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Re: PK Ontology

From: Richard Boyce <rdb20@pitt.edu>
Date: Tue, 5 Feb 2013 14:34:58 -0500
Message-ID: <51115EE2.2080103@pitt.edu>
To: <public-semweb-lifesci@w3.org>
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.

- 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 

- 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 
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: 


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] *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 Pittsburgh
Office: 412-648-9219
Twitter: @bhaapgh
Received on Tuesday, 5 February 2013 19:35:26 UTC

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