomas Maurel700
1
gravatar for arielpaulson
19 months ago by
arielpaulson20
arielpaulson20 wrote:

Hi Amonida,

The error message in my post shows that this is not a quoting problem. I cut and pasted the blog-post code into reply, but in the code I ran, I had replaced the quotes.  Bad quotes would return a completely different error message, since R would not be able to parse the function arguments in the first place.

I assume the problem is on Ensembl's end, since the call ' listMarts(host="www.ensembl.org") ' does technically succeed, but the result is empty, thus no marts at www.ensembl.org.  Recently Ensembl has changed their default host from www.biomart.org to www.ensembl.org, which broke the biomaRt defaults.  Then, they changed the mart names and core dataset names for ensemblgenomes.org marts.  I suspect they have changed something yet again.

Thanks,

Ariel

ADD COMMENTlink written 19 months ago by arielpaulson20
Hi Ariel, Sorry for the late reply. Can you please paste in the exact command line you're running as I can't reproduce the error message you're getting. Below is what I get when testing the examples from Ensembl website (http://www.ensembl.org/info/data/biomart/biomart_r_package.html): > library(biomaRt) > listMarts(host='www.ensembl.org') biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 84 2 ENSEMBL_MART_SNP Ensembl Variation 84 3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 84 4 ENSEMBL_MART_VEGA Vega 64 > listEnsembl() biomart version 1 ensembl Ensembl Genes 84 2 snp Ensembl Variation 84 3 regulation Ensembl Regulation 84 4 vega Vega 64 > ensembl=useEnsembl(biomart='ensembl') > head(listDatasets(ensembl)) dataset description version 1 oanatinus_gene_ensembl Ornithorhynchus anatinus genes (OANA5) OANA5 2 cporcellus_gene_ensembl Cavia porcellus genes (cavPor3) cavPor3 3 gaculeatus_gene_ensembl Gasterosteus aculeatus genes (BROADS1) BROADS1 4 itridecemlineatus_gene_ensembl Ictidomys tridecemlineatus genes (spetri2) spetri2 5 lafricana_gene_ensembl Loxodonta africana genes (loxAfr3) loxAfr3 6 choffmanni_gene_ensembl Choloepus hoffmanni genes (choHof1) choHof1 The reason that the default host changed in biomaRt was that the www.biomart.org portal was down and hence the biomaRt developers changed it to www.ensembl.org. Can you also please give an example of the changes you mention for the ensemblgenomes.org marts, as far as I know these have not been modified. Best regards, Amonida -- Amonida Zadissa Ensembl Production Team EMBL-EBI Hinxton England On 15/04/2016 22:28, arielpaulson [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User arielpaulson <https: support.bioconductor.org="" u="" 10099=""/> wrote Answer: > Ensembl release 84 is out! <https: support.bioconductor.org="" p="" 79474="" #80914="">: > > Hi Amonida, > > The error message in my post shows that this is not a quoting problem. I cut and > pasted the blog-post code into reply, but in the code I ran, I had replaced the > quotes. Bad quotes would return a completely different error message, since R > would not be able to parse the function arguments in the first place. > > I assume the problem is on Ensembl's end, since the call ' > listMarts(host="www.ensembl.org") ' does technically succeed, but the result is > empty, thus no marts at www.ensembl.org. Recently Ensembl has changed their > default host from www.biomart.org to www.ensembl.org, which broke the biomaRt > defaults. Then, they changed the mart names and core dataset names for > ensemblgenomes.org marts. I suspect they have changed something yet again. > > Thanks, > > Ariel > > -------------------------------------------------------------------------------- > > Post tags: ensembl, mart, release84, biomart, ensembl release, News > > You may reply via email or visit A: Ensembl release 84 is out! >
ADD REPLYlink written 19 months ago by amonida10

running R 3.2.2 with biomart 2.28.0, I get the following

> library(biomaRt)

> listMarts(host="www.ensembl.org")
[1] biomart version
<0 rows> (or 0-length row.names)
> ens <- useEnsembl(biomart="ensembl")

Error in useMart(biomart = biomart, dataset = dataset, host = host, verbose = verbose) : 
  Incorrect BioMart name, use the listMarts function to see which BioMart databases are available

 

ADD REPLYlink written 18 months ago by glocke010
1
gravatar for arielpaulson
19 months ago by
arielpaulson20
arielpaulson20 wrote:

Hi Amonida,

I've discovered the problem is on our end.  We have a CentOS 6 sitewide environment, but someone has built the sitewide biomaRt package on an "experimental" server running CentOS7 -- apparently -- because biomaRt will only work on that server.  Everywhere else it fails like: 

> library(biomaRt)

> listMarts(host='www.ensembl.org')
[1] biomart version
<0 rows> (or 0-length row.names)

