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Re: [BioRDF] BioSIOC / aTag task

From: Kei Cheung <kei.cheung@yale.edu>
Date: Tue, 06 Jan 2009 21:14:19 -0500
Message-ID: <49640FFB.7020401@yale.edu>
To: Matthias Samwald <samwald@gmx.at>
CC: public-semweb-lifesci@w3.org

Hi Matthias,

What you proposed sounds like an interesting project to be included as 
part of the BioRDF task force. I like the idea of exploring a fit 
between folksonomy and ontology. Currently, the BioRDF group has the 
query federation project that explores how to pose federated queries 
across multiple data/knowledge sources including the HCLS KB's (hosted 
at DERI and Free Univ. Berlin). The possibility that the BioSIOC project 
can add more data/knowledge to the HCLS KB hosted at DERI is 
complementary to the query federation project.

I look forward to working with you.



Matthias Samwald wrote:

> 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 
> Knowledge
> 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/
> [4]
> http://en.wikipedia.org/wiki/Konrad_Lorenz_Institute_for_Evolution_and_Cognition_Research 
> [5] http://kli.ac.at/
> Cheers,
> Matthias Samwald
> DERI Galway, Ireland
> http://deri.ie/
> Konrad Lorenz Institute for Evolution & Cognition Research, Austria
> http://kli.ac.at/
Received on Wednesday, 7 January 2009 02:15:10 UTC

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