- From: Kei Cheung <kei.cheung@yale.edu>
- Date: Wed, 13 Feb 2008 11:55:16 -0500
- 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 UTC