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Re: BioRDF Brainstorming

From: Kei Cheung <kei.cheung@yale.edu>
Date: Tue, 12 Feb 2008 15:58:16 -0500
To: Alan Ruttenberg <alanruttenberg@gmail.com>, olivier@nlm.nih.gov
Cc: eric neumann <ekneumann@gmail.com>, Matthias Samwald <samwald@gmx.at>, Susie M Stephens <STEPHENS_SUSIE_M@lilly.com>, public-semweb-lifesci@w3.org, Holger Stenzhorn <holger.stenzhorn@deri.org>, Ernest.Lim@Yale.edu, Luis Marenco <luis.marenco@yale.edu>
Message-id: <47B20868.6040806@yale.edu>

Hi Olivier, Alan, et al,

A prototype version of our neuroscience semantic web portal is 
accessible at: http://neuroweb3.med.yale.edu

Bear in mind, this is a working prototype for proof of concept and it is 
still under active development. The Web interface has 3 panels: search 
panel (on top), facet panel (below the search panel on the left) and 
data panel (below the search panel on the right). The user can enter a 
key word and select a facet and data sources (ontologies) against which 
the key word is searched. The search results are displayed and organized 
based on the selected facet. Each leaf node (neuron, neuron property, 
gene, or drug target (receptor)) of the facet tree can be selected for 
retrieving more detailed information from each of the selected data 
sources. Currently, we have implemented 4 facets: neuron (default), 
neuron properties, gene, and drug. While the first two facets were 
created based on the SenseLab and CCDB ontologies, gene facet was 
created based on GO's molecular functions and the drug facet was created 
based on ChEBI.

I think MeSH can potentially be a source for creating new facets (e.g., 
diseases, drug actions, etc) ...

Also, I have a question regarding retrieval of entez gene information 
including gene ids, symbols, and snyonyms. Is such information available 
from the HCLS KB and/or RDF entrez gene dataset that Olivier's group had 



Alan Ruttenberg wrote:
> On Feb 11, 2008, at 3:34 PM, Olivier Bodenreider wrote:
>> eric neumann wrote:
>>> I haven't been good at following the calls lately, but still am 
>>> sympathetic to the endeavor and committed to helping as I can (just 
>>> not quite efficiently).
>> Starting with MeSH might be a good idea as it it does not have the 
>> intellectual restrictions inherent to other sources in the UMLS. 
>> Moreover, MeSH is available in XML and could be easily transformed 
>> into RDF, allowing for a possible resolution of the URIs.
> There is already one RDF translation in the KB (script from Van Assem 
> et. al., modified by Jonathan). This is in to SKOS. There's also a 
> prototype uri scheme that we used in the demo, if you are looking for 
> a model.
> -Alan
>> -- Olivier
>>> Eric
>>> On Feb 11, 2008 9:58 AM, Matthias Samwald <samwald@gmx.at 
>>> <mailto:samwald@gmx.at>> wrote:
>>>     I have also added several ideas to the wiki page [1]:
>>>     * OBO Structured Digital Abstracts
>>>     * SIOC for Science
>>>     * OntoWiki and Semantic MediaWiki
>>>     * HCLS KB Decentralisation
>>>     * Define a simplified OWL-to-RDF mapping for a subset of OWL
>>>     Cheers,
>>>     Matthias Samwald
>>>     Semantic Web Company / DERI Galway / Yale Center for Medical
>>>     Informatics
>>>     [1] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Brainstorming
Received on Tuesday, 12 February 2008 22:21:44 UTC

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