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RE: Updated Invitation: Pharmacogenomics for Drug Discovery @ Thu 2012-07-19 11:00 - 12:00 (public-semweb-lifesci@w3.org)

From: Freimuth, Robert, Ph.D. <Freimuth.Robert@mayo.edu>
Date: Thu, 19 Jul 2012 12:08:57 -0500
Message-ID: <BEDC94A68947954BA999E99DD926FE1B0BCDDA@msgebe49.mfad.mfroot.org>
To: "Lin MD, Simon" <LINMD.SIMON@mcrf.mfldclin.edu>, <rdb20@pitt.edu>, <public-semweb-lifesci@w3.org>
> Based on the loaded data, can we make a graph showing the complex
relationship between drugs and biomarkers (n-to-n)? 
 
I think this would be relatively easy to do with Cytoscape (following a
trivial transform of the data), but the semweb gurus probably know of a
way to do this natively using the RDF.

Thanks, 
Bob 

 


________________________________

	From: public-semweb-lifesci-request@listhub.w3.org
[mailto:public-semweb-lifesci-request@listhub.w3.org] On Behalf Of Lin
MD, Simon
	Sent: Thursday, July 19, 2012 12:01 PM
	To: rdb20@pitt.edu; public-semweb-lifesci@w3.org
	Subject: RE: Updated Invitation: Pharmacogenomics for Drug
Discovery @ Thu 2012-07-19 11:00 - 12:00 (public-semweb-lifesci@w3.org)
	
	

	Richard, 

	 

	Fabulous results! Sorry I was unable to make the call today. 

	 

	For "3) drug product with CYPD6", can you make the query to show
the drug names? Right now, it is showing a link. 

	 

	Here is a  scientific question to make it more interesting: 

	Based on the loaded data, can we make a graph showing the
complex relationship between drugs and biomarkers (n-to-n)? The drugs
and biomarkers can be nodes. I suspect a CYP gene will be a hub to many
drugs. For drug nodes, we can color code them with different therapeutic
areas.

	 

	What do you think?

	 

	Simon

	 

	==================================================

	Simon Lin, MD

	Director, Biomedical Informatics Research Center 

	Marshfield Clinic Research Foundation 

	1000 N Oak Ave, Marshfield, WI 54449 

	Office 715-221-7299 

	Lin.Simon@mcrf.mfldclin.edu 

	www.marshfieldclinic.org/birc

	 

	For scheduling assistance, please contact

	      Crystal Gumz, Administrative Secretary

	      gumz.crystal@mcrf.mfldclin.edu

	      715-221-6403

	 

	 

	From: Richard Boyce [mailto:rdb20@pitt.edu] 
	Sent: Thursday, July 19, 2012 9:29 AM
	To: public-semweb-lifesci@w3.org
	Subject: Re: Updated Invitation: Pharmacogenomics for Drug
Discovery @ Thu 2012-07-19 11:00 - 12:00 (public-semweb-lifesci@w3.org)

	 

	Re: " I also want to talk about making that list of FDA labels
that containing PGx info."... 
	
	If its of interest, I can share my initial load and mapping of
the data from the FDA's pharmacogenomic biomarker table
<http://www.fda.gov/Drugs/ScienceResearch/ResearchAreas/Pharmacogenetics
/ucm083378.htm>
<http://www.fda.gov/Drugs/ScienceResearch/ResearchAreas/Pharmacogenetics
/ucm083378.htm>  into linkedSPLs. You can test it out now....
	
	INSTRUCTIONS:
	1) go to <http://dbmi-icode-01.dbmi.pitt.edu:8080/sparql>
<http://dbmi-icode-01.dbmi.pitt.edu:8080/sparql> 
	2) enter the following in the field "Default IRI":
http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/
	3) Delete the text in the query box
	4) enter in any of test of a sample query below (the text in
between dashed lines)
	5) to enter a new query, just use the back button, delete the
olde query, and enter the new one.
	
	Example queries:
	
	1) show the entire FDA pharmgx table:
	
