[ensembl-dev] Biomart connection

Anne Lyle annelyle at ebi.ac.uk
Fri Apr 20 10:57:18 BST 2018


Hi again Pankaj

It looks like biomaRt is being directed towards our useast mirror, which is the correct behaviour for your location - but unfortunately the biomart human gene set is missing from that mirror. If it’s possible to explictily direct biomaRt to our UK or uswest sites, that will fix your problem; in the meantime we’ll work on fixing the useast machine.

Thanks again for letting us know

Anne

> On 19 Apr 2018, at 22:58, Pankaj Agarwal <p.agarwal at duke.edu> wrote:
> 
> I am connecting to the default (not specifying any server in particular).
> Here is my code
>  
> > library("biomaRt")
> > listMarts()
>                biomart               version
> 1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 92
> 2   ENSEMBL_MART_MOUSE      Mouse strains 92
> 3     ENSEMBL_MART_SNP  Ensembl Variation 92
> 4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 92
>  
> >ensembl=useMart("ensembl")
>  
> I cannot see "hsapiens_gene_ensembl" in the dataset list now
>  
> > listDatasets(ensembl)$dataset
> [1] "mcaroli_gene_ensembl"           "pabelii_gene_ensembl"
> [3] "odegus_gene_ensembl"            "mfuro_gene_ensembl"
> [5] "psinensis_gene_ensembl"         "cjacchus_gene_ensembl"
> [7] "sharrisii_gene_ensembl"         "tbelangeri_gene_ensembl"
> [9] "mlucifugus_gene_ensembl"        "cchok1gshd_gene_ensembl"
> [11] "amelanoleuca_gene_ensembl"      "caperea_gene_ensembl"
> [13] "pmarinus_gene_ensembl"          "mpahari_gene_ensembl"
> [15] "pbairdii_gene_ensembl"          "mochrogaster_gene_ensembl"
> [17] "ggorilla_gene_ensembl"          "gaculeatus_gene_ensembl"
> [19] "lchalumnae_gene_ensembl"        "amexicanus_gene_ensembl"
> [21] "dnovemcinctus_gene_ensembl"     "scerevisiae_gene_ensembl"
> [23] "mmusculus_gene_ensembl"         "mauratus_gene_ensembl"
> [25] "pvampyrus_gene_ensembl"         "ppaniscus_gene_ensembl"
> [27] "saraneus_gene_ensembl"          "dmelanogaster_gene_ensembl"
> [29] "fcatus_gene_ensembl"            "tnigroviridis_gene_ensembl"
> [31] "oprinceps_gene_ensembl"         "ccrigri_gene_ensembl"
> [33] "neugenii_gene_ensembl"          "cpalliatus_gene_ensembl"
> [35] "aplatyrhynchos_gene_ensembl"    "mspretus_gene_ensembl"
> [37] "vpacos_gene_ensembl"            "sscrofa_gene_ensembl"
> [39] "chircus_gene_ensembl"           "falbicollis_gene_ensembl"
> [41] "csabaeus_gene_ensembl"          "clanigera_gene_ensembl"
> [43] "ecaballus_gene_ensembl"         "ngalili_gene_ensembl"
> [45] "nleucogenys_gene_ensembl"       "oaries_gene_ensembl"
> [47] "ogarnettii_gene_ensembl"        "pformosa_gene_ensembl"
> [49] "anancymaae_gene_ensembl"        "ttruncatus_gene_ensembl"
> [51] "csyrichta_gene_ensembl"         "itridecemlineatus_gene_ensembl"
> [53] "hmale_gene_ensembl"             "trubripes_gene_ensembl"
> [55] "mdomestica_gene_ensembl"        "drerio_gene_ensembl"
> [57] "xmaculatus_gene_ensembl"        "catys_gene_ensembl"
> [59] "mleucophaeus_gene_ensembl"
>  
>  
>  
> > mymart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
> Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) :
>   The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names c
>  
> This same code was working last week.
>  
> mymart = useMart("ensembl", dataset="pabelii_gene_ensembl")         
>  
> - this works fine
>  
> > mm = useMart("ensembl", dataset="mmusculus_gene_ensembl")
> - mouse works fine too
>  
> Curious why hsapiens_gene_ensembl is not in the dataset anymore?
>  
> Thanks,
>  
> - Pankaj
>  
> From: Dev [mailto:dev-bounces at ensembl.org] On Behalf Of Anne Lyle
> Sent: Thursday, April 19, 2018 4:29 AM
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] Biomart connection
>  
> Hi Pankaj
>  
> Which database server are you connecting to? We are experiencing some network issues here in the UK, but if you’re connecting to the US East mirror I will need to look for possible server problems in the cloud.
>  
> Thanks
>  
> Anne
>  
> 
> 
> On 18 Apr 2018, at 19:27, Pankaj Agarwal <p.agarwal at duke.edu <mailto:p.agarwal at duke.edu>> wrote:
>  
> Hi,
> I am trying to connect to biomart through R as follows and sometimes it works fine and sometimes I get the following error (today it only giving the error)
>  
> library("biomaRt")
> listMarts()
>                biomart               version
> 1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 92
> 2   ENSEMBL_MART_MOUSE      Mouse strains 92
> 3     ENSEMBL_MART_SNP  Ensembl Variation 92
> 4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 92
>  
> mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
> Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) :
>   The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.
>  
> This same command has worked several times in the past.
>  
> Thanks,
>  
> - Pankaj
>  
> ----------------------------------------------------------------
> Pankaj Agarwal, M.S
> Bioinformatician
> Database Analyst II
> Surgical Sciences Applied Therapeutics Section
> Department of Surgery
> Duke University
> 919-681-2251
> p.agarwal at duke.edu <mailto:p.agarwal at duke.edu>
>  
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> Anne Lyle
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