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> - Identify the initial data sources to be used in the demo. -
I recommend that you have a look at "Gateway to Neuroscience Resources on the Web" at SfN: http://big.sfn.org/NDG/site/eavObList.asp?c=81&menu_item=dblist
I also recommend that the demo should be based on the BioPAX OWL ontology, or a simplified/modified version thereof:
The BioPAX ontology is probably one of the most useful biological ontologies that are out there at the moment. In the context of this demo, its main drawback is that it still makes a lot of compromises to 'classic', non-ontological bioinformatics systems. For instance, you have the possibilty to make "XREFs", which point to database entries in classic databases via a database-id/record-id key pair. This is vital for the transition between current systems and the new Semantic Web systems, but should be obsolete once the Semantic Web has fully overtaken the bioinformatics world. I think the demo should be a simulation of this 'visionary, all-Semantic-Web' scenario, because its advantages are better recognizable that way. Therefore, it might be warranted to modify BioPAX in some way for the demo.
There is already some data available in the current BioPAX format, so there would be no need to start at zero. At the moment, I am also busy with converting the following databases to an extended version of BioPAX:
BIND (molecular interactions): http://bind.ca IUPHAR-DB (receptor classification of the International Union of Pharmacology): http://www.iuphar-db.org/ Ligand Gated Ion Channel Database: http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php PDSP KiDB (quantitative information about drug-receptor binding): http://kidb.bioc.cwru.edu/ Voltage-gated potassium channel database: http://vkcdb.biology.ualberta.ca/ (maybe:) The DopaNet Ontology: http://dopanet.org
kind regards, Matthias Samwald
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- Re: [BIORDF]Telcon Matthias Samwald
- Re: [BIORDF]Telcon Olivier Bodenreider