	---------------
	
	PREFIX prv: <http://purl.org/net/provenance/ns#>
<http://purl.org/net/provenance/ns> 
	PREFIX dc: <http://purl.org/dc/elements/1.1/>
<http://purl.org/dc/elements/1.1/> 
	PREFIX db:
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/resource/>
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/resource/> 
	PREFIX diseasome:
<http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/>
<http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/> 
	PREFIX drugbank:
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/>
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/> 
	PREFIX prvFiles: <http://purl.org/net/provenance/files#>
<http://purl.org/net/provenance/files> 
	PREFIX foaf: <http://xmlns.com/foaf/0.1/>
<http://xmlns.com/foaf/0.1/> 
	PREFIX meta:
<http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/metadata#>
<http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/metadata> 
	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
<http://www.w3.org/2000/01/rdf-schema> 
	PREFIX obo: <http://purl.obolibrary.org/obo/>
<http://purl.obolibrary.org/obo/> 
	PREFIX ncbit:
<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl> 
	PREFIX prvTypes: <http://purl.org/net/provenance/types#>
<http://purl.org/net/provenance/types> 
	PREFIX d2r:
<http://sites.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/config.rdf#>
<http://sites.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/config.rdf> 
	PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
<http://www.w3.org/2001/XMLSchema> 
	PREFIX prvIV: <http://purl.org/net/provenance/integrity#>
<http://purl.org/net/provenance/integrity> 
	PREFIX map:
<file:/home/rdb20/linkedSPLs/dailymed_d2r_map_config.n3#>
<file:///\\home\rdb20\linkedSPLs\dailymed_d2r_map_config.n3> 
	PREFIX owl: <http://www.w3.org/2002/07/owl#>
<http://www.w3.org/2002/07/owl> 
	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
<http://www.w3.org/1999/02/22-rdf-syntax-ns> 
	PREFIX dailymed:
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/vocab/resource/>
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/vocab/resource/> 
	PREFIX bpRxnorm: <http://purl.bioontology.org/ontology/RXNORM/>
<http://purl.bioontology.org/ontology/RXNORM/> 
	
	
	SELECT DISTINCT * WHERE {
	  ?s rdf:type dailymed:pharmgxData.
	  ?s dailymed:activeMoiety ?activeMoiety.
	  ?s dailymed:activeMoietyRxCUI ?rxNormCUI.
	  ?s dailymed:pharmgxBiomarker ?biomarker.
	  ?s dailymed:therapeuticApplication ?therapeuticApplication.
	  ?s dailymed:setId ?productLabelSetId.
	  ?s dailymed:SPLSection ?labelSection.
	} ORDER BY ?productLabelSetId
	
	---------------
	
	2) Get sections containing pharmgx recommendations for Psych
drugs
	
	---------------
	
	PREFIX prv: <http://purl.org/net/provenance/ns#>
<http://purl.org/net/provenance/ns> 
	PREFIX dc: <http://purl.org/dc/elements/1.1/>
<http://purl.org/dc/elements/1.1/> 
	PREFIX db:
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/resource/>
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/resource/> 
	PREFIX diseasome:
<http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/>
<http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/> 
	PREFIX drugbank:
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/>
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/> 
	PREFIX prvFiles: <http://purl.org/net/provenance/files#>
<http://purl.org/net/provenance/files> 
	PREFIX foaf: <http://xmlns.com/foaf/0.1/>
<http://xmlns.com/foaf/0.1/> 
	PREFIX meta:
<http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/metadata#>
<http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/metadata> 
	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
<http://www.w3.org/2000/01/rdf-schema> 
	PREFIX obo: <http://purl.obolibrary.org/obo/>
<http://purl.obolibrary.org/obo/> 
	PREFIX ncbit:
<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl> 
	PREFIX prvTypes: <http://purl.org/net/provenance/types#>
<http://purl.org/net/provenance/types> 
	PREFIX d2r:
<http://sites.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/config.rdf#>
<http://sites.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/config.rdf> 
	PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
<http://www.w3.org/2001/XMLSchema> 
	PREFIX prvIV: <http://purl.org/net/provenance/integrity#>
<http://purl.org/net/provenance/integrity> 
	PREFIX map:
<file:/home/rdb20/linkedSPLs/dailymed_d2r_map_config.n3#>
<file:///\\home\rdb20\linkedSPLs\dailymed_d2r_map_config.n3> 
	PREFIX owl: <http://www.w3.org/2002/07/owl#>
<http://www.w3.org/2002/07/owl> 
	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
<http://www.w3.org/1999/02/22-rdf-syntax-ns> 
	PREFIX dailymed:
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/vocab/resource/>
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/vocab/resource/> 
	PREFIX bpRxnorm: <http://purl.bioontology.org/ontology/RXNORM/>
<http://purl.bioontology.org/ontology/RXNORM/> 
	
	SELECT DISTINCT ?setId ?moiety ?biomarker ?sectionTag
?sectionText WHERE {
	  ?s dailymed:setId ?setId.
	  ?pharmgxData dailymed:setId ?setId.
	  ?pharmgxData dailymed:therapeuticApplication ncbit:Psychiatry.
	  ?pharmgxData dailymed:activeMoiety ?moiety.
	  ?pharmgxData dailymed:pharmgxBiomarker ?biomarker.
	  ?pharmgxData dailymed:SPLSection ?sectionTag.
	  ?s ?sectionTag ?sectionText.
	}
	
	---------------
	
	3) return all setIds and drug product rxcuis for product labels
that contain sections with FDA pharmgx data for biomarker "CYPD6"
	
