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Re: BioRDF Brainstorming

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Tue, 12 Feb 2008 23:01:55 -0500
Message-Id: <03433B5C-3C68-461B-8719-1C45633C6CF5@gmail.com>
Cc: olivier@nlm.nih.gov, 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>
To: Kei Cheung <kei.cheung@yale.edu>


On Feb 12, 2008, at 3:58 PM, Kei Cheung wrote:

> Hi Olivier, Alan, et al,
>
> A prototype version of our neuroscience semantic web portal is  
> accessible at: http://neuroweb3.med.yale.edu

Nice :)

> 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) ...

If you can supply a list of genes, you can retrieve a set of mesh  
terms by linking via entrez gene to pubmed, then to mesh. Same if you  
supply a list of pubmed ids. You can also limit to a specific branch  
of mesh easily enough. If that's the sort of think you had in mind,  
let me know and I can construct the query, or Matthias can.

> 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 created?

Separate email.

For educational purposes, perhaps have an option to show the sparql  
queries you use to retrieve the information and offer a sparql  
endpoint to let people play with fiddling the queries.

Regards,
Alan

> Cheers,
>
> -Kei
>
> 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 Wednesday, 13 February 2008 04:56:19 GMT

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