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Re: [biordf] Progress with PDSP Ki database

From: Kei Cheung <kei.cheung@yale.edu>
Date: Thu, 25 Oct 2007 10:51:27 -0400
To: samwald@gmx.at
Cc: public-semweb-lifesci@w3.org
Message-id: <4720AD6F.7040101@yale.edu>

Well done, Matthias.

As the number of semantic web resources (e.g., owl ontologies) is 
increasing, the next step is to develop intuitive user interface that 
will exploit and integrate these ontologies without requiring the users 
(e.g., neuroscientists) to learn SPARQL and/or a specific OWL-based 
query language. To this end, the SenseLab team (including Matthias) in 
collaboration with the CCDB team has developed a prototype interface 
called "Entrez Neuron" (http://ycmi.med.yale.edu/entrez_neuron.html), 
which allows users to query across several neuroscience ontologies 
(NeuronDB, ModelDB, and CCDB) using keywords. These ontologies are 
currently stored in Oracle RDF Data Model (Oracle 10g). We are planning 
to migrate to Oracle 11g, which supports OWL. In addition, we plan to 
incorporate more neuroscience-related sources as well as expand the 
interface/querying capabilities in the future. Entrez Neuron is still 
under active development. Feedback and suggestions are welcome.



samwald@gmx.at wrote:
> I have made some progress with the conversion of the PDSP Ki database (containing quantitative information about ligand-receptor interactions with a focus on neuroscience).
> Ontology URL:
> http://purl.org/ycmi/ki/core.owl
> Associated Wiki page:
> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Data/KI_database
> This ontology extends the NeuronDB ontology (part of SenseLab, developed at the Yale Center for Medical Informatics). It also makes use of various OBO ontologies and Science Commons URIs.
> Please note that Protege does not display all of the information in the ontology, which is (mostly?) a fault of the application, not the ontology. I suggest that you just look at the source code to get an overview.
> The ontology does not currently contain all of the entries in the original PDSP Ki database -- the mapping between receptor entries in the Ki database and receptor class URIs in NeuronDB (or other ontologies) is still incomplete. Where no mapping exists, the database entry is currently missing from the ontology.
> I am still not really happy with the ontological representation ('exemplary' instances, representation of Ki values etc.), so some minor changes might still be made in this regard. Feedback is appreciated. 
> Thanks to Kei Cheung for supporting this work.
> cheers,
> Matthias Samwald
Received on Thursday, 25 October 2007 14:51:53 UTC

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