[biomart-users] Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still conne

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[biomart-users] Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still conne

Darya Vanichkina
Hi! I"m having issues connecting to biomaRt from Australia.
I'm running the following code:

ensemblNew=useMart(host="dec2015.archive.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl")
annotationNew <- getBM(attributes=c("ensembl_gene_id","mgi_symbol", "description", "gene_biotype"), filters = "ensembl_gene_id", values=row.names(mydataTable), mart=ensemblNew)



Even if I do the query without any filters, I get the same error. And I'm obviously online etc.

getBM(attributes=c("ensembl_gene_id","mgi_symbol", "description", "gene_biotype"), mart=ensemblNew)



I've tried doing the following, and it's also giving me a 404 error

wget -O registry_test.xml http://www.biomart.org/biomart/martservice?type=registry

--2016-02-10 13:51:09--  http://www.biomart.org/biomart/martservice?type=registry
Resolving www.biomart.org... 79.170.44.95
Connecting to www.biomart.org|79.170.44.95|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2016-02-10 13:51:25 ERROR 404: Not Found.



Please let me know whether I'm doing something wrong, or if it's just the system is down. Thanks!


I can do the following successfully:

listMarts(ensemblNew)
              biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 83
2     ENSEMBL_MART_SNP  Ensembl Variation 83
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 83
4    ENSEMBL_MART_VEGA               Vega 63
5                pride        PRIDE (EBI UK)





 listAttributes
(ensemblNew)[1:10,]
                   name           description
1        ensembl_gene_id       Ensembl Gene ID
2  ensembl_transcript_id Ensembl Transcript ID
3     ensembl_peptide_id    Ensembl Protein ID
4        ensembl_exon_id       Ensembl Exon ID
5            description           Description
6        chromosome_name       Chromosome Name
7         start_position       Gene Start (bp)
8           end_position         Gene End (bp)
9                 strand                Strand
10                  band                  Band


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Re: [biomart-users] Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still conne

Amonida Zadissa
Hi Darya,

I just tried a modified version of your query and got results back. I
changed your query slightly because I didn't have the 'mydataTable' data
set and also replaced the 'ensembl_gene_id' as filter to
'external_gene_name' and the values to a list of gene names, see below.

> annotationNew <- getBM(attributes=c("ensembl_gene_id","mgi_symbol", "description", "gene_biotype"), filters = "external_gene_name", values="ESPN,MYH9,USH1C,CISD2,THRB,DFNB31", mart=ensemblNew)
> annotationNew
      ensembl_gene_id mgi_symbol
                         description   gene_biotype
1 ENSMUSG00000022443       Myh9 myosin, heavy polypeptide 9, non-muscle
[Source:MGI Symbol;Acc:MGI:107717] protein_coding
2 ENSMUSG00000021779       Thrb            thyroid hormone receptor beta
[Source:MGI Symbol;Acc:MGI:98743] protein_coding
3 ENSMUSG00000028943       Espn                                  espin
[Source:MGI Symbol;Acc:MGI:1861630] protein_coding
4 ENSMUSG00000028165      Cisd2             CDGSH iron sulfur domain 2
[Source:MGI Symbol;Acc:MGI:1914256] protein_coding
5 ENSMUSG00000030838      Ush1c                      Usher syndrome 1C
[Source:MGI Symbol;Acc:MGI:1919338] protein_coding

I hope this helps. If the problem persists please contact us again and
we'll investigate further.

Best regards,
Amonida

--
Amonida Zadissa
Ensembl Production Team
EMBL-EBI
Hinxton
England

On 10/02/2016 03:03, Darya Vanichkina wrote:

> Hi! I"m having issues connecting to biomaRt from Australia.
> I'm running the following code:
>
> ensemblNew=useMart(host="dec2015.archive.ensembl.org", biomart=
> "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl")
> annotationNew <- getBM(attributes=c("ensembl_gene_id","mgi_symbol",
> "description", "gene_biotype"), filters = "ensembl_gene_id", values=row.
> names(mydataTable), mart=ensemblNew)
>
>
>
> Even if I do the query without any filters, I get the same error. And I'm
> obviously online etc.
>
> getBM(attributes=c("ensembl_gene_id","mgi_symbol", "description",
> "gene_biotype"), mart=ensemblNew)
>
>
>
> I've tried doing the following, and it's also giving me a 404 error
>
> wget -O registry_test.xml http:
> //www.biomart.org/biomart/martservice?type=registry
>
> --2016-02-10 13:51:09--  http:
> //www.biomart.org/biomart/martservice?type=registry
> Resolving www.biomart.org... 79.170.44.95
> Connecting to www.biomart.org|79.170.44.95|:80... connected.
> HTTP request sent, awaiting response... 404 Not Found
> 2016-02-10 13:51:25 ERROR 404: Not Found.
>
>
>
> Please let me know whether I'm doing something wrong, or if it's just the
> system is down. Thanks!
>
>
> I can do the following successfully:
>
> listMarts(ensemblNew)
>                biomart               version
> 1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 83
> 2     ENSEMBL_MART_SNP  Ensembl Variation 83
> 3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 83
> 4    ENSEMBL_MART_VEGA               Vega 63
> 5                pride        PRIDE (EBI UK)
>
>
>
>
>
>   listAttributes(ensemblNew)[1:10,]
>                     name           description
> 1        ensembl_gene_id       Ensembl Gene ID
> 2  ensembl_transcript_id Ensembl Transcript ID
> 3     ensembl_peptide_id    Ensembl Protein ID
> 4        ensembl_exon_id       Ensembl Exon ID
> 5            description           Description
> 6        chromosome_name       Chromosome Name
> 7         start_position       Gene Start (bp)
> 8           end_position         Gene End (bp)
> 9                 strand                Strand
> 10                  band                  Band
>
>

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