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

From: Matthias Samwald <samwald@gmx.at>
Date: Tue, 14 Aug 2007 17:10:17 +0200
To: <brandizi@ebi.ac.uk>, Eric Neumann <eneumann@teranode.com>
CC: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>, "M. Scott Marshall" <marshall@science.uva.nl>
Message-ID: <2007814171017.484663@cqueberel>

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.

I made the same experience while presenting the HCLS poster at the Bio-Ontologies special interest group meeting. I was also surprised that some of them are already silently subscribed to this mailing but did not dare to mention their work so far. While this mailing list should probably not be overloaded with traffic, I think it would be constructive if those that are subscribed and have so far been silent write a short introduction about their work to the list.

Marco Brandizi wrote:
> 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).

The demo was, in part, made possible through building upon foundational ontologies like the OBO relation ontology [1] and BFO [2] that promote consistency between ontologies. Furthermore, domain ontologies from the OBO repository [3] were used where possible. I think that anyone interested in producing Semantic Web content should take a little time to understand these resources and the surrounding literature. Of course there are generic algorithms that allow you to convert an arbitrary Excel file or XML document into a RDF document, but the result is much more useful when some basic ontology design criteria are met and the information in the source databases is re-interpreted to form a meaningful ontology. Unfortunately I cannot point you to a short, comprehensive document that would describe the design philosophy I am thinking of -- this is something that still needs to be written, I guess.

[1] http://www.obofoundry.org/ro/
[2] http://www.ifomis.uni-saarland.de/bfo/
[3] http://obofoundry.org/

Matthias Samwald
Received on Tuesday, 14 August 2007 15:10:34 UTC

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