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[BioRDF] PDSP Ki Database in OWL / BioPAX

From: Matthias Samwald <samwald@gmx.at>
Date: Fri, 21 Apr 2006 11:21:11 +0200
To: <public-semweb-lifesci@w3.org>
Message-ID: <2006421112354.413334@cqueberel>

Hello all,

I am almost finished with a conversion of the PDSP Ki Database [1] to an OWL - based format. Accoring to its website, the Ki database is a...

"[...] unique resource in the public domain which provides information on the abilities of drugs to interact with an expanding number of molecular targets. The Ki database serves as a data warehouse for published and internally-derived Ki, or affinity, values for a large number of drugs and drug candidates at an expanding number of G-protein coupled receptors, ion channels, transporters and enzymes."

This kind of data is especially important for the neurosciences.

I have attached a small demo-file to this message. The file of the OWL - version of the whole Ki database is 25 MB large and contains around 280.000 triples (and some minor bugs that have yet to be eliminated). The namespaces and URIs might still be subject to change. The OWL version of the KiDB also contains some annotations that do not exist in the original database, namely annotations with codes from the IUHPHAR receptor database [2], classification of receptors according to the classes in the IUPHAR-DB, and annotation of organisms with their respective code in the Entrez Taxonomy database [3]. These annotations are based on manual mappings between terms in the KiDB and the databases.

The OWL ontology used to represent the data from the KiDB is an extension of the BioPAX ontology. The ontology imports the original BioPAX ontology and some extension ontologies via the internet -- this means that you have to be online to load the ontology.

It seems that this is the first time an existing (and used) SemWeb - ontology is extended like this. This might be an interesting study case about seeing ontology extension and 'evolution' in action. I can also see that making such extensions to the core BioPAX ontology is problematic for the BioPAX project, which seeks to provide a common and clearly-defined ontology for data exchange. However, it should be quite easy for tools supporting BioPAX to ignore the extensions made in subclasses of the original BioPAX classes -- just using the information that is understandable to the application.

Suggestions?

kind regards,
Matthias Samwald

[1] http://kidb.cwru.edu/
[2] http://www.iuphar-db.org/GPCR/
[3] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy

http://neuroscientific.net






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Received on Friday, 21 April 2006 09:24:05 UTC

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