[ensembl-dev] Biomart connection

Pankaj Agarwal p.agarwal at duke.edu
Mon Apr 23 12:42:01 BST 2018


Hi Anne,
I tried connecting other mirrors and there is an issue with all of them.  Some have even less datasets available.

> mymart3 = useEnsembl("ENSEMBL_MART_ENSEMBL", mirror="uswest")
>
> listDatasets(mymart3)$dataset
[1] "oaries_gene_ensembl"        "oniloticus_gene_ensembl"
[3] "pcoquereli_gene_ensembl"    "dmelanogaster_gene_ensembl"
[5] "oanatinus_gene_ensembl"     "ocuniculus_gene_ensembl"
[7] "saraneus_gene_ensembl"      "drerio_gene_ensembl"
[9] "cporcellus_gene_ensembl"
>
>

> mymart4 = useEnsembl("ENSEMBL_MART_ENSEMBL", mirror="asia")
>
> listDatasets(mymart4)$dataset
[1] "cjacchus_gene_ensembl"       "pmarinus_gene_ensembl"
[3] "ptroglodytes_gene_ensembl"   "csabaeus_gene_ensembl"
[5] "psinensis_gene_ensembl"      "rbieti_gene_ensembl"
[7] "xmaculatus_gene_ensembl"     "ogarnettii_gene_ensembl"
[9] "caperea_gene_ensembl"        "loculatus_gene_ensembl"
[11] "amexicanus_gene_ensembl"     "gmorhua_gene_ensembl"
[13] "ocuniculus_gene_ensembl"     "cfamiliaris_gene_ensembl"
[15] "ccapucinus_gene_ensembl"     "sboliviensis_gene_ensembl"
[17] "ppaniscus_gene_ensembl"      "ttruncatus_gene_ensembl"
[19] "chircus_gene_ensembl"        "aplatyrhynchos_gene_ensembl"
[21] "ccrigri_gene_ensembl"        "mauratus_gene_ensembl"
[23] "celegans_gene_ensembl"       "anancymaae_gene_ensembl"
[25] "gaculeatus_gene_ensembl"     "clanigera_gene_ensembl"
[27] "cporcellus_gene_ensembl"     "choffmanni_gene_ensembl"
[29] "rroxellana_gene_ensembl"     "ggallus_gene_ensembl"
[31] "drerio_gene_ensembl"         "eeuropaeus_gene_ensembl"
[33] "ggorilla_gene_ensembl"       "oaries_gene_ensembl"
[35] "odegus_gene_ensembl"         "saraneus_gene_ensembl"
[37] "mmurinus_gene_ensembl"       "sharrisii_gene_ensembl"
[39] "panubis_gene_ensembl"        "xtropicalis_gene_ensembl"
[41] "mdomestica_gene_ensembl"     "mnemestrina_gene_ensembl"
[43] "falbicollis_gene_ensembl"
>
>

Can you please check and let me know the status of these mirrors.  Is it possible there is an issue with BiomartR.  Can someone in your team test BIomartR to find if they see the same issues.

Thanks,

- Pankaj

From: Dev [mailto:dev-bounces at ensembl.org] On Behalf Of Anne Lyle
Sent: Friday, April 20, 2018 5:57 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] Biomart connection

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<mailto: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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