Genomic CDS An RDF/OWL Knowledge Base for Query Answering and Decision Support in Clinical Pharmacogenetics Matthias Samwald Medical University of Vienna.

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Harnessing the Semantic Web to Answer Scientific Questions:

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Genomic CDS An RDF/OWL Knowledge Base for Query Answering and Decision Support in Clinical Pharmacogenetics Matthias Samwald Medical University of Vienna W3C Semantic Web for Healthcare and Life Science Interest Group

Drug efficacy and toxicity can vary drastically between patients with different genetic profiles Significant cause of morbidity and mortality! One reason why many promising therapeutics in development fail to reach patients!

Pharmacogenetic assays and treatment algorithms are becoming more and more numerous

Sequencing-based: PGRNseq … Microarray-based: 23andMe Affymetrix DMET chip Florida/Stanford chip …

We are creating an ontology-based (OWL 2 DL) framework for representing pharmacogenetic knowledge and providing pharmacogentic clinical decision support

Small variations are scattered throughout genome, usually there are two copies of each gene One copy from the mother: One copy from the father: … …

Alleles / haplotypes (specific variants of genes) can be defined through logical axioms

Logical axioms can be used to infer alleles from partial, ambiguous test results A) Allele definitions, B) simple case, C) ambiguous case requiring haplotype resolution

Of course, some of the genes in the ontology are far larger than that

This is how it actually looks in the ontology 1 Class: 'human with CYP2C9*3' 2 EquivalentTo: 3 has some rs _C 4 SubClassOf: 5 has some 'CYP2C9 *3', 6 (has some rs _C) and 7 (has some rs _A) and 8 (has some rs _C) and 9 (has some rs _A) and 10 (has some rs _C) and 11 (has some rs _AGAAATGGAA) and 12 (has some rs _G) and 13 (has some rs _C)...

This is how it actually looks in the ontology 1 Class: 'human with CYP2C9*18' 2 EquivalentTo: 3 (has some rs _C) and 4 (has some rs _T) and 5 (has some rs _C) 6 SubClassOf: 7 has some 'CYP2C9 *18', 8 (has some rs _C) and 9 (has some rs _T) and 10 (has some rs _C) and 11 (has some rs _A) and 12 (has some rs _C) and...

Experimental extension for haplotype resolution for ambiguous test results Class: 'human with GENE1*3' SubClassOf: human EquivalentTo: (has some (rs1_T that (taken_by some GENE1*3))) and (has some (rs2_G that (taken_by some GENE1*3))), has some GENE1*3 SubClassOf: has some (rs3_A that (taken_by some GENE1*3) Class: polymorphism SubClassOf: 'taken by' exactly 1 allele Class: GENE1 EquivalentTo: GENE1_star_1 or GENE1_star_2 or GENE1_star_3 or GENE1_star_4 or GENE1_star_5

Dosing guideline from an FDA drug label

1 Class: 'human triggering CDS rule 9' 2 Annotations: 3 CDS_message "0.5-2 mg warfarin per day should be considered 4 as a starting dose range for a patient with this genotype 5 according to the warfarin drug label." 6 EquivalentTo: 7 (has some 'CYP2C9 *1') and 8 (has some 'CYP2C9 *3') and 9 (has exactly 2 rs _T)

Describing an individual patient in OWL 1 Individual: example_patient 2 Types: 3human, 4(has some rs1208_A) and (has some rs1208_G), 5(has some rs _C) and (has some rs _T), 6(has some rs _A) and (has some rs _G), 7has exactly 2 rs _C, 8has exactly 2 rs _T, 9has exactly 2 rs _C, 10(has some ‘CYP2C9 *1’) and (has some ‘CYP2C9 *3’), 11has exactly 2 ‘CYP2C19 *1’, 12(has exactly 3 CYP2D6) and (has exactly 2 ‘CYP2D6 *1’) 13and (has exactly 1 ‘CYP2D6 *2’)... heterozygous SNP variants homozygous SNP variants allelic variants and copy num- ber variations

Describing an individual patient in OWL 1 Individual: example_patient 2 Types: 3human, 4(has some rs1208_A) and (has some rs1208_G), 5(has some rs _C) and (has some rs _T), 6(has some rs _A) and (has some rs _G), 7has exactly 2 rs _C, 8has exactly 2 rs _T, 9has exactly 2 rs _C, 10(has some ‘CYP2C9 *1’) and (has some ‘CYP2C9 *3’), 11has exactly 2 ‘CYP2C19 *1’, 12(has exactly 3 CYP2D6) and (has exactly 2 ‘CYP2D6 *1’) 13and (has exactly 1 ‘CYP2D6 *2’)... heterozygous SNP variants homozygous SNP variants allelic variants and copy num- ber variations " mg warfarin per day should be considered as a starting dose range for a patient with this genotype according to the warfarin drug label." OWL Reasoner

We are running our OWL 2 reasoner over hundreds of publicly available human genomes to analyse how pharmacogenetic decisions support would influence treatment in patient populations. A virtual patient cohort

OWL 2 DL reasoning needs to be fast!!

TrOWL is significantly more performant than other openly available reasoners for our demo ontology TrOWL 1.1: 5,8 s HermiT 1.3.8: did not terminate within 1 h Fact++: did not terminate within 1 h Pellet: did not terminate within 1 h JFact: did not terminate within 1 h MORe JFact 0.1.5: did not terminate within 1 h MORe Hermit 0.1.5: did not terminate within 1 h Demo ontology has ALCQ expressivity and approx classes, axioms. The demo ontology also includes the genetic profile of a single patient. Tested with reasoner plugins in Protégé 4.3, Running on an Amazon EC2 “High-Memory Extra Large Instance” virtual machine, Microsoft Windows Server 2008, 17.1 GB of memory, 64-bit platform, two virtual cores with 3.25 EC2 compute units each

We are creating a barrier-free system for storing and interpreting personal pharmacogenetic information (based on 2D barcodes and web-based decision support)

Next steps Integrating with HL7 standards for clinical genomics and decision support (OpenCDS?) Forming collaborations with stakeholders from o clinical practice (early adopters of prospective pharmacogenetic testing) o pharmaceutical companies o health insurance providers o genetic testing service providers Testing in realistic clinical settings

Take-home messages Genomic CDS ontology + Medicine Safety Code system provide a comprehensive solution for clinical pharmacogenetics RDF/OWL 2 is capabale of providing both decision support functionality as well as flexible knowledge bases for molecular, personalized medicine in an integrated model OWL 2 reasoner perfomance continues to improve significantly (what we are doing today was not possible 1-2 years ago)

Thanks! Local team: Jose Antonio Miñarro Gimenez Klaus-Peter Adlassnig W3C partners: Richard Boyce (University of Pittsburgh) Robert R. Freimuth (Mayo Clinic) Michel Dumontier (Carleton University) Simon Lin (Marshfield Clinic) Robert L. Powers (Predictive Medicine, Inc.) Joanne S. Luciano (Rensselaer Polytechnic Institute) Eric Prud’hommeaux (W3C) M. Scott Marshall (MAASTRO Clinic) Funding: Austrian Science Fund (FWF): [PP N15] Links: