[ensembl-dev] Biomart connection

[Pankaj Agarwal]

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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