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[BioRDF] BioSIOC / aTag task

From: Matthias Samwald <samwald@gmx.at>
Date: Tue, 6 Jan 2009 17:24:47 +0100
Message-ID: <D23A0EA87F9C4F30B5C0E23BE0C37EEA@ms>
To: <public-semweb-lifesci@w3.org>

In the coming weeks / months I will create some RDF/OWL resources that make
use of the basic SIOC vocabulary together with biomedical domain ontologies
for the representation of biomedical knowledge (let's call this task 
"BioSIOC", since I intend to do it as part of the BioRDF task force [1]).

The basic idea is to represent a high-level view of biomedical knowledge in
the form of small statements, represented as SIOC items that are annotated
with entities from OBO ontologies and UniProt entries. So instead of
representing the full semantics of the biological statements in RDF/OWL
(with the associated problems of complexity and inter-dataset heterogeneity
that  made it difficult to create practical applications out of the
biomedical RDF/OWL resources that have been created in recent years), the
statements will be represented a small snippets of text and sets of
associated tags ('aTags'). Finding the right trade-off between expressivity
and simplicity while optimizing for usefulness in realistic biomedical
research scenarios will be a major focus. The project will be documented on
a wiki page [2].

Through the use of SIOC, these statements can also be integrated into simple
(micro-) blogging environments or more specialized and sophisticated
discourse databases such as those described with the SWAN ontology. I will
also be working on developing user interfaces for creating, embedding and
querying such SIOC items.

If the other participants of the BioRDF task agree, the RDF/OWL that is
produced by this project will also be added to the HCLS Knowledge Base
hosted at DERI [3] (which currently solely consits of the Neurocommons 
Base). The technologies and data developed by this project will also be
employed for the creation of a Drupal-based knowledge repository that will
be hosted by the Konrad Lorenz Institute for Evolution and Cognition
Research [4, 5] (which I will describe in more detail at a later time).

[1] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup
[2] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags
[3] http://hcls.deri.org/
[5] http://kli.ac.at/

Matthias Samwald

DERI Galway, Ireland

Konrad Lorenz Institute for Evolution & Cognition Research, Austria
Received on Tuesday, 6 January 2009 16:25:09 UTC

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