RE: Updated Invitation: Pharmacogenomics for Drug Discovery @ Thu 2012-07-19 11:00 - 12:00 (public-semweb-lifesci@w3.org) from Lin MD, Simon on 2012-07-19 (public-semweb-lifesci@w3.org from July 2012)

From: Lin MD, Simon <LINMD.SIMON@mcrf.mfldclin.edu>
Date: Thu, 19 Jul 2012 17:11:58 +0000
To: "Freimuth, Robert, Ph.D." <Freimuth.Robert@mayo.edu>, "rdb20@pitt.edu" <rdb20@pitt.edu>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>
Message-ID: <A5BD550FC766564987DA2A59779890303DFB2493@MCL-EXMB02.mfldclin.org>
Bob, I completely agree. Given the sophisticated layout options available in Cytoscape, that could be the way to go for visualization! -Simon

From: Freimuth, Robert, Ph.D. [mailto:Freimuth.Robert@mayo.edu]
Sent: Thursday, July 19, 2012 12:09 PM
To: Lin MD, Simon; 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)

> 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> [mailto:public-semweb-lifesci-request@listhub.w3.org]<mailto:[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<mailto:rdb20@pitt.edu>; public-semweb-lifesci@w3.org<mailto: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<mailto: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<mailto:Lin.Simon@mcrf.mfldclin.edu>
www.marshfieldclinic.org/birc<http://www.marshfieldclinic.org/birc>

For scheduling assistance, please contact
      Crystal Gumz, Administrative Secretary
      gumz.crystal@mcrf.mfldclin.edu<mailto:gumz.crystal@mcrf.mfldclin.edu>
      715-221-6403


From: Richard Boyce [mailto:rdb20@pitt.edu]<mailto:[mailto:rdb20@pitt.edu]>
Sent: Thursday, July 19, 2012 9:29 AM
To: public-semweb-lifesci@w3.org<mailto: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<mailto: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<mailto:w3.hcls@gmail.com> wrote:

Microsoft Outlook Web Access: https://exchange.pitt.edu/owa?ae=Item&a=open&t=IPM.Schedule.Meeting.Request&id=RgAAAABIJ%2FzGAGFgTKLiK5T2HHYjBwCgDb8iAQTaTJ1WnLL6a2ItAAABKG9eAACUhAUmmNbBR6ow1bEXCKFKACQGgySHAAAL

This event has been changed.
more details ><https://www.google.com/calendar/event?action=VIEW&eid=dWRsdXAwcDlpcjhvZHBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAdzMub3Jn&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2IzZjcwMmRjYmFmZTU2N2FiMzM0ODNm&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=AFQjCNG0MKmcRl77RYagVfKU9ZZl91H2Uw> 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

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w3.hcls@gmail.com<mailto:w3.hcls@gmail.com> - organizer

*

public-semweb-lifesci@w3.org<mailto:public-semweb-lifesci@w3.org>

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pharmacogenomicspaper@googlegroups.com<mailto:pharmacogenomicspaper@googlegroups.com>



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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<mailto:rdb20@pitt.edu>

412-648-9219 (W), 206-371-6186 (C)

Twitter: @bhaapgh

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Received on Thursday, 19 July 2012 17:12:38 UTC