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.rob...@mayo.edu] Sent: Thursday, July 19, 2012 12:09 PM To: Lin MD, Simon; rd...@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-requ...@listhub.w3.org<mailto:public-semweb-lifesci-requ...@listhub.w3.org> [mailto:public-semweb-lifesci-requ...@listhub.w3.org]<mailto:[mailto:public-semweb-lifesci-requ...@listhub.w3.org]> On Behalf Of Lin MD, Simon Sent: Thursday, July 19, 2012 12:01 PM To: rd...@pitt.edu<mailto:rd...@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.si...@mcrf.mfldclin.edu<mailto:lin.si...@mcrf.mfldclin.edu> www.marshfieldclinic.org/birc<http://www.marshfieldclinic.org/birc> For scheduling assistance, please contact Crystal Gumz, Administrative Secretary gumz.crys...@mcrf.mfldclin.edu<mailto:gumz.crys...@mcrf.mfldclin.edu> 715-221-6403 From: Richard Boyce [mailto:rd...@pitt.edu]<mailto:[mailto:rd...@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.h...@gmail.com<mailto:w3.h...@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:za...@voip.w3.org<mailto:sip%3aza...@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.h...@gmail.com<mailto:w3.h...@gmail.com> - organizer * public-semweb-lifesci@w3.org<mailto:public-semweb-lifesci@w3.org> * pharmacogenomicspa...@googlegroups.com<mailto:pharmacogenomicspa...@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 rd...@pitt.edu<mailto:rd...@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. 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