W3C HCLS – Pharmacogenomics

02 Aug 2012

See also: IRC log


Michel Dumontier


<harryhoch> hello +1 412 648 9300 is harryhoch -Harry Hochheiser at Pittsburgh

pgx ontology

matthias: satisfying results with spreadsheet constructed ontology
... in the past tried to build over tmo, other ontologies
... this time tried to focus on the task of inferring haplotypes from pgx data
... snps to haplotypes and alleles; alleles to definitions in cpic or dutch pgx group
... from very basic patient data to clinical interpretations
... results posted to the pgx mailing list
... got some good feedback
... powerful - seems to have what we need
... challenge is to get it to work in practice
... small subset of kb; most reasoners are not working well; not responding
... next thing on the todo reduce the complexity ; possibly throw out some features
... must work with large datases
... scalable; fast results
... michel offered suggestions to improve performance
... TrOWL reasoner in particular

<Joanne> TrOWL classifies in about a second

<Joanne> ...Michel: TrOWL classifies in about a second

<Joanne> ...Matthias using 4.2 build 278

<Joanne> ... of Protege

<Joanne> ...Michel using 4.1, not using too much of 4.2 and will double check (he's found an inconsistency)

<Joanne> ...TrOWL fast, but doesn't seem to support all features (may not so DLQuery, for example) but that is important because the SNPs are submitted as a DLQuery

<Joanne> ...TrOWL may not be up-to-date version .9 in May // Michel will download latest version

<Joanne> ... issue with cardinality restrictions also

<Joanne> Michel - switching to representation discussion:


matthias: polymorphic variants are held by all individuals, for which each variant can have 2 values

<Joanne> For example, ApoE contains two SNPs that result in three possible alleles for this gene: E2, E3, and E4. Each allele differs by one DNA base (is this what we're talking about?)

<Joanne> Discussion about the excel spreadsheet that the clinicians can update and OWL generated automatically (through Visual Basic programming within the spreadsheet) (Matthias correct if I didn't get this right)

<Joanne> output is Manchester Syntax


michel: after removing the snp from the disjoint set, i still get 6 unsatisfiable classes - H1,H2,H5,H7,H8,H9 for homozygous

<BobF> VKORC1 rs2884737 and rs7196161

<BobF> rs2884737 can be A or C

<BobF> rs7196161 can be G or A

<BobF> if patient is heterozygous at both loci

<BobF> the patient could be H1 (A at 737 and G at 161) and H5 (C and A, respectively)

<BobF> or H2 (C and G) and H?? (A and A)

<Joanne> How do you know you have found a new allele that hasn't been identified? [Did I get your question correct? Correct if not]

bobf: affy has a genotype to star nomenclature converter

<harryhoch> thanks all.

Summary of Action Items

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