At any rate, thanks for your help,

Ariel

ADD COMMENTlink written 19 months ago by arielpaulson20
Hi Ariel, Glad you've identified the source of the issue. Please let us know if you come across any Ensembl related issues in the future. Best regards, Amonida -- Amonida Zadissa Ensembl Production Team EMBL-EBI Hinxton England On 20/04/2016 20:39, arielpaulson [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User arielpaulson <https: support.bioconductor.org="" u="" 10099=""/> wrote Answer: > Ensembl release 84 is out! <https: support.bioconductor.org="" p="" 79474="" #81090="">: > > Hi Amonida, > > I've discovered the problem is on our end. We have a CentOS 6 sitewide > environment, but someone has built the sitewide biomaRt package on an > "experimental" server running CentOS7 -- apparently -- because biomaRt will only > work on that server. Everywhere else it fails like: > >> library(biomaRt) > >> listMarts(host='www.ensembl.org') > [1] biomart version > <0 rows> (or 0-length row.names) > > At any rate, thanks for your help, > > Ariel > > -------------------------------------------------------------------------------- > > Post tags: ensembl, mart, release84, biomart, ensembl release, News > > You may reply via email or visit A: Ensembl release 84 is out! >
ADD REPLYlink written 19 months ago by amonida10

Hi Ariel,

I am having the exact same problem you are. When I try the command

> useMart("ensembl") 
Error in useMart("ensembl") : Incorrect BioMart name, use the listMarts function to see which BioMart databases are available

>listMarts(host = "www.ensembl.org")
[1] biomart version
<0 rows> (or 0-length row.names)

However, I'm operating on what I thought was a pretty standard version of x86_64 GNU/Linux. I'm not sure what the problem is, but if you found a workaround or have any insights about this problem, I would be grateful to hear!

Thank you,

Maureen

ADD REPLYlink written 19 months ago by maureen.pittman0
0
gravatar for arielpaulson
19 months ago by
arielpaulson20
arielpaulson20 wrote:

Trying the above command -- useEnsembl(biomart=“ensembl") -- today on R 3.2.2 and R 3.2.0, it does not work, gives error "Incorrect BioMart name, use the listMarts function to see which BioMart databases are available".  Also, using listMarts() with core host "www.ensembl.org" returns a data frame with 0 rows, although "metazoa.ensembl.org" still works.  Where do we get the vertebrate marts from now?

ADD COMMENTlink written 19 months ago by arielpaulson20
Hi Arial The problem is with the formatting of the command. The first double-quote in the command is causing the issue. If you replace it with plain double-quotes the command should work fine: ensembl_mart_84 <- useEnsembl(biomart="ensembl") You can also use single-quotes: ensembl_mart_84 <- useEnsembl(biomart='ensembl') Hope this helps, Amonida On 14/04/2016 20:50, arielpaulson [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User arielpaulson <https: support.bioconductor.org="" u="" 10099=""/> wrote Answer: > Ensembl release 84 is out! <https: support.bioconductor.org="" p="" 79474="" #80854="">: > > Trying the above command -- useEnsembl(biomart=“ensembl") -- today on R 3.2.2 > and R 3.2.0, it does not work, gives error "Incorrect BioMart name, use the > listMarts function to see which BioMart databases are available". Also, using > listMarts() with core host "www.ensembl.org" returns a data frame with 0 rows, > although "metazoa.ensembl.org" still works. Where do we get the vertebrate > marts from now? > > -------------------------------------------------------------------------------- > > Post tags: ensembl, mart, release84, biomart, ensembl release, News > > You may reply via email or visit A: Ensembl release 84 is out! >
ADD REPLYlink written 19 months ago by amonida10

@Ariel, I have the same problem too. I am trying to fetch human transcripts and protein domain data via biomaRt and I get the same error "

> listMarts("www.ensembl.org")
[1] biomart version
<0 rows> (or 0-length row.names)
> ensembl_mart_84 <- useEnsembl(biomart=“ensembl")
Error: unexpected input in "ensembl_mart_84 <- useEnsembl(biomart=�"
> ensembl_mart_84 <- useEnsembl(biomart='ensembl')
Error in useMart(biomart = biomart, dataset = dataset, host = host, verbose = verbose) :
  Incorrect BioMart name, use the listMarts function to see which BioMart databases are available"

This is literally blocking me from finishing up my work!
@Amonida, is there any work around for this situation. I am trying to generate lollipop plots using GeneVisR packages lolliplot() command. This requires ensembl annotation. I am running R v3.3.0 on 64bit linux-gnu Ubuntu 14.04.

any help would be very much appreciated.

TIA,

Venkatesh Chellappa

ADD REPLYlink written 17 months ago by genomics0
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