Accessing local installation of biomart results in "Unexpected format to the list of available marts"
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anhvo711 • 0
@e5f68b8c
Last seen 9 months ago

I have downloaded and launched the webserver for a local installation of Biomart 0.9 using these directions. After using MartConfigurator to download a mart, I am attempting to access the webserver using

listMarts(host = "IP.address", port = 9000, path = "/martservice/marts")

This results in the R error:

"Error: Unexpected format to the list of available marts. Please check the following URL manually, and try ?listMarts for advice."

When visiting the URL, I get the following warning and a page that is supposed to start with "MartRegistry", but does not.

This XML file does not appear to have any style information associated with it. The document tree is shown below.

<marts>
<mart mart="gene_ensembl" config="gene_ensembl_config" group="" isHidden="false" meta="" operation="SINGLESELECT" description="gene_ensembl_config" displayName="ensembl_mart_ensembl" name="gene_ensembl_config"/>
<mart mart="gene_ensembl" config="gene_ensembl_config_1" group="" isHidden="false" meta="" operation="SINGLESELECT" description="gene_ensembl_config_1" displayName="gene_ensembl_config_1" name="gene_ensembl_config_1"/>
</marts>

Any idea on what I am doing wrong & how to fix this issue?

mart martconfigurator biomaRt xml • 264 views
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Mike Smith ★ 5.1k
@mike-smith
Last seen 5 hours ago
EMBL Heidelberg / de.NBI

First off I'll just point out that while biomaRt is a Bioconductor package, the BioMart software is not related to Bioconductor and you might get some better help elsewhere. However, I'm the maintainer of biomaRt and can probably offer some insights.

I think you're going to struggle here, mostly because the BioMart project has been dead for quite a few years. It's no longer actively developed or maintained, and the number of BioMart instances is decreasing as time goes by. The Ensembl BioMart still gets a lot of traffic, but most other projects have either moved their data into the main Ensembl BioMart or moved to another software platfom for giving access to their data. For that reason the biomaRt package focuses almost exclusively on working with Ensembl.

I can't find anything concrete to prove this right now, but I'm pretty confident that Ensembl are running version 0.7 of BioMart. However your local installation is version 0.9. I don't know the full scope of the differences, but immediately I can tell you is no /martservice/marts endpoint on version 0.7. The list of marts is access via martservice?type=registry e.g. http://www.ensembl.org/biomart/martservice?type=registry. Given this fundamental difference I'm afraid biomaRt doesn't support version 0.9.

Maybe you have a really good reason for using BioMart, but if you really need to run your own data query webserver I think your life might be easier in the long run to try using another platform that has developer support. One example you might want to look at is Intermine.

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