- From: Richard Boyce <rdb20@pitt.edu>
- Date: Thu, 19 Jul 2012 14:10:42 -0400
- To: "Lin MD, Simon" <LINMD.SIMON@mcrf.mfldclin.edu>
- CC: "Freimuth, Robert, Ph.D." <Freimuth.Robert@mayo.edu>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>
- Message-ID: <50084DA2.8020309@pitt.edu>
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 > attendee of this event. > > To stop receiving future notifications for this event, decline > this event. Alternatively you can sign up for a Google account > at https://www.google.com/calendar/ and control your > notification settings for your entire calendar. > > > > -- > > 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 412-648-9219 (W), 206-371-6186 (C) Twitter: @bhaapgh
Received on Thursday, 19 July 2012 18:11:09 UTC