W3C HCLS – Clinical Pharmacogenomics

21 Nov 2012

See also: IRC log


Michel Dumontier


michel: new directions to solution problems

rich: working on clinical proposal - product labeling; solidify the resource, making it useful for NLP folks. links back to the LOD
... drug interactions and pharmacogenomics; colleagues in school of pharmacy, pgx guidelines of interest; pharmacy-specific use cases
... going to brainstorm specific tasks in next meeting
... modeling the semantics of pgx claims in product labels
... have a semantic model to capture 29 statements from product labels

michel: sounds really good - looking forward to the requirements, and determine how we can support or collaborate in this work

matthias: what semantic model are you referring to?

rich: met with clinical pharmacology and pharmacy people to pull out pgx sections and developed a model rather organically

bob: working with rich for a few months to structure some of the product labels, in a way that we can access and mine
... will be really useful with the linked data clouds, like pharmgkb

<matthias_samwald> lots of typing noise!

<boycerd> leaving now, happy thanksgiving.

bye rich!

bob: amia group - significant interest in clinical pharmacogenomics. overlap - could grow our ranks to advertise to that channel

michel +1

matthias: the additional focus will help to bring more people to the table

bob: graduate students

matthias; one goal should be to align our interests

rich: work that matthias presented on 2d bar codes - really neat application. would like to consider how to apply this more broadly to other knowledge sources

sorry - bob said the above

bob: hla application is ripe for this - number of loci should be containable in the bar code, but extreme variety in the population
... blood typing?
... would like to think of additional ways in which we can coordinate that

paul courtney - dana farber cancer institute - blood and marrow transplant group there; hla typing is really important. how we match donors with recipients.

matthias: definitely applicable

bob: invovled in national bone marrow donor program

matthias: a standard - shared ontology, shared design pattern - for representing pgx / immunogenetic data

lost my connection

<matthias_samwald> me too

<matthias_samwald> back on again

bob: structured product labels - the pgx section is a big paragraph of (mixed) text; knowledge is completely unstructured. e.g authors can say whatever they want about gene interactions - just an association with a gene and drug, or it could be a specific allele
... how can we mark this up so they can be mined later
... rich has a tool to extract triples out of the markup; however, they vary enormously about what they say

matthias: manual annotation is really required

bob: +1
... at the point where we can take the resource and find associations between genes and drugs; but more detailed evidence of the nature of the interaction is not guaranteed

paul: is it that pharma just doesn't have access to that information to provide more specific details?

bob: personal opinion - not an unwillingness to share the information - but it's up to the label author to make an assertion without all the evidence
... don't want to make an incorrect assertion - it may be more prudent to state the association

michel: cds ontology

matthias: genomic cds ontology http://www.genomic-cds.org/ont/genomic-cds.owl
... demo with patient data: http://www.genomic-cds.org/ont/genomic-cds-demo.owl
... extracted data from dbsnp and pharmgkb, ontology that contains the snps and logical definitions
... clinical guidelines are represented - 50 separate rules to match specific patient profile with specific clinical guidelines
... some guidelines refer to snps, alleles and genotypes
... with the ontology, can infer one from the other
... open question on how to represent phasing rules in the ontology; ambiguous combination of snps;
... missing representation of copy number variations
... ontology assumes one copy of each allele on each strand
... CNV have significant clinical impact
... more information about genetic assays for testing specific alleles
... process for annotating the rules and extracting the data need to be automated; better provenance
... in the email, definitions provided in owl manchester syntax; possible to have a sentence and generate an axiom

bob: great work !

michel: +1

matthias: mostly script generated. uses dbsnp service to get more information
... uses 2 excel spreadsheets - allele/haplotype definitions from pharmgkb; clinical decision support rules that were manually curated
... spreadsheets make it possible for domain experts to validate
... move this to google doc and collaborate

michel: michel asks bob what the status of the clinical guidelines are

bob: developed a information model for the guidelines, currently evaluating it
... hope to have one of those CPIC guidelines in a structured format
... by the end of the year
... captures detailed information about the guidelines - includes link outs
... as specific and necessary to capture that important information, but general enough to capture numerous different guidelines
... just wants to convince himself about the approach

matthias: drug + genetic markers + evidence - just basic info

bob: guideline with hlad genotype; needs revision; until i get to fix this, i want to keep working on it, but will present asap
... HL7 clinical genomics group?

matthias: conflicting / heterogeneous / overlapping projects ;

ericP: CDA (xml representation of v3 (RIM) concepts), FHIR (based on v3); similar, but a number of false equivalences between these. RIM is like an upper level ontology

bob: use cases that hl7 clinical genomics could be used for us

michel/ericp: in theory we could use FHIR data to translate into genomic-cds

Summary of Action Items

[End of minutes]

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Got date from IRC log name: 21 Nov 2012
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