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Question: BiomaRt package not working
0
gravatar for Didi
22 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.

 

biomart getbm • 791 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by Didi10
Answer: BiomaRt package not working
1
gravatar for James W. MacDonald
22 months ago by
United States
James W. MacDonald49k 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 22 months ago by James W. MacDonald49k

Thanks a lot. 

ADD REPLYlink written 22 months ago by Didi10
Answer: BiomaRt package not working
0
gravatar for Michael Steinbaugh
22 months ago by
Harvard
Michael Steinbaugh20 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 22 months ago by Michael Steinbaugh20
Answer: BiomaRt package not working
0
gravatar for Mike Smith
22 months ago by
Mike Smith3.2k
EMBL Heidelberg / de.NBI
Mike Smith3.2k 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 22 months ago by Mike Smith3.2k

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 22 months ago by Thomas Maurel770

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 22 months ago • written 22 months ago by Mike Smith3.2k

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

Thomas

ADD REPLYlink written 22 months ago by Thomas Maurel770
Answer: BiomaRt package not working
0
gravatar for Didi
22 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 22 months ago by Didi10
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