Question: Ensembl version from non-vertebrate biomaRt
gravatar for arielpaulson
2.6 years ago by
arielpaulson20 wrote:


I used to be able to get Ensembl version numbers from non-vertebrate marts, but sometime between Ensembl 81 and 84 this has been lost.

 For instance, vertebrate marts clearly show their version numbers:

> listMarts(host="")
                                    biomart                         version
1 ENSEMBL_MART_ENSEMBL        Ensembl Genes 84
2          ENSEMBL_MART_SNP     Ensembl Variation 84
3 ENSEMBL_MART_FUNCGEN  Ensembl Regulation 84
4        ENSEMBL_MART_VEGA                       Vega 64

But non-vertebrate marts do not, for instance fungi:

> listMarts(host="")
               biomart                       version
1        fungal_mart                Fungal Mart
2 fungal_variations  Fungal Variation Mart

The version data used to show "Fungal Mart ##" with an actual version number.  Can we get this back please?



ADD COMMENTlink modified 2.6 years ago by Dan Staines70 • written 2.6 years ago by arielpaulson20
gravatar for Dan Staines
2.6 years ago by
Dan Staines70
Dan Staines70 wrote:

Hi Ariel,

The version number was recently removed in the biomart name for Ensembl Genomes marts to make URLs reusable between releases (as is the case for Ensembl) but it also appears to be absent from the display name (rendered as "version" in your example). I'll look into rectifying this.

Note that the non-vertebrate marts come from the Ensembl Genomes project, which has a different (but parallel) release cycle and versioning system (e.g. the current release of EG is 31, whilst the current release of Ensembl is 84) and the display name of the mart will reflect this.



ADD COMMENTlink written 2.6 years ago by Dan Staines70
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