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>.
-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-requ...@listhub.w3.org
[mailto:public-semweb-lifesci-requ...@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
rd...@pitt.edu
Office: 412-648-9219
Twitter: @bhaapgh
