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Re: Reminder: Clinical Pharmacogenomics Telecon (was Re: PK Ontology)

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Wed, 6 Feb 2013 11:15:43 -0500
Message-ID: <CALcEXf5gb==pHaFyVwgYAJdzac1qLCSbueAvVoB9D4pfFs8qCg@mail.gmail.com>
To: Matthias Samwald <matthias.samwald@meduniwien.ac.at>
Cc: Richard Boyce <rdb20@pitt.edu>, public-semweb-lifesci@w3.org
During the call we discussed:

- having a HCLS meeting at CSHALS during lunch on Friday March 1.
- AMIA posters need to be ready by March 11
- BobF has one clinical guideline in RDF. includes RxNorm drug codes and
PharmGKB identifiers
- Rich's FDA list uses unique ingredient identifiers (unii), which are
mapped to rxnorm, and others from there
- Michel - to prioritize RxNorm RDFization and add to Bio2RDF
- Michel - got scripts to generate dbSNP subset from BobF

- next call in 2 weeks, will discuss published PGx ontology and corpus


On Tue, Feb 5, 2013 at 3:14 PM, Matthias Samwald <
matthias.samwald@meduniwien.ac.at> wrote:

> **
> There is a Clinical Pharmacogenomics telecon scheduled for tomorrow,
> Wednesday, 10:15 Eastern Time (remember that we decided to have the telecon
> a bit earlier). I suggest that we use the teleconference to discuss this!
> If you have other agenda items to suggest, please add them to the wiki
> page.
>
>
> http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-02-06_Conference_Call
>
> Meeting:      HCLS Pharmacogenomics
> Date:         February 06, 2013
> Time:         10:15 Eastern Time (16:15 Middle European Time)
> Frequency:    1st and 3rd Wednesday of the month
> Convener:     Michel Dumontier, Matthias Samwald
> Dial-In #:    +1.617.761.6200 (Cambridge, MA)
> VoIP address: sip:zakim@voip.w3.org
> Participant   Access Code: 4257 ("HCLS")
> IRC Channel:  irc.w3.org port 6665 channel #HCLS
>
> *Suggested Agenda*
>
>    - PK Ontology
>    - Discussing a potential HCLS IG / task force meetup around CSHALS
>    2013 in Boston this year
>    - (add other agenda items to the wiki page)
>
> Cheers,
> Matthias
>
>
>  *From:* Richard Boyce <rdb20@pitt.edu>
> *Sent:* Tuesday, February 05, 2013 8:34 PM
> *To:* public-semweb-lifesci@w3.org
> *Subject:* Re: PK Ontology
>
> This is relevant, thanks for finding Bob. Lang Li's group has been doing
> some interesting work. This ontology is a start in the right direction but
> has some issues (see below). I  would certainly be interested in discussing
> this and related work on a call. As you know, I would like to lead an
> effort to build a DDI ontology for the semantic web that meets pharmacist
> use cases.
>
> Comments:
> - The ontology uses almost no formal definitions except for those
> imported.
>
> - It is inconsistent according to Hermit 1.3.6 and Fact++ (Protege 4.2)
>
> - a quick inspection finds evidence that formal relationships are not
> being used e.g., why are CYP probe inhibitors and inducers sub-classes of
> specific CYP families? As it is, Omeprazole is_a CYP1A2-inducer-probe is_a
> CYP1A2 is_a Metabolism-enzyme!? Seems this should be a relationship between
> a set of a drug/chemicals as the domain and a CYP family as the range.
>
> - The enzymes themselves are not mapped to anything!
>
> - Its good to see muon's and positrons in there just in case... ;)
>
> - variants come from the Sequence ontology
>
> - the paper refers to a 2006 guidance to industry on drug-drug interaction
> studies for probe inhibitors, inducers, and substrates (see page 7 URL).
> This was updated in 2012 (
> http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/ucm292362.pdf)
> and its not clear if the ontology has been updated with it (I know that I
> need to update the Drug Interaction Knowledge Base).
>
> - There are at least two other DDI corpuses out there besides Li's and the
> SemEval 2011. SemEval 2013 has a new corpus with MedLine and DrugBank
> annotations that will be publicly released in a couple of months when this
> years' the SemEval DDI challenge is completed (
> http://www.cs.york.ac.uk/semeval-2013/task9/). Also, we have made public
> a corpus of pharmacokinetic PDDIs manually annotated from drug product
> labeling:
> <http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/package-insert-DDI-NLP-corpus.html><http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/package-insert-DDI-NLP-corpus.html>.
>
>
> -Rich
>
> On 02/05/2013 12:04 PM, Freimuth, Robert, Ph.D. wrote:
>
