W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > August 2007

Re: HCLS Demo at ISMB/ECCB, How to contribute to the demo?

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Fri, 17 Aug 2007 19:00:37 -0400
Message-Id: <F234DB08-D40C-41DB-9C88-AF705E444847@gmail.com>
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>, Helen Parkinson <parkinson@ebi.ac.uk>
To: Marco Brandizi <brandizi@ebi.ac.uk>


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 <brandizi@ebi.ac.uk>
>
> 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
>
>
>
>
Received on Friday, 17 August 2007 23:00:45 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:49 GMT