	----------------
	PREFIX prv: <http://purl.org/net/provenance/ns#>
<http://purl.org/net/provenance/ns> 
	PREFIX dc: <http://purl.org/dc/elements/1.1/>
<http://purl.org/dc/elements/1.1/> 
	PREFIX db:
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/resource/>
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/resource/> 
	PREFIX diseasome:
<http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/>
<http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/> 
	PREFIX drugbank:
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/>
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/> 
	PREFIX prvFiles: <http://purl.org/net/provenance/files#>
<http://purl.org/net/provenance/files> 
	PREFIX foaf: <http://xmlns.com/foaf/0.1/>
<http://xmlns.com/foaf/0.1/> 
	PREFIX meta:
<http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/metadata#>
<http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/metadata> 
	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
<http://www.w3.org/2000/01/rdf-schema> 
	PREFIX obo: <http://purl.obolibrary.org/obo/>
<http://purl.obolibrary.org/obo/> 
	PREFIX ncbit:
<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl> 
	PREFIX prvTypes: <http://purl.org/net/provenance/types#>
<http://purl.org/net/provenance/types> 
	PREFIX d2r:
<http://sites.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/config.rdf#>
<http://sites.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/config.rdf> 
	PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
<http://www.w3.org/2001/XMLSchema> 
	PREFIX prvIV: <http://purl.org/net/provenance/integrity#>
<http://purl.org/net/provenance/integrity> 
	PREFIX map:
<file:/home/rdb20/linkedSPLs/dailymed_d2r_map_config.n3#>
<file:///\\home\rdb20\linkedSPLs\dailymed_d2r_map_config.n3> 
	PREFIX owl: <http://www.w3.org/2002/07/owl#>
<http://www.w3.org/2002/07/owl> 
	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
<http://www.w3.org/1999/02/22-rdf-syntax-ns> 
	PREFIX dailymed:
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/vocab/resource/>
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/vocab/resource/> 
	PREFIX bpRxnorm: <http://purl.bioontology.org/ontology/RXNORM/>
<http://purl.bioontology.org/ontology/RXNORM/> 
	
	SELECT DISTINCT ?setId ?rxcuiDrugProduct ?sectionTag
?sectionText WHERE {
	  ?pharmgxData dailymed:pharmgxBiomarker "CYP2D6".
	  ?pharmgxData dailymed:setId ?setId.
	  ?pharmgxData dailymed:SPLSection ?sectionTag.
	  ?spl dailymed:setId ?setId.
	  ?spl ?sectionTag ?sectionText.
	  ?spl dc:subject ?rxcuiDrugProduct.
	} LIMIT 10
	----------------
	
	
	On 07/19/2012 10:09 AM, w3.hcls@gmail.com wrote:

		
		Microsoft Outlook Web Access:
https://exchange.pitt.edu/owa?ae=Item&a=open&t=IPM.Schedule.Meeting..Requ
est&id=RgAAAABIJ%2FzGAGFgTKLiK5T2HHYjBwCgDb8iAQTaTJ1WnLL6a2ItAAABKG9eAAC
UhAUmmNbBR6ow1bEXCKFKACQGgySHAAAL
		
		
		

This event has been changed. 

more details >
<https://www.google.com/calendar/event?action=VIEW&eid=dWRsdXAwcDlpcjhvZ
HBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAd
zMub3Jn&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2IzZjcwMmRj
YmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en> 

Pharmacogenomics for Drug Discovery

Changed: Dial-In #: +1.617.761.6200 (Cambridge, MA)
VoIP address: sip:zakim@voip.w3.org <mailto:sip%3Azakim@voip.w3.org> 
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org
<http://www.google.com/url?q=http%3A%2F%2Firc.w3.org&usd=2&usg=AFQjCNG0M
KmcRl77RYagVfKU9ZZl91H2Uw>  port 6665 channel #HCLS
IRC Web: http://goo.gl/A6WZn
Duration: ~1 hour
Frequency: 1st and 3rd Thursday
Convener: Michel Dumontier

Hi,
At today's meeting I hope to discuss some additional sources of SNP
associations - I've been looking at OMIM, but I would love your feedback
on other resources. I also want to talk about making that list of FDA
labels that containing PGx info.

Cheers,

m.

 

 

When

Thu 2012-07-19 11:00 - 12:00 Eastern Time

Calendar

public-semweb-lifesci@w3.org

Who

*

w3.hcls@gmail.com - organizer

*

public-semweb-lifesci@w3.org

*

pharmacogenomicspaper@googlegroups.com

 

Going?   Yes
<https://www.google.com/calendar/event?action=RESPOND&eid=dWRsdXAwcDlpcj
hvZHBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2
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zZjcwMmRjYmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en>  - Maybe
<https://www.google.com/calendar/event?action=RESPOND&eid=dWRsdXAwcDlpcj
hvZHBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2
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zZjcwMmRjYmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en>  - No
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options >
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HBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAd
zMub3Jn&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2IzZjcwMmRj
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	-- 
	Richard Boyce, PhD
	Assistant Professor of Biomedical Informatics
	Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics
Research and Training Program
	Scholar, Comparative Effectiveness Research Program
	University of Pittsburgh
	rdb20@pitt.edu
	412-648-9219 (W), 206-371-6186 (C)
	Twitter: @bhaapgh
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Received on Thursday, 19 July 2012 17:19:57 GMT

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