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to add our VectorBase source to their public instance, as VectorBase sourced-data (either biomart instance) may be out-of-date.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.orghttp://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 <dan@bx.psu.edumailto:dan@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vector data (e.g. BioMart) from our NIH Bioinformatics Resource Center (BRC) VectorBase into Galaxy, but some are outdated and some of our users would like a direct source.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.orghttp://www.vectorbase.org/.
I noticed our sister BRC EuPathDB has made their data available via http://main.g2.bx.psu.eduhttp://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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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