[biomart-users] mouse genes

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[biomart-users] mouse genes

Roxy J

Hi guys,

what dataset do I ask for when trying to retrieve information for mouse and pig genes in BioMart?
My code:
>m <- useMart("ENSEMBL_MART_MOUSE"); listDatasets(m)
>m <- useMart("ENSEMBL_MART_MOUSE", dataset="mmusculus_gene_ensembl")
>listAttributes(m)

ERROR: dataset not found

Also in:

> go <- getBM(attributes=c("go_id", "mmusculus_locus", "namespace_1003"), mart=m)
 Error in getBM(attributes = c("go_id", "mmusculus_locus", "namespace_1003"),  :
 
Invalid attribute(s): mmusculus_locus

I am actually having a hard time knowing how to find the datasets and attibutes for different species.  Now i m working on Mouse and pig.  If someone could help that will be greatly appreciated.


Thanks

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Re: [biomart-users] mouse genes

Thomas Maurel
Dear Roxy,

The Ensembl mouse mart only contains the Ensembl mouse strains: http://www.ensembl.org/Mus_musculus/Info/Strains
You can query mouse and pig by doing the following queries when using the Ensembl Gene mart:

Mouse: 

> m <- useMart("ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl")
> go <- getBM(attributes=c(“go_id", "namespace_1003"),filters = 'chromosome_name', values = '1', mart=m)
> go[2,]
       go_id     namespace_1003
2 GO:0005737 cellular_component

Pig: 

> m <- useMart("ENSEMBL_MART_ENSEMBL", dataset="sscrofa_gene_ensembl")
> go <- getBM(attributes=c("go_id", "namespace_1003"),filters = 'chromosome_name', values = '1', mart=m)
> go[2,]
       go_id     namespace_1003
2 GO:0005654 cellular_component

PS: The BioMart software is not designed for genome wide queries please make sure to use some filters in your query. Please see: “listFilters(m)"

I am afraid the “mmusculus_locus” attribute don’t exist in our mart, where did you got it from?

Hope this helps,
Kind Regards,
Thomas

On 21 Sep 2017, at 21:34, Roxy J <[hidden email]> wrote:


Hi guys,

what dataset do I ask for when trying to retrieve information for mouse and pig genes in BioMart?
My code:
>m <- useMart("ENSEMBL_MART_MOUSE"); listDatasets(m)
>m <- useMart("ENSEMBL_MART_MOUSE", dataset="mmusculus_gene_ensembl")
>listAttributes(m)

ERROR: dataset not found

Also in:

> go <- getBM(attributes=c("go_id", "mmusculus_locus", "namespace_1003"), mart=m)
 Error in getBM(attributes = c("go_id", "mmusculus_locus", "namespace_1003"),  :
 
Invalid attribute(s): mmusculus_locus

I am actually having a hard time knowing how to find the datasets and attibutes for different species.  Now i m working on Mouse and pig.  If someone could help that will be greatly appreciated.


Thanks

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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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