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RE: Updated Invitation: Pharmacogenomics for Drug Discovery @ Thu 2012-07-19 11:00 - 12:00 (public-semweb-lifesci@w3.org)

From: Erich Gombocz <egombocz@io-informatics.com>
Date: Thu, 19 Jul 2012 15:49:33 -0700
Message-ID: <08AE3015BD5DF149951910A5E851F010D40DCD@MAIL-02.io-informatics.com>
To: <rdb20@pitt.edu>, "Lin MD, Simon" <LINMD.SIMON@mcrf.mfldclin.edu>
Cc: "Freimuth, Robert, Ph.D." <Freimuth.Robert@mayo.edu>, <public-semweb-lifesci@w3.org>
Dear Richard,  Simon and All,

 

I don't want to contribute confusion to this very good discussion
thread, but want to let you know, that the Import Mapper in our Sentient
Knowledge Explorer supports script-based transformations when creating
the RDF triples; so you could use this function to separate multiple
terms into individual ones automatically as long as you can set up the
rules (e.g. for string truncation).

 

Hope, this helps.

 

Cordially,

 

Erich

 

 

Erich A. Gombocz

Vice President, Chief Scientific Officer

 

IO Informatics, Inc.

2550 Ninth Street, Suite 114

Berkeley, CA 94710-2552, USA

 

Phone:   (510) 705-8470

Fax:       (510) 705-8476

Mobile:  (415) 740-9416

Email:      <mailto:egombocz@io-informatics.com>
egombocz@io-informatics.com

Web:        <http://www.io-informatics.com/> www.io-informatics.com

 

 

From: Richard Boyce [mailto:rdb20@pitt.edu] 
Sent: Thursday, July 19, 2012 3:42 PM
To: Lin MD, Simon
Cc: Freimuth, Robert, Ph.D.; 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)

 

Hi Simon....

 
I took a look at the error log. Did you manually break some of the lines
into two? For instance,
  TRAMADOL AND ACETAMINOPHEN

REPLY: I am consulting with a clinical pharmacologist colleague on how
to best handle products with combined ingredients...here are the known
issues: 

"This import currently does not contain data for the table entries with
combined active ingredients: chlordiazepoxide and amitriptyline,
desloratadine and pseudoephedrine, dextromethorphan and quinidine,
drospirenone and ethinyl estradiol, fluoxetine and olanzapine,
isosorbide and hydralazine, tramadol and acetaminophen.
    
(7/12/12) Other issues with the very initial import of the FDA
Pharmacogenetic Biomarker Table include: 1) none of the "Patient
Counseling" sections referenced in the table currently exist in
LinkeSPLs (These will appear at a future date) 2) currently, "Metabolic
and Endocrinology" therapeutic application is mapped only to
ncbit:Endocrinology, "Dermatology and Dental" to ncbit:Dermatology, and
"Reproductive and Urologic" to ncbit:Urology."
    
......



 

With the current setup, are you able to query the total number of FDA
approved drugs in a certain therapeutic area, for instance, Psychiatry
or Hematology?      



REPLY: that is coming soon...working with Bob and Quin at Mayo to load
the SPL EPC mappings...will let you know when it is testable.

kind regards,
-Rich



 

Thanks!

 

Simon

 

 

From: Richard Boyce [mailto:rdb20@pitt.edu] 
Sent: Thursday, July 19, 2012 1:11 PM
To: Lin MD, Simon
Cc: Freimuth, Robert, Ph.D.; 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)

 

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] On Behalf Of Lin
MD, Simon
Sent: Thursday, July 19, 2012 12:01 PM
To: 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)

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 

www.marshfieldclinic.org/birc

 

For scheduling assistance, please contact

      Crystal Gumz, Administrative Secretary

      gumz.crystal@mcrf.mfldclin.edu

      715-221-6403

 

 

From: Richard Boyce [mailto:rdb20@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:///\\%5C%5C%5C%5Chome%5Crdb20%5ClinkedSPLs%5Cdailymed_d2r_map_conf
ig.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:///\\%5C%5C%5C%5Chome%5Crdb20%5ClinkedSPLs%5Cdailymed_d2r_map_conf
ig.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:///\\%5C%5C%5C%5Chome%5Crdb20%5ClinkedSPLs%5Cdailymed_d2r_map_conf
ig.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.hcls@gmail.com wrote:


Microsoft Outlook Web Access: https://exchange.pitt.edu/owa?ae=Item
<https://exchange.pitt.edu/owa?ae=Item&a=open&t=IPM.Schedule.Meeting.Req
uest&id=RgAAAABIJ%2FzGAGFgTKLiK5T2HHYjBwCgDb8iAQTaTJ1WnLL6a2ItAAABKG9eAA
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This event has been changed.

 
<https://www.google.com/calendar/event?action=VIEW&eid=dWRsdXAwcDlpcjhvZ
HBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAd
zMub3Jn&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2IzZjcwMmRj
YmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en> more details >

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=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.hcls@gmail.com - organizer


*

public-semweb-lifesci@w3.org


*

pharmacogenomicspaper@googlegroups.com

 

Going?
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hvZHBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2
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zZjcwMmRjYmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en> Yes -
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lAdzMub3Jn&rst=2&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2I
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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

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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
  _____  


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 22:50:05 GMT

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