We would like to demonstrate query federation with UCSC data. We will
eventually (dynamically) translate SPARQL queries into SQL as part of
the exercise. However, we would really appreciate a little advice on a
few UCSC databases that we could link (i.e. query across), preferrably
framed in a biology use case. Could somebody recommend a few databases
to link, possibly even with an example query? We were hoping to work
Uniprot into the story but that can come later. Please use Reply-All.
One idea might be to extend a previous study of overlaps between
ENCODE data set of ChIP-on-chip for H3K4Me3 and transcription factor
binding sites [1] to putatively related proteins.
BTW, we found that we couldn't perform joins across tables using Mr.
'genome' user in the genome-mysql.cse.ucsc.edu database. Any way to
query across tables without having to create local copies? Is there
another user/database combination that is slightly less restricted?
A few people will meet tomorrow (Nov. 24) at 9AM PST 12PM EST 6PM CET
to discuss this, mini-hackathon style. Anybody interested in joining
should use the following dial-in information:
Date of Call: Tuesday, November 23, 2010
Time of Call: 12:00 pm Eastern Time, 5 pm UK, 6 pm CET
Dial-In #: +1.617.761.6200 (Cambridge, MA)
Participant Access Code: 4257 ("HCLS2")
IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see W3C IRC page for
details, or see Web IRC), Quick Start: Use
http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls2
Cheers,
Scott
--
M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
Leiden University Medical Center / University of Amsterdam
http://staff.science.uva.nl/~marshall
[1] Some old work details this:
http://www.integrativebioinformatics.nl/histone/HistoneDataIntegration.html
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