> URLs to save you time...
>
> The article abstract and provisional pdf are available at:
> http://www.biomedcentral.com/1471-2105/14/35/abstract
>
> The ontology is at:
> http://rweb.compbio.iupui.edu/corpus/ontology/
>
> The PK corpuses that were used are at:
> http://rweb.compbio.iupui.edu/corpus/
>
>
> Thanks,
> Bob
>
>
>  ------------------------------
> *From:* public-semweb-lifesci-request@listhub.w3.org [
> mailto:public-semweb-lifesci-request@listhub.w3.org<public-semweb-lifesci-request@listhub.w3.org>]
> *On Behalf Of *Freimuth, Robert, Ph.D.
> *Sent:* Tuesday, February 05, 2013 10:20 AM
> *To:* public-semweb-lifesci@w3.org
> *Subject:* PK Ontology
>
>
>
> Hi All,
>
> I haven't read this yet, but thought the abstract sounded interesting.
> Perhaps it is a topic for a future meeting?
>
> Thanks,
> Bob
>
>
> *BMC Bioinformatics.* <http://www.ncbi.nlm.nih.gov/pubmed/23374886#> 2013
> Feb 1;14(1):35. [Epub ahead of print]
>
> *An integrated pharmacokinetics ontology and corpus for text mining.*
>
> *Wu HY*<http://www.ncbi.nlm.nih.gov/pubmed?term=Wu%20HY%5BAuthor%5D&cauthor=true&cauthor_uid=23374886>,
> *Karnik S*<http://www.ncbi.nlm.nih.gov/pubmed?term=Karnik%20S%5BAuthor%5D&cauthor=true&cauthor_uid=23374886>,
> *Subhadarshini A*<http://www.ncbi..nlm.nih.gov/pubmed?term=Subhadarshini%20A%5BAuthor%5D&cauthor=true&cauthor_uid=23374886>,
> *Wang Z*<http://www..ncbi.nlm.nih.gov/pubmed?term=Wang%20Z%5BAuthor%5D&cauthor=true&cauthor_uid=23374886>,
> *Philips S*<http://www.ncbi.nlm.nih.gov/pubmed?term=Philips%20S%5BAuthor%5D&cauthor=true&cauthor_uid=23374886>,
> *Han X*<http://www.ncbi.nlm.nih.gov/pubmed?term=Han%20X%5BAuthor%5D&cauthor=true&cauthor_uid=23374886>,
> *Chiang C*<http://www.ncbi.nlm.nih.gov/pubmed?term=Chiang%20C%5BAuthor%5D&cauthor=true&cauthor_uid=23374886>,
> *Liu L*<http://www.ncbi..nlm.nih.gov/pubmed?term=Liu%20L%5BAuthor%5D&cauthor=true&cauthor_uid=23374886>,
> *Boustani M*<http://www.ncbi.nlm.nih.gov/pubmed?term=Boustani%20M%5BAuthor%5D&cauthor=true&cauthor_uid=23374886>,
> *Rocha LM*<http://www.ncbi.nlm.nih.gov/pubmed?term=Rocha%20LM%5BAuthor%5D&cauthor=true&cauthor_uid=23374886>,
> *Quinney SK*<http://www.ncbi..nlm.nih.gov/pubmed?term=Quinney%20SK%5BAuthor%5D&cauthor=true&cauthor_uid=23374886>,
> *Flockhart D*<http://www.ncbi.nlm..nih.gov/pubmed?term=Flockhart%20D%5BAuthor%5D&cauthor=true&cauthor_uid=23374886>,
> *Li L*<http://www.ncbi.nlm.nih.gov/pubmed?term=Li%20L%5BAuthor%5D&cauthor=true&cauthor_uid=23374886>
> .
>
> *Abstract*
>
>
> ABSTRACT: BACKGROUND: Drug pharmacokinetics parameters, drug interaction
> parameters, and pharmacogenetics data have been unevenly collected in
> different databases and published extensively in the literature. Without
> appropriate pharmacokinetics ontology and a well annotated pharmacokinetics
> corpus, it will be difficult to develop text mining tools for
> pharmacokinetics data collection from the literature and pharmacokinetics
> data integration from multiple databases.Description: A comprehensive
> pharmacokinetics ontology was constructed. It can annotate all aspects of
> in vitro pharmacokinetics experiments and in vivo pharmacokinetics studies.
> It covers all drug metabolism and transportation enzymes. Using our
> pharmacokinetics ontology, a PK-corpus was constructed to present four
> classes of pharmacokinetics abstracts: in vivo pharmacokinetics studies, in
> vivo pharmacogenetic studies, in vivo drug interaction studies, and in
> vitro drug interaction studies. A novel hierarchical three level annotation
> scheme was proposed and implemented to tag key terms, drug interaction
> sentences, and drug interaction pairs. The utility of the pharmacokinetics
> ontology was demonstrated by annotating three pharmacokinetics studies; and
> the utility of the PK-corpus was demonstrated by a drug interaction
> extraction text mining analysis. CONCLUSIONS: The pharmacokinetics ontology
> annotates both in vitro pharmacokinetics experiments and in vivo
> pharmacokinetics studies. The PK-corpus is a highly valuable resource for
> the text mining of pharmacokinetics parameters and drug interactions.
>
>
>
>
>
>
>
> --
> Richard D 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 Pittsburghrdb20@pitt.edu
> Office: 412-648-9219
> Twitter: @bhaapgh
>
>


-- 
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com
Received on Wednesday, 6 February 2013 16:16:37 GMT

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