> 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] On Behalf Of Lin
MD, Simon
Sent: Thursday, July 19, 2012 12:01 PM
To: 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)
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
www.marshfieldclinic.org/birc
For scheduling assistance, please contact
Crystal Gumz, Administrative Secretary
gumz.crys...@mcrf.mfldclin.edu
715-221-6403
From: Richard Boyce [mailto:rd...@pitt.edu]
Sent: Thursday, July 19, 2012 9:29 AM
To: 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)
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 wrote:
Microsoft Outlook Web Access:
https://exchange.pitt.edu/owa?ae=Item&a=open&t=IPM.Schedule.Meeting..Requ
est&id=RgAAAABIJ%2FzGAGFgTKLiK5T2HHYjBwCgDb8iAQTaTJ1WnLL6a2ItAAABKG9eAAC
UhAUmmNbBR6ow1bEXCKFKACQGgySHAAAL
This event has been changed.
more details >
<https://www.google.com/calendar/event?action=VIEW&eid=dWRsdXAwcDlpcjhvZ
HBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAd
zMub3Jn&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2IzZjcwMmRj
YmFmZTU2N2FiMzM0ODNm&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=AFQjCNG0M
KmcRl77RYagVfKU9ZZl91H2Uw> 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
Who
*
w3.h...@gmail.com - organizer
*
public-semweb-lifesci@w3.org
*
pharmacogenomicspa...@googlegroups.com
Going? Yes
<https://www.google.com/calendar/event?action=RESPOND&eid=dWRsdXAwcDlpcj
hvZHBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2
lAdzMub3Jn&rst=1&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2I
zZjcwMmRjYmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en> - Maybe
<https://www.google.com/calendar/event?action=RESPOND&eid=dWRsdXAwcDlpcj
hvZHBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2
lAdzMub3Jn&rst=3&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2I
zZjcwMmRjYmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en> - No
<https://www.google.com/calendar/event?action=RESPOND&eid=dWRsdXAwcDlpcj
hvZHBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2
lAdzMub3Jn&rst=2&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2I
zZjcwMmRjYmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en> more
options >
<https://www.google.com/calendar/event?action=VIEW&eid=dWRsdXAwcDlpcjhvZ
HBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAd
zMub3Jn&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2IzZjcwMmRj
YmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en>
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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
rd...@pitt.edu
412-648-9219 (W), 206-371-6186 (C)
Twitter: @bhaapgh
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