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Re: BioRDF Brainstorming

From: Kei Cheung <kei.cheung@yale.edu>
Date: Sun, 10 Feb 2008 21:13:00 -0500
Message-ID: <47AFAF2C.6020608@yale.edu>
CC: public-semweb-lifesci@w3.org, Matthias Samwald <matthias.samwald@meduniwien.ac.at>, Luis Marenco <luis.marenco@yale.edu>, Ernest.Lim@yale.edu

Hi Susie et al.,

Since SenseLab’s Semantic Web development has been a part of the HCLS 
activities, I would like to suggest its new development as part of the 
future HCLS activities. One suggestion is the extension of “Entrez 
Neuron” to become a Semantic Web portal for mashing up neuroscientific 
data provided by different sources. I added a description of this 
project to the wiki page, but I also appended the project description below.



Project title: Semantic Web Portal for Neuroscientific Data Mashup

As the need for neuroscience data integration is growing and the number 
of neuroscientific datasets available in RDF/OWL format is increasing, 
we are presently at the neuroinformatics frontier of exploring the full 
potential of Semantic Web technologies in enabling integrative 
neuroscience research (including translational research) that requires 
integration of diverse types of neuroscientific data provided by 
different sources in heterogeneous formats. As a pilot project, we have 
prototyped a user-friendly Web application called “Entrez Neuron” that 
allows the user to perform keyword searches for neuron-related 
information across multiple data sources (OWL ontologies) including 
SenseLab (NeuronDB and ModelDB) ontologies and CCDB (Cell Centered 
Database) ontologies. Our future plan is to expand this pilot 
application to become a Semantic Web Portal that allows semantic mashup 
of diverse types of data in neuroscientifically meaningful ways. To 
achieve this, we propose to include additional data/ontology sources and 
create different facets that represent user-centric aspects (or views) 
of ontologies. For example, “Entrez Neuron” currently features a “brain 
region/neuron” facet for organizing query results (about neurons) based 
on anatomical structure. Such a hierarchical structure is intuitive to 
neuroscientists, while benefiting from the machine use of ontologies in 
terms of querying, organizing, and integrating data. Additional facets 
that we are implementing/considering include (but not limited to) drug, 
disease, pathway, phenotype, gene functions, etc.

Project members: Kei Cheung, Matthias Samwald, Ernest Lim, Luis Marenco

Susie M Stephens wrote:

>I've created a Wiki page where people can propose projects for BioRDF to
>work on until the end of April [1]. It'd be great if you could post any
>ideas that you may have.
>[1] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Brainstorming
Received on Monday, 11 February 2008 02:13:24 UTC

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