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

From: Eric Neumann <eneumann@teranode.com>
Date: Tue, 14 Aug 2007 09:08:57 -0400
Message-ID: <E7092F10DB73FA43AE0E59F2DCDAA6360A91BE@MI8NYCMAIL04.Mi8.com>
To: "Marco Brandizi" <brandizi@ebi.ac.uk>
cc: "W3C HCLSIG hcls" <public-semweb-lifesci@w3.org>, "M. Scott Marshall" <marshall@science.uva.nl>


Thanks for the acknowledgement!  Many folks were intersted in participating, so we need to offer them useful examples and tools. As I mentioned, we can already get the community to begin using uniprot.rdf for proteins, and EcoCYC+HumCYC pathways RDF via BioPAX from the VBI folks (who should also normalize on the uniprot URIs). I believe if we can get MESH/UMLS as URIs, there will be a core set of items for the community to begin adopting...

In terms of converting various forms of data to RDF, you can use the on-line Babel facility at MIT... http://simile.mit.edu/babel/

It can convert a number fo formats to and from RDF. You can also call it directly within code via an http request (see http://simile.mit.edu/wiki/Babel/How_to_call_translator_using_HTTP_GET ).  Be sure to use a browser like Firefox-- seems to not show up properly using Safari.


-----Original Message-----
From: public-semweb-lifesci-request@w3.org on behalf of Marco Brandizi
Sent: Mon 8/13/2007 1:31 PM
To: Eric Neumann
Cc: W3C HCLSIG hcls; M. Scott Marshall
Subject: Re: HCLS Demo at ISMB/ECCB, How to contribute to the demo?

Eric Neumann wrote:
> I'll also add that there were many (young) researchers wanting to get 
> involved in Semantic Web activities. I strongly encouraged them to 
> participate with HCLSIG and pointed them to our pages and mailing list.  

Hi all,

I'd like as well make my congratulations to Eric for his presentation. I 
am one of those who expressed interest in collaboration.

Eric, during his presentation briefly mentioned that it should be 
relatively easy to "cook" some data one may have available in non-RDF 
format, so that they may be integrated in the demo. My idea is to 
experiment the export of gene expression data available in public 
repositories (mainly ArrayExpress). At the moment I am trying to review 
ISMB materials and I wonder if there are pointers, on the wiki or 
somewhere else, about this point. Something like a brief tutorial, that 
  could guide me from choosing proper ontologies which are already used 
by the demo, to using the technology the demo is using too, to getting 
some simple result.

Thanks in advance for any help.


Marco Brandizi <brandizi@ebi.ac.uk>

NET Project - Software Engineer

European Bioinformatics Institute
Hinxton, CB10 1SD, United Kingdom
Tel.: +44 (0)1223 49 2613
Fax: +44 (0)1223 49 4468

Received on Tuesday, 14 August 2007 13:10:01 UTC

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