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; 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/
>     <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.*
>
>         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/
>
>         	
>
>         public-semweb-lifesci@w3.org <mailto:public-semweb-lifesci@w3.org>
>
>         /Who/
>
>         	
>
>         •
>
>         	
>
>         w3.hcls@gmail.com <mailto:w3.hcls@gmail.com>- organizer
>
>         •
>
>         	
>
>         public-semweb-lifesci@w3.org <mailto:public-semweb-lifesci@w3.org>
>
>         •
>
>         	
>
>         pharmacogenomicspaper@googlegroups.com
>         <mailto:pharmacogenomicspaper@googlegroups.com>
>
>         Going? *Yes*
>         <https://www.google.com/calendar/event?action=RESPOND&eid=dWRsdXAwcDlpcjhvZHBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAdzMub3Jn&rst=1&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2IzZjcwMmRjYmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en>*-
>         **Maybe*
>         <https://www.google.com/calendar/event?action=RESPOND&eid=dWRsdXAwcDlpcjhvZHBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAdzMub3Jn&rst=3&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2IzZjcwMmRjYmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en>*-
>         **No*
>         <https://www.google.com/calendar/event?action=RESPOND&eid=dWRsdXAwcDlpcjhvZHBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAdzMub3Jn&rst=2&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2IzZjcwMmRjYmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en>more
>         options »
>         <https://www.google.com/calendar/event?action=VIEW&eid=dWRsdXAwcDlpcjhvZHBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAdzMub3Jn&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2IzZjcwMmRjYmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en>
>
>         Invitation from Google Calendar
>         <https://www.google.com/calendar/>
>
>         You are receiving this courtesy email at the account
>         public-semweb-lifesci@w3.org
>         <mailto:public-semweb-lifesci@w3.org> because you are an
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>         To stop receiving future notifications for this event, decline
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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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-- 
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

Received on Thursday, 19 July 2012 18:11:09 UTC