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 20:40:30 +0000
To: "rdb20@pitt.edu" <rdb20@pitt.edu>
CC: "Freimuth, Robert, Ph.D." <Freimuth.Robert@mayo.edu>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>
Message-ID: <A5BD550FC766564987DA2A59779890303DFB252E@MCL-EXMB02.mfldclin.org>
Hi Richard,



that works!



I took a look at the error log. Did you manually break some of the lines into two? For instance,

  TRAMADOL AND ACETAMINOPHEN

With the current setup, are you able to query the total number of FDA approved drugs in a certain therapeutic area, for instance, Psychiatry or Hematology?

Thanks!

Simon


From: Richard Boyce [mailto:rdb20@pitt.edu]
Sent: Thursday, July 19, 2012 1:11 PM
To: Lin MD, Simon
Cc: Freimuth, Robert, Ph.D.; 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)

Hi Simon, I like your idea. If I understand your request, it should be as simple as adding " ?spl dailymed:activeMoiety ?drug." to the query:

SELECT DISTINCT ?drug ?setId ?rxcuiDrugProduct ?sectionTag ?sectionText WHERE {
  ?pharmgxData dailymed:pharmgxBiomarker "CYP2D6".
  ?pharmgxData dailymed:setId ?setId.
  ?pharmgxData dailymed:SPLSection ?sectionTag.
  ?spl dailymed:setId ?setId.
  ?spl dailymed:activeMoiety ?drug.
  ?spl ?sectionTag ?sectionText.
  ?spl dc:subject ?rxcuiDrugProduct.
} LIMIT 1

FYI: Near future work will bring drug class info per NDFRT into linkedSPLs and map the biomarkers to PRO and Uniprot. I think that things will only get more when we start playing with federated queries.

-R

On 07/19/2012 01:11 PM, Lin MD, Simon wrote:
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<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>)

> 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:///\\%5C%5Chome%5Crdb20%5ClinkedSPLs%5Cdailymed_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:///\\%5C%5Chome%5Crdb20%5ClinkedSPLs%5Cdailymed_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:///\\%5C%5Chome%5Crdb20%5ClinkedSPLs%5Cdailymed_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.
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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
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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<mailto:public-semweb-lifesci@w3.org>

Who

*

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

*

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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

________________________________
The contents of this message may contain private, protected and/or privileged information. If you received this message in error, you should destroy the e-mail message and any attachments or copies, and you are prohibited from retaining, distributing, disclosing or using any information contained within. Please contact the sender and advise of the erroneous delivery by return e-mail or telephone. Thank you for your cooperation.
________________________________
The contents of this message may contain private, protected and/or privileged information. If you received this message in error, you should destroy the e-mail message and any attachments or copies, and you are prohibited from retaining, distributing, disclosing or using any information contained within. Please contact the sender and advise of the erroneous delivery by return e-mail or telephone. Thank you for your cooperation.




--

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

______________________________________________________________________
The contents of this message may contain private, protected and/or privileged information.  If you received this message in error, you should destroy the e-mail message and any attachments or copies, and you are prohibited from retaining, distributing, disclosing or using any information contained within.  Please contact the sender and advise of the erroneous delivery by return e-mail or telephone.  Thank you for your cooperation.
Received on Thursday, 19 July 2012 20:45:29 UTC