Question: Problem Querying Archived Ensembl 73 With Biomart
gravatar for neelroop
5.2 years ago by
neelroop10 wrote:

I regularly use biomaRt, the R package, to query archived versions of Ensembl. I had been querying Ensembl 65 for over a year with no issues, and I've tried Ensembl 72 and 74 and they work fine, too.

However, for my current project, I want to use Ensembl 73 (the rest of the project uses Gencode v18), and when I obtain this mart, I cannot identify any datasets in it (using the same commands that work for the other archives).

Could someone please advise me on what I might be doing wrong or if the archived version of Ensembl 73 is known to have problems with biomaRt? Does it work just fine for others? Some code and version information below:

R version, etc: R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit)

Here is some sample code/output: Ensembl 65 querying:

> library(biomaRt) ## from biomaRt_2.18.0.tgz
> listMarts(host="")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 65
2     ENSEMBL_MART_SNP  Ensembl Variation 65
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 65
4    ENSEMBL_MART_VEGA               Vega 45
5             REACTOME    REACTOME (CSHL US)
6                pride        PRIDE (EBI UK)

> mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",host="")#,dataset="hsapiens_gene_ensembl")
> listDatasets(mart)
                          dataset                                   description
1          oanatinus_gene_ensembl        Ornithorhynchus anatinus genes (OANA5)
2           tguttata_gene_ensembl       Taeniopygia guttata genes (taeGut3.2.4)
3         cporcellus_gene_ensembl               Cavia porcellus genes (cavPor3)
4         gaculeatus_gene_ensembl        Gasterosteus aculeatus genes (BROADS1)
5          lafricana_gene_ensembl            Loxodonta africana genes (loxAfr3)
6         mlucifugus_gene_ensembl              Myotis lucifugus genes (myoLuc2)
7           hsapiens_gene_ensembl                Homo sapiens genes (GRCh37.p5)
## etc. - it loads just fine

Ensembl 73 querying:

> library(biomaRt)
> listMarts(host="")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 73
2     ENSEMBL_MART_SNP  Ensembl Variation 73
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 73
4    ENSEMBL_MART_VEGA               Vega 53
5                pride        PRIDE (EBI UK)
> mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",host="")
> listDatasets(mart)
[1] dataset     description version
<0 rows> (or 0-length row.names)

Note that I get an empty query with the "" while other archives appear to work fine.

Thank you in advance for your help!

ensembl biomart annotation • 1.6k views
ADD COMMENTlink modified 5.2 years ago by Emily_Ensembl17k • written 5.2 years ago by neelroop10
gravatar for Emily_Ensembl
5.2 years ago by
Emily_Ensembl17k wrote:

Please do not cross post to both Biostar and Ensembl helpdesk - it means duplicate work. See rule 8.

Other Biostars - no need to respond, this is already being dealt with by Ensembl helpdesk.

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Emily_Ensembl17k
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