On Aug 17, 2007, at 6:54 PM, Marco Brandizi wrote:
Hi all,
sorry for late reply. I've been a bit busy.
thank you for the interesting replies. The Nigam tutorial, it is a
really good introduction to the world of BioOntologies.
In addition to that topics, I'd like to understand some further
details
about the demo, and about how to put hands in it. For instance:
- How to expose RDF data to the demo? Via Joseki?
We use Virtuoso, an open source triple store that is integrated into
a relational database engine.
http://virtuoso.openlinksw.com/wiki/main/
- Does the demo consist of code that have to be downloaded, changed
and
run on my own server? Do I have to proceed like that if I want to
extend
it with my own RDF data?
You may download and install the software and data if you wish.
Instructions are on the way but at the moment you would have to email
me to get instructions on where to get the data an upload it.
If you want to extend the demo with your own data there are several
options:
1) Generate the RDF in one of the standard formats and we can load it
up in to the running demo
2) Set up a SPARQL endpoint of your own (using any technology) and do
queries that select from multiple graphs, one from the neurocommons
data store, and one from your SPARQL endpoint.
3) Create a mirror of the demo and then add your own data.
The easiest way is 1), so that's what I'd recommend - it will let you
focus just on generating RDF for the moment.
I guess some of the above questions may be answered by screening
better
the Wiki and the mailing list. Help welcome anyway!
Hope this helps.
best,
Alan
Alan Ruttenberg wrote:
1) Representing the information about the samples, experiment,
protocols leading to the hybridization, technical aspects of the
hybridization, etc.
2) Representing what the computed intensity of the spots on an
array, as well as how those were computed (e.g. MAS5, rma, d-chip,
etc)
3) Representing which genes are thought to be relatively highly
expressed by interpreting the intensity of the spots as amount of
expression of certain genes.
I am thinking to something quite simple: AE is able to show the
experiments and conditions under which a gene is expressed [1],
obviously according to stored microarray data. So it would be nice to
jump from genes to the conditions under which they're expressed, and
optionally show the expression levels.
Also I wonder how much complex would be attempting to expose only this
simple information. Certainly they're not enough, cause you would like
to add what supports the results, so things mentioned in 1) and 2).
But
as a starting point...
I personally have worked in something similar in the past [2]. But
probably my work should be revised, and is not as simple as what I am
thinking of here.
Thanks a lot for replying.
[1]http://www.ebi.ac.uk/microarray-as/aew/DW?
queryFor=gene&gene_query=nfkbia&species=&exp_query=leukemia
[2]http://gca.btbs.unimib.it/brandizi/mysite/phdv3
--
======================================================================
=========
Marco Brandizi <[EMAIL PROTECTED]>
NET Project - Software Engineer
http://www.ebi.ac.uk/net-project
European Bioinformatics Institute
Hinxton, CB10 1SD, United Kingdom
Tel.: +44 (0)1223 49 2613
Fax: +44 (0)1223 49 4468
http://www.ebi.ac.uk/~brandizi
