BiomaRt package not working
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Didi ▴ 10
@didi-10905
Last seen 10 months ago

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 • 1.4k views
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@james-w-macdonald-5106
Last seen 29 minutes ago
United States

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"                    
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Thanks a lot. 

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@mjsteinbaugh
Last seen 9 months ago
28-7 Therapeutics

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

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Mike Smith ★ 5.2k
@mike-smith
Last seen 2 hours ago
EMBL Heidelberg / de.NBI

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)
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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

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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.

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

Thomas

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Didi ▴ 10
@didi-10905
Last seen 10 months ago

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.

 

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