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Question: BiomaRt package not working
0
gravatar for Didi
7 months ago by
Didi10
Didi10 wrote:

Hi,

I usually use this script to get the GO IDs but I'm getting the error below since yesterday.

library("biomaRt")

listMarts(host="plants.ensembl.org") 
m <- useMart("plants_mart", host="plants.ensembl.org");
listDatasets(ensembl)
ensembl= useDataset("athaliana_eg_gene", mart=ensembl)
go <- getBM(attributes=c("go_accession", "tair_locus", "go_namespace_1003"), mart=ensembl)

Error in getBM(attributes = c("go_accession", "tair_locus", "go_namespace_1003"),  : 
  Invalid attribute(s): go_accession, go_namespace_1003 
Please use the function 'listAttributes' to get valid attribute names

Thanks a lot.

 

ADD COMMENTlink modified 7 months ago • written 7 months ago by Didi10
1
gravatar for James W. MacDonald
7 months ago by
United States
James W. MacDonald45k wrote:

Ensembl just updated to Ensembl plants 35, which includes changes to the Biomart.

> library(biomaRt)
> mart <- useMart("plants_mart", host = "plants.ensembl.org")
> mart <- useMart("plants_mart", "athaliana_eg_gene", host = "plants.ensembl.org")
> grep("go", listAttributes(mart)[,1], value = TRUE)
 [1] "go_id"                                             
 [2] "go_linkage_type"                                   
 [3] "goslim_goa_accession"                              
 [4] "goslim_goa_description"      

That's all the GO stuff they have now, so far as I can tell. I have no idea what a go_namespace_1003 might be, so I can't say if any of those things are what you are looking for. You can always use the archive, however:

> mart2 <- useMart("plants_mart", "athaliana_eg_gene",host = "archive.plants.ensembl.org")
> grep("go", listAttributes(mart2)[,1], value = TRUE)
 [1] "go_accession"                               
 [2] "go_name_1006"                               
 [3] "go_definition_1006"                         
 [4] "go_linkage_type"                            
 [5] "go_namespace_1003"                          
 [6] "goslim_goa_accession"                       
 [7] "goslim_goa_description"                    
ADD COMMENTlink written 7 months ago by James W. MacDonald45k

Thanks a lot. 

ADD REPLYlink written 7 months ago by Didi10
0
gravatar for Michael Steinbaugh
7 months ago by
Harvard
Michael Steinbaugh0 wrote:

The Ensembl website is down for maintenance, which could also be causing your biomaRt requests to error out at the moment.

ADD COMMENTlink written 7 months ago by Michael Steinbaugh0
0
gravatar for Mike Smith
7 months ago by
Mike Smith2.1k
EMBL Heidelberg / de.NBI
Mike Smith2.1k wrote:

Did you try using the listAttributes() function as suggested in the output message you've highlighted?

As James says a new Ensembl plants has  been release, and some of the attribute names have changed.  These are documented here although I'm not sure that list is accurate since, for example, there is no attribute named simply go.  I think the code you require is:

go <- getBM(attributes = c("go_id", "tair_locus", "namespace_1003"), 
            mart=ensembl)
ADD COMMENTlink written 7 months ago by Mike Smith2.1k

Dear Mike,

Thanks a lot for spotting this. I've now updated the following file: ftp://ftp.ensemblgenomes.org/pub/release-35/release_35_biomart_changes.txt

Kind Regards,

Thomas

ADD REPLYlink written 7 months ago by Thomas Maurel700

Cool, I made my suggested substitutions based on the 'Description' field, so point out if that was incorrect.

Should there still be an entry in the file for go_accession -> go_id? I can't see one, but go_accession is no longer listed as an attribute.

ADD REPLYlink modified 7 months ago • written 7 months ago by Mike Smith2.1k

Opps sorry, you are right. I've added "go_accession -> go_id" to the file. 
Thanks,

Thomas

ADD REPLYlink written 7 months ago by Thomas Maurel700
0
gravatar for Didi
7 months ago by
Didi10
Didi10 wrote:

Thank you so much. It's working now by using :

go <- getBM(attributes = c("go_id", "tair_locus", "namespace_1003"), 
            mart=ensembl)

It was really helpful.

Thanks again.

 

ADD COMMENTlink written 7 months ago by Didi10
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