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15:59:47 <michel> Meeting: W3C HCLS – Clinical Pharmacogenomics
15:59:52 <michel> Chair: Michel Dumontier
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16:05:08 <michel> michel: new directions to solution problems
16:05:43 <michel> rich: working on clinical proposal - product labeling; solidify the resource, making it useful for NLP folks. links back to the LOD
16:06:37 <michel> ... drug interactions and pharmacogenomics; colleagues in school of pharmacy, pgx guidelines of interest; pharmacy-specific use cases
16:07:21 <michel> ... going to brainstorm specific tasks in next meeting
16:07:29 <michel> ... modeling the semantics of pgx claims in product labels
16:07:51 <michel> ... have a semantic model to capture 29 statements from product labels
16:09:02 <michel> michel: sounds really good - looking forward to the requirements, and determine how we can support or collaborate in this work
16:09:12 <michel> matthias: what semantic model are you referring to?
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16:09:46 <michel> rich: met with clinical pharmacology and pharmacy people to pull out pgx sections and developed a model rather organically
16:10:47 <michel> bob: working with rich for a few months to structure some of the product labels, in a way that we can access and mine
16:11:20 <michel> ... will be really useful with the linked data clouds, like pharmgkb
16:12:24 <matthias_samwald> lots of typing noise!
16:13:56 <boycerd> leaving now, happy thanksgiving.
16:14:36 <michel> bye rich!
16:15:04 <michel> bob: amia group - significant interest in clinical pharmacogenomics. overlap - could grow our ranks to advertise to that channel
16:15:12 <michel> michel +1
16:16:05 <michel> matthias: the additional focus will help to bring more people to the table
16:16:09 <michel> bob: graduate students
16:16:25 <michel> matthias; one goal should be to align our interests
16:17:18 <michel> 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
16:17:27 <michel> sorry - bob said the above
16:18:15 <michel> bob: hla application is ripe for this - number of loci should be containable in the bar code, but extreme variety in the population
16:18:47 <michel> bob: blood typing?
16:19:22 <michel> bob: would like to think of additional ways in which we can coordinate that
16:20:46 <michel> paul courtney - dana farber cancer institute - blood and marrow transplant group there; hla typing is really important. how we match donors with recipients.
16:21:55 <michel> matthias: definitely applicable
16:22:18 <michel> bob: invovled in national bone marrow donor program
16:24:56 <michel> matthias: a standard - shared ontology, shared design pattern - for representing pgx / immunogenetic data
16:25:14 <michel> lost my connection
16:25:22 <matthias_samwald> me too
16:26:03 <matthias_samwald> back on again
16:28:42 <michel> 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
16:29:02 <michel> ... how can we mark this up so they can be mined later
16:30:01 <michel> bob: rich has a tool to extract triples out of the markup; however, they vary enormously about what they say
16:30:27 <michel> matthias: manual annotation is really required
16:30:30 <michel> bob: +1
16:32:20 <michel> bob: 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
16:32:55 <michel> paul: is it that pharma just doesn't have access to that information to provide more specific details?
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16:33:20 <michel> 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
16:34:05 <michel> ... don't want to make an incorrect assertion - it may be more prudent to state the association
16:34:59 <michel> michel: cds ontology
16:35:17 <michel> matthias: genomic cds ontology  http://www.genomic-cds.org/ont/genomic-cds.owl
16:35:33 <michel> ... demo with patient data: http://www.genomic-cds.org/ont/genomic-cds-demo.owl
16:37:09 <michel> ... extracted data from dbsnp and pharmgkb, ontology that contains the snps and logical definitions
16:37:55 <michel> ... clinical guidelines are represented - 50 separate rules to match specific patient profile with specific clinical guidelines
16:38:16 <michel> ... some guidelines refer to snps, alleles and genotypes
16:38:23 <michel> ... with the ontology, can infer one from the other
16:38:40 <Zakim> - +1.507.269.aabb
16:38:59 <michel> zakim, +aadd is michel
16:38:59 <Zakim> sorry, michel, I do not recognize a party named '+aadd'
16:39:06 <michel> zakim, .aadd is michel
16:39:06 <Zakim> sorry, michel, I do not recognize a party named '.aadd'
16:39:12 <michel> zakim, aadd is michel
16:39:12 <Zakim> +michel; got it
16:39:58 <michel> ... open question on how to represent phasing rules in the ontology; ambiguous combination of snps;
16:40:06 <michel> ... missing representation of copy number variations
16:40:19 <michel> ... ontology assumes one copy of each allele on each strand
16:40:30 <michel> ... CNV have significant clinical impact
16:40:44 <michel> ... more information about genetic assays for testing specific alleles
16:41:03 <michel> ... process for annotating the rules and extracting the data need to be automated; better provenance
16:42:20 <michel> ... in the email, definitions provided in owl manchester syntax; possible to have a sentence and generate an axiom
16:42:44 <michel> bob: great work !
16:44:23 <michel> michel: +1
16:44:38 <michel> matthias: mostly script generated.  uses dbsnp service to get more information
16:45:10 <michel> matthias: uses 2 excel spreadsheets - allele/haplotype definitions from pharmgkb; clinical decision support rules that were manually curated
16:45:25 <michel> ... spreadsheets make it possible for domain experts to validate
16:45:35 <michel> ... move this to google doc and collaborate
16:51:33 <michel> michel: michel asks bob what the status of the clinical guidelines are
16:51:48 <michel> bob: developed a information model for the guidelines, currently evaluating it
16:52:31 <michel> bob: hope to have one of those CPIC guidelines in a structured format
16:52:36 <michel> ... by the end of the year
16:53:37 <michel> bob: captures detailed information about the guidelines - includes link outs
16:54:10 <michel> ... as specific and necessary to capture that important information, but general enough to capture numerous different guidelines
16:54:29 <michel> ... just wants to convince himself about the approach
16:55:05 <michel> matthias: drug + genetic markers + evidence - just basic info
16:56:25 <michel> bob: guideline with hlad genotype; needs revision; until i get to fix this, i want to keep working on it, but will present asap
17:00:00 <michel> bob: HL7 clinical genomics group?
17:01:22 <michel> matthias: conflicting / heterogeneous / overlapping projects ;
17:03:08 <michel> 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
17:04:45 <michel> bob: use cases that hl7 clinical genomics could be used for us
17:06:15 <michel> michel/ericp: in theory we could use FHIR data to translate into genomic-cds
17:06:38 <Zakim> -Tony
17:06:41 <Zakim> -michel
17:06:42 <Zakim> - +1.240.753.aaee
17:06:50 <michel> rrsagent, draft minutes
17:06:50 <RRSAgent> I have made the request to generate http://www.w3.org/2012/11/21-HCLS-minutes.html michel
17:06:56 <michel> rrsagent, make log world-visible
17:10:13 <Zakim> -ericP
17:10:24 <Zakim> -[IPcaller]
17:10:25 <Zakim> SW_HCLS(LODD)11:00AM has ended
17:10:25 <Zakim> Attendees were [IPcaller], +1.613.293.aaaa, +1.507.269.aabb, +1.240.753.aacc, +1.613.293.aadd, +1.240.753.aaee, Tony, ericP, michel
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