Re: Preview of OWL 2 ontology for clinical pharmacogenomics and decision support (now called 'Genomic CDS')

Quick reply: SNPs and drugs are already linked to the Bio2RDF versions of dbSNP and DrugBank, i.e., the ontology is already part of the linked data cloud! The entities are linked via rdfs:seeAlso.

Cheers,
Matthias

From: Michel Dumontier 
Sent: Wednesday, November 21, 2012 6:40 PM
To: Matthias Samwald 
Cc: public-semweb-lifesci@w3.org ; Simon Lin MD 
Subject: Re: Preview of OWL 2 ontology for clinical pharmacogenomics and decision support (now called 'Genomic CDS')


Matthias, 
 First, great work. I think this embodies an initial approach we've envisioned for using OWL ontologies for clinical pharmacogenomics.  It's able to 
i) define complex genotypes (as a union/conjunction of alleles)
ii) it can define copy number variation (zero, one or more copies of a gene/gene variant), or capture uncertainty in the copy number (e.g. at least one). 
iii) it points to specific snps variants for a given variant


so, here are some comments:
1. can you provide a description of the specific snp-containing entry e.g. rs9332239_C - i'll generate the appropriate descriptions for Bio2RDF version dbsnp that i'm working on.


2. The class 'Human' specifies 2 of all the genes, so this restricts our cases where CNV plays an important role (from 0 copies to dozens). To what extent is the use of the cardinality restriction on this parent class *essential* for generating the inferred classification?   Should this instead be done at the patient level?


3. We should be generating linked data -> Warfarin can point to any of : drugbank or SPL (since PharmGKB and PubChem gets their drug information from DrugBank). Since Bio2RDF hosts Drugbank, we could use those URIs.


m.


On Wed, Nov 21, 2012 at 10:19 AM, Matthias Samwald <matthias.samwald@meduniwien.ac.at> wrote:

  Dear all,

  A preview release (version 0.8) of the Genomic CDS ontology is now available at 
  http://www.genomic-cds.org/ont/genomic-cds.owl

  There is also a demo version that contains some example patient data:
  http://www.genomic-cds.org/ont/genomic-cds-demo.owl

  Among other things, it contains logical representations of pharmacogenetic alleles and their defining SNPs, as well as logical representations of selected pharmacogenetic guidelines from the Clinical Pharmacogenetics Implementation Consortium and the Dutch Pharmacogenetics Working Group. The Genomic CDS ontology aims to unify several functionalities in a single resource, being:
  * A knowledge base for clinical pharmacogenomics/pharmacogenetics that can be used for question-answering (e.g., which SNPs are associated with this drug?)
  * A rule base for clinical decision support (e.g., inferring that a patient with a specific set of SNPs requires a lowered dose of warfarin and generating a CDS message that can be viewed by clinicians)
  * A tool for checking data consistency (e.g., highlighting which allele definitions in PharmGKB are overlapping, or which clinical decision support rules are matching the same group of patients)

  The ontology is OWL 2 DL serialized in Manchester Syntax. Protege 4 with the TrOWL reasoner plugin is recommended for working with the ontology. Please note that it the ontology is quite complex, so reasoning only works on decent hardware.

  The use of OWL 2 (and Manchester Syntax) makes it possible to capture complex pharmacogenetic definitions and data in a relatively intuitive, yet ontology-based and machine-readable format. For example, the OWL description of a few SNPs of a patient looks like this:
-----------Individual: example_patient
Types:
	human,
	(has some rs10929302_A)  and (has some rs10929302_G),
	(has some rs1208_A)  and (has some rs1208_G),
	(has some rs12571421_A)  and (has some rs12571421_G),
	(has some rs12769205_A)  and (has some rs12769205_G),
	has exactly 2 rs10264272_C,
	has exactly 2 rs10276036_T,
	has exactly 2 rs1041983_C,
	has exactly 2 rs1042713_G,
-----------Equally, a logical description of SNPs associated with the CYP2C9*3 allele look like this...-----------Class: 'human with CYP2C9 *3'        EquivalentTo:         has some rs1057910_C

        SubClassOf:         has some 'CYP2C9 *3',        (has some rs1057910_C)         and (has some rs1057911_A)         and (has some rs1799853_C)         and (has some rs2256871_A)
         and (has some rs28371685_C)
         and (has some rs28371686_C)         and (has some rs56165452_T)         and (has some rs57505750_C)         and (has some rs67807361_C)         and (has some rs72558184_G)         and (has some rs72558187_T)

         and (has some rs72558188_AGAAATGGAA)         and (has some rs72558189_G)         and (has some rs72558190_C)         and (has some rs72558192_A)         and (has some rs72558193_A)         and (has some rs7900194_G)

         and (has some rs9332130_A)         and (has some rs9332131_A)         and (has some rs9332239_C),-----------... and a logical description of the group of humans that might require a specific initial warfarin dose based on their genetic traits looks like this:-----------Class: 'human triggering CDS rule 7'    Annotations:         label "human triggering CDS rule 7",        'CDS message' "3-4 mg warfarin per day should be considered as a starting dose range for a patient with this genotype according to the Warfarin drug label (Bristol-Myers Squibb).",

        'relevant for' <http://www.genomic-cds.org/ont/genomic-cds.owl#Warfarin>        EquivalentTo:         (has some 'CYP2C9 *1')

         and (has some 'CYP2C9 *3')         and (has exactly 2 rs9923231_C)        SubClassOf:         'Human triggering CDS rule'-----------To make long-term development and maintenance easier, the ontology is generated from intuitive spreadsheets (so that independent domain experts can easily edit and validate the knowledge) and automated imports from primary datasets such as dbSNP.An issue tracker for ontology development is available athttp://code.google.com/p/genomic-cds/issues/listAlso, a website for the project is under construction at
  http://www.genomic-cds.org/

  The ontology also has a home on BioPortal at
  http://bioportal.bioontology.org/ontologies/3179

  Needless to say, all of this is just a partial research prototype. Not all required information is in the ontology, some information might be several months out of date, and accuracy and quality have not been validated. 
  We can discuss the ontology in today's teleconference call (the first in the new Wednesday timeslot, an announcement will be sent out soon).

  Cheers,
  Matthias Samwald
  http://samwald.info/








-- 

Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com