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Re: BioRDF Brainstorming

From: Kei Cheung <kei.cheung@yale.edu>
Date: Wed, 13 Feb 2008 11:55:16 -0500
Message-ID: <47B320F4.1060300@yale.edu>
To: Alan Ruttenberg <alanruttenberg@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>

Alan Ruttenberg wrote:

>
> 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 :)
>
Thanks :-) . There is still a lot of room for improvement.

>> 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.

Thanks for bringing this up. I have also thought about that. The only 
thing is that I'd like to spend a little bit time to think about how to 
constraint the MeSH facet tree in a meaningful context.

>
>> 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.
>
Although we have everything loaded into Oracle triplestore at the 
moment, we  have also thought about the possibility of using sparql 
endpoints to query other triplestores live.

I think I just got a flu, need to go offline ...

-Kei

> 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 16:56:05 GMT

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