- From: Richard Boyce <rdb20@pitt.edu>
- Date: Thu, 19 Jul 2012 10:28:57 -0400
- To: <public-semweb-lifesci@w3.org>
- Message-ID: <500819A9.5040205@pitt.edu>
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>
into linkedSPLs. You can test it out now....
INSTRUCTIONS:
1) go to <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#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX db: <http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/resource/>
PREFIX diseasome:
<http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/>
PREFIX drugbank:
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/>
PREFIX prvFiles: <http://purl.org/net/provenance/files#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX meta: <http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/metadata#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX ncbit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX prvTypes: <http://purl.org/net/provenance/types#>
PREFIX d2r:
<http://sites.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/config.rdf#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX prvIV: <http://purl.org/net/provenance/integrity#>
PREFIX map: <file:/home/rdb20/linkedSPLs/dailymed_d2r_map_config.n3#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dailymed:
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/vocab/resource/>
PREFIX bpRxnorm: <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#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX db: <http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/resource/>
PREFIX diseasome:
<http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/>
PREFIX drugbank:
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/>
PREFIX prvFiles: <http://purl.org/net/provenance/files#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX meta: <http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/metadata#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX ncbit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX prvTypes: <http://purl.org/net/provenance/types#>
PREFIX d2r:
<http://sites.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/config.rdf#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX prvIV: <http://purl.org/net/provenance/integrity#>
PREFIX map: <file:/home/rdb20/linkedSPLs/dailymed_d2r_map_config.n3#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dailymed:
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/vocab/resource/>
PREFIX bpRxnorm: <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#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX db: <http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/resource/>
PREFIX diseasome:
<http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/>
PREFIX drugbank:
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/>
PREFIX prvFiles: <http://purl.org/net/provenance/files#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX meta: <http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/metadata#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX ncbit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX prvTypes: <http://purl.org/net/provenance/types#>
PREFIX d2r:
<http://sites.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/config.rdf#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX prvIV: <http://purl.org/net/provenance/integrity#>
PREFIX map: <file:/home/rdb20/linkedSPLs/dailymed_d2r_map_config.n3#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dailymed:
<http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/vocab/resource/>
PREFIX bpRxnorm: <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 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
> /Who/
> • w3.hcls@gmail.com- organizer
> • public-semweb-lifesci@w3.org
> • 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>
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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 14:29:26 UTC