- From: Alan Ruttenberg <alanruttenberg@gmail.com>
- Date: Tue, 12 Feb 2008 23:01:55 -0500
- To: Kei Cheung <kei.cheung@yale.edu>
- 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>
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 UTC