Running R Biomart With Local Installation

Question

[Assa Yeroslaviz]

Hi everybody,

I installed the local version of the biomart 0.8 using the user manual. It was very easy and unproblematic. I tested it with a web browser (Firefox) and it run correctly. I downloaded the example database they give in the quickstart.xml example (msd) and than also the enseml database. When starting the web server I see these four options:

* msd_config
* dmelanogaster_gene_ensembl_config
* mmusculus_gene_ensembl_config
* hsapiens_gene_ensembl_config

I can also than run the queries in the webserver.

My problems start when I am trying to run it in my R session. Somehow I can't get it to find the server.

> listMarts(host="my server IP address",port=9000, path="biomart0.8/release-0_8-candidate_6/registry/biomart0.8ensembl.xml")
Request to BioMart web service failed. Verify if you are still connected to the internet. 
Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and 
verify if this website is available.
Error:   does not seem to be XML, nor to identify a file name

Somehow I am not sure exactly what XML file is looks for. After compilation I started the martconfigurator and did as in the manual. I thought this is also the same path I need to out into the listMarts command in R. But this is apperently wrong.

Has anyone tried it before and can help me with these paths? What path do I need to use?

Thanks A.

[Neilfws]

I have never tried to connect to a local instance from biomaRt, but the first argument of listMarts() is supposed to be a mart object created using useMart(). Could that be the problem?

[Neilfws]

My second thought: I think "path" does not refer to file path but to a URL suffix. Skimming through the manual, it looks like "martservice/marts" might work?

[Assa Yeroslaviz]

well, I tried both options, but it didn't work.

I crated the mart:

mart=useMarts('ensembl')

[Assa Yeroslaviz]

well, I tried both options, but it didn't work. I crated the mart:

mart=useMarts('ensembl') listMarts(ensembl, host="XXX.XXX.XXX.XXX", port=9000, path='martservice/marts') but I got the same error.

Answer 1

[Joachim]

I think the biomaRt package uses the REST API of BioMart to retrieve data for you. The REST API has changed from BioMart 0.7 to 0.8, so that might be the reason why your listMarts() attempt fails.

Can you test biomaRt on one of the public BioMart 0.7 marts, please? For example, it should work on http://www.ensembl.org/biomart/martview/ but it probably fails on http://central.biomart.org/.

[Assa Yeroslaviz]

If I am running the command listMarts() or listMarts("www.ensembl.org") I do get the right list, so I guess the connection is there Is it than possible to do it at all, or do I need to install biomart 0.7?

[Joachim]

Those two commands do not access your local installation according to http://rss.acs.unt.edu/Rdoc/library/biomaRt/html/listMarts.html

Please try these two things: leaving "path"/"port" out and only using the "host" parameter with your BioMart running on port 80. I expect that this fails because of the 0.8 incompatibility I mentioned.

Since you are using an 0.7 mart dump anyway (the Ensembl marts are 0.7 marts), try then setting the "mysql", "port", "user" and "password" parameters to access your database directly. This should definitely work.