I am asking for galaxy to add our VectorBase source to their public instance, 
as VectorBase sourced-data (either biomart instance) may be out-of-date.  The 
UCSC data is even older.  As EuPath has their latest release data available 
from the public interface, we were interested in doing the same.

This delay should be at most two months, though, from talking to EBI so we'll 
advocate VectorBase users to use the biomart xml/public interface and you 
should be fine Gus.       I'll look at the XML spec tomorrow just in case.

- S

On Sep 6, 2011, at 3:40 PM, W. Augustine Dunn III wrote:

I suppose what I meant to say was that since I was able to add the 
metazoa.ensembl.org<http://metazoa.ensembl.org/> biomart by modifying the 
existing biomart xml, would this not also work for VB's biomart instance?  Or 
would this not be what you are looking for?

Actually, re-reading your OP, is it that you are asking for galaxy to add this 
source to their public instances?

Gus

On Tue, Sep 6, 2011 at 11:54 AM, Daniel Blankenberg 
<d...@bx.psu.edu<mailto:d...@bx.psu.edu>> wrote:
Hi Scott,

For information on adding Datasource tools to Galaxy, please see:
http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources
http://www.ncbi.nlm.nih.gov/pubmed/21531983

If your resource is using software that is already Galaxy-aware, you can often 
take an existing xml configuration (GALAXY_ROOT/tools/data_source/*.xml) and 
make a copy to modify for your needs. Please let us know if we can provide 
additional information.


Thanks for using Galaxy,

Dan


On Sep 4, 2011, at 10:29 AM, Scott Emrich wrote:

> Dear team,
>
> There are multiple 3rd party sources to import arthropod vector data (e.g. 
> BioMart) from our NIH Bioinformatics Resource Center (BRC) VectorBase into 
> Galaxy, but some are outdated and some of our users would like a direct 
> source.  Given this increase of Galaxy in our vector biology community, what 
> is the policy for adding a new server to "Get Data" and is there information 
> on formatting our results appropriately (i.e., using a REST interface)?   Our 
> NIH BRC server is www.vectorbase.org<http://www.vectorbase.org/>.
>
> I noticed our sister BRC EuPathDB has made their data available via 
> http://main.g2.bx.psu.edu<http://main.g2.bx.psu.edu/>, and we have similar 
> developer resources to make our server compatible; however, I couldn't find 
> this information online besides addressing this list.
>
> Thanks in advance, and best regards,
>
> - S
>
> ---
>
> Scott Emrich, PhD
> Scientific Manager, VectorBase
> Assistant Professor, Computer Science and Engineering
> University of Notre Dame
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perverse to withhold provisional assent." I suppose that apples might start to 
rise tomorrow, but the possibility does not merit equal time in physics 
classrooms.
-Stephen Jay Gould


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