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HCLS knowledgebase extension: PDSP Ki database uploaded to DERI triplestore

From: <samwald@gmx.at>
Date: Wed, 31 Oct 2007 19:10:59 +0100
Cc: public-semweb-lifesci@w3.org <public-semweb-lifesci@w3.org>
Message-ID: <20071031181059.294750@gmx.net>
To: Kei Cheung <kei.cheung@yale.edu>, alanruttenberg@gmail.com <alanruttenberg@gmail.com>, giovanni.tummarello@deri.org <giovanni.tummarello@deri.org>

I have uploaded the 'beta version' of the OWL conversion of the PDSP Ki database to the SPARQL endpoint hosted by DERI.

The address is:
http://hcls.deri.ie/sparql

Alternatively, you can also use the SPARQL endpoint of the Yale Center for Medical Informatics (only contains the SenseLab ontologies):
http://neuroweb.med.yale.edu:8890/sparql

Since the datasets makes use of the SenseLab URIs for receptors, the queries can also be connected to further information about neuronal cell types, cellular properties, brain regions etc.

A possible SPARQL query showing some ligands of the serotonin receptor 5-HT2A, together with their affinity (lower values mean higher affinity, i.e. the substance is of higher pharmacological interest):

=====

PREFIX neurondb: <http://purl.org/ycmi/senselab/neuron_ontology.owl#>
PREFIX obo_essentials: <http://purl.org/zen/obo_essentials.owl#>
PREFIX ro:
<http://www.obofoundry.org/ro/ro.owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?name_of_ligand ?ki_value FROM <http://purl.org/ycmi/ki/core.owl> WHERE  {?nicotinic_receptor a neurondb:_5-HT2A .
?ligand a ?ligand_class .
?process a obo_essentials:GO_0005488_process .
?process ro:has_participant ?nicotinic_receptor . 
?process ro:has_participant ?ligand .
?ligand_class rdfs:label ?name_of_ligand .
?ligand ro:bearer_of ?quality .
?quality rdf:value ?ki_value .
 } 

=====
First three results:

name_of_ligand -- ki_value
--------------------------
tryptamine -- 218.7761623949
(R)-noradrenaline --455970.15
yohimbine -- 4790
chlorpromazine -- 1.8 

Some of the ligands have the name 'null', this still needs to be fixed.

The PDSP Ki datasets can be mirrored on other installations of Virtuoso with the following iSQL command:

DB.DBA.RDF_LOAD_RDFXML(
xml_uri_get('http://neuroweb.med.yale.edu/svn/trunk/ontology/ki/core.owl', 'http://neuroweb.med.yale.edu/svn/trunk/ontology/ki/core.owl'), 
'http://purl.org/ycmi/ki/core.owl', 'http://purl.org/ycmi/ki/core.owl'
)


Please note that the current HCLS demo knowledge base contains outdated namespaces for the SenseLab ontologies (we are using PURLs now), so the PDSP Ki datasets do not readily connect to the rest of the knowledge base. The namespaces in the demo KB will soon be updated (at least I would like to do so).

cheers,
Matthias Samwald
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Received on Wednesday, 31 October 2007 18:18:08 GMT

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