Bacterial Biomart

[Joy Yang]

Hi biomart users,

This is my first time posting, so please tip me off if I'm using bad etiquette or if this is a terrible question. But my question/problem is:

I'm having trouble accessing bacterial mart, and I was wondering if anyone has had any luck with it recently. I'm using the biomaRt package from Bioconductor. What I found so far from googling: 

It seems that initially it was a mart listed from listMarts(), but I can't seem to find it anymore.

(https://stat.ethz.ch/pipermail/bioconductor/attachments/20100827/ead26694/attachment.pl)

but then it looks like later it moved to a different host, but it could still be found by changing the host

listMarts(host="bacteria.ensembl.org") 

(https://lists.biomart.org/pipermail/users/2012-March/002510.html)

but when I tried this, I got a long error starting "Entity 'hellip' not defined". However, if I try this for fungi (just as a test - the fungal mart can already be seen just using listMarts() ), this seems to work

> listMarts(host="fungi.ensembl.org") 

            biomart               version

1       fungal_mart           Fungal Mart

2 fungal_variations Fungal Variation Mart

If anyone has had any luck recently with this, I would really, extremely appreciate your advice!

Thanks in advance,

Joy

[Arek Kasprzyk]

Hi Joy,

as far as I know the bacterial mart is no longer maintained. Dan (cc'ed on this email) may want to correct me on this

a

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to biomart-user...@googlegroups.com.
Visit this group at http://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--

“You have enemies? Good. That means you've stood up for something, sometime in your life.”

― Winston Churchill

[Joy]

Ok, thanks for the quick reply! I realized later on that I already had in annotations the data that I was trying to use biomaRt to retrieve. I just had such great impressions of biomaRt from playing around with it in the past that it was the first place I went to :) Anyway, thanks again!

Joy

[Dan Staines]

On 08/29/2014 04:56 PM, Arek Kasprzyk wrote:
> Hi Joy,
> as far as I know the bacterial mart is no longer maintained. Dan (cc'ed
> on this email) may want to correct me on this
>
>

No, thats quite correct - since switching to a bacterial release model
where we have over 15,000 bacterial genomes, we can no longer provide a
biomart as we do for other divisions of Ensembl Genomes. We are however
looking at alternative solutions to making bacterial data available.

--
Dan Staines, PhD
Technical Coordinator, Ensembl Genomes
European Bioinformatics Institute (EMBL-EBI)
http://www.ebi.ac.uk/
http://www.ensemblgenomes.org/