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Question: Ensembl bacteria not accessible from biomaRt
0
gravatar for arielpaulson
18 months ago by
arielpaulson20
arielpaulson20 wrote:

Hi,

I need to know how to access Ensembl bacteria via biomaRt, if it can be done.  

I can access all the non-vertebrate marts (fungi, plants, metazoa, protists) by their respective ensembl.org subdomains, but not bacteria.  When I try:

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

I get this crazy result:

Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'nbsp' not defined
Entity 'raquo' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Opening and ending tag mismatch: img line 78 and li
Opening and ending tag mismatch: img line 78 and li
Opening and ending tag mismatch: img line 78 and li
Opening and ending tag mismatch: li line 78 and ul
Opening and ending tag mismatch: img line 78 and li
Opening and ending tag mismatch: li line 78 and ul
Opening and ending tag mismatch: li line 78 and div
Opening and ending tag mismatch: ul line 78 and div
Opening and ending tag mismatch: img line 78 and div
Entity 'copy' not defined
Opening and ending tag mismatch: img line 145 and a
Opening and ending tag mismatch: a line 144 and p
Opening and ending tag mismatch: img line 148 and a
Opening and ending tag mismatch: a line 147 and p
Opening and ending tag mismatch: p line 147 and div
Opening and ending tag mismatch: p line 144 and div
Opening and ending tag mismatch: li line 78 and div
Opening and ending tag mismatch: ul line 77 and body
Opening and ending tag mismatch: div line 73 and html
Premature end of data in tag div line 72
Premature end of data in tag div line 71
Premature end of data in tag div line 21
Premature end of data in tag div line 20
Premature end of data in tag body line 19
Premature end of data in tag html line 2
Error: 1: Entity 'hellip' not defined
2: Entity 'hellip' not defined
3: Entity 'nbsp' not defined
4: Entity 'raquo' not defined
5: Entity 'hellip' not defined
6: Entity 'hellip' not defined
7: Entity 'hellip' not defined
8: Entity 'hellip' not defined
9: Opening and ending tag mismatch: img line 78 and li
10: Opening and ending tag mismatch: img line 78 and li
11: Opening and ending tag mismatch: img line 78 and li
12: Opening and ending tag mismatch: li line 78 and ul
13: Opening and ending tag mismatch: img line 78 and li
14: Opening and ending tag mismatch: li line 78 and ul
15: Opening and ending tag mismatch: li line 78 and div
16: Opening and ending tag mismatch: ul line 78 and div
17: Opening and ending tag mismatch: img line 78 and div
18: Entity 'copy' not defined
19: Opening and ending tag mismatch: img line 145 and a
20: Opening and ending tag mismatch: a line 144 and p
21: Opening and ending tag mismatch: img line 148 and a
22: Opening and ending tag mismatch: a line 147 a

Again, for fungi, plants, metazoa, and protists, this approach works just fine.

Thanks,

Ariel

 

 

ADD COMMENTlink modified 18 months ago by Martin Morgan ♦♦ 20k • written 18 months ago by arielpaulson20
1
gravatar for Dan Staines
18 months ago by
Dan Staines70
EMBL-EBI
Dan Staines70 wrote:

Hi Ariel,

Since the expansion in early 2013 of Ensembl Bacteria from a few hundred to tens of thousands of bacteria, Ensembl Genomes has not provided a mart, as BioMart does not scale to this number of genomes. We're actively working on an alternative to provide access to all Ensembl and Ensembl Genomes data, and will be working with the BioConductor community to make sure this new service meets key requirements for data retrieval.

As for the odd response, I imagine that biomaRt is trying to access the old mart address and trying to parse the redirect page, so if there is a URL for the old bacteria mart in biomaRt, it needs to be removed.

Best regards,

Dan

 

ADD COMMENTlink written 18 months ago by Dan Staines70

Yes, adding verbose=TRUE to listMarts(host="bacteria.ensembl.org", verobse=TRUE) will print the URL biomaRt it is trying to connect to; copy paste to your browser and it is a redirection to the page for documentation.

 

ADD REPLYlink written 18 months ago by Martin Morgan ♦♦ 20k
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