14:14:42 <RRSAgent> RRSAgent has joined #HCLS
14:14:42 <RRSAgent> logging to http://www.w3.org/2013/04/03-HCLS-irc
14:14:52 <matthias_samwald> :(
14:14:52 <michel> michel has changed the topic to: #hcls  W3C HCLS – Clinical Pharmacogenomics
14:14:57 <michel> Meeting: W3C HCLS – Clinical Pharmacogenomics
14:15:01 <JeremyCarroll> Zakim, who is here?
14:15:02 <Zakim> sorry, JeremyCarroll, I don't know what conference this is
14:15:03 <Zakim> On IRC I see RRSAgent, Zakim, michel, JeremyCarroll, matthias_samwald, bobP, TallTed, ericP
14:15:09 <michel> zakim, this is hcls
14:15:09 <Zakim> ok, michel; that matches SW_HCLS(LODD)10:15AM
14:15:14 <JeremyCarroll> Zakim, who is here?
14:15:14 <Zakim> On the phone I see Bob_Powers, +1.415.586.aaaa, [IPcaller], michel
14:15:15 <Zakim> On IRC I see RRSAgent, Zakim, michel, JeremyCarroll, matthias_samwald, bobP, TallTed, ericP
14:15:21 <JeremyCarroll> Zakim, aaaa is me
14:15:21 <Zakim> +JeremyCarroll; got it
14:15:35 <JeremyCarroll> Zakim, mute me
14:15:35 <Zakim> JeremyCarroll should now be muted
14:16:05 <Zakim> + +1.206.371.aabb
14:16:06 <loriy> loriy has joined #HCLS
14:16:21 <matthias_samwald> zakim, [IPcaller] is me
14:16:21 <Zakim> +matthias_samwald; got it
14:16:30 <Zakim> - +1.206.371.aabb
14:17:03 <Zakim> + +1.206.371.aacc
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14:17:43 <matthias_samwald> zakim, +1.206.371.aacc is richard_boyce
14:17:43 <Zakim> +richard_boyce; got it
14:17:51 <Zakim> + +1.215.239.aadd
14:17:58 <boycer> boycer has joined #HCLS
14:18:24 <iker> zakim, +1.215.239.aadd is iker
14:18:24 <Zakim> +iker; got it
14:19:11 <Zakim> + +1.507.269.aaee
14:19:16 <michel> topic: pgx of depression use case
14:20:30 <michel> matthias: depression is common disease, significant burden.
14:20:57 <michel> ... electronic representation of EHR and clinical decision support
14:21:13 <michel> ... joanne and michel have some work in this area
14:21:54 <matthias_samwald> michel: yes, we had a paper in briefings in bioinformatics about early work
14:22:19 <matthias_samwald> michel: we looked at papers, made a spreadsheet and converted that to RDF triples.
14:22:36 <matthias_samwald> michel: even back then there was quite a bit of knowledge on pharmacogenomics of depression
14:22:50 <JeremyCarroll> Zakim, unmute me
14:22:50 <Zakim> JeremyCarroll should no longer be muted
14:23:30 <matthias_samwald> Richard: It is an interesting topic.
14:23:47 <matthias_samwald> ... U Pittsburgh has one of the leading centers studying depression in the elderly.
14:24:16 <matthias_samwald> ... my mentor has a few large grants in the area. Large number of nursing homes involved, large number of studies.
14:24:50 <matthias_samwald> ... we would have use-cases driven by these researchers
14:25:05 <matthias_samwald> ... treatment, interventions, estimating risk of transition to major depression
14:25:43 <matthias_samwald> ... other piece that is interesting: a colleague did work on biomarker discovery/genotyping for 800/900 patients
14:26:02 <matthias_samwald> ... of course that would require negotiation and IRB approval
14:26:15 <michel> my paper: http://dumontierlab.com/publications/2008_BIB_pharmacogenomics.pdf
14:26:58 <matthias_samwald> ... two basic branches of work: 1) pgx associated with effectiveness. limited number of pathways is affected by common antidepressants.
14:27:18 <matthias_samwald> 2) safety of antidepressants. this is more worked out than (1).
14:27:20 <bobP> http://bib.oxfordjournals.org/content/early/2009/02/24/bib.bbn056.full
14:28:06 <matthias_samwald> ... also there can be concerns specific to elderly
14:28:27 <matthias_samwald> ... i am working on statistical models about falling and other adverse events in such situations
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14:29:28 <matthias_samwald> matthias: for the 800/900 patients, does data contain also clinical data / drug response?
14:30:20 <michel> jeremy: first time joining the call, what's semantic web about pharmacogenomics
14:30:50 <michel> matthias: we have an interest in the topic, and use semantic web to represent and reason about the underlying data
14:31:29 <YinXu> YinXu has left #hcls
14:31:32 <ericP> Zakim, please dial ericP-office
14:31:32 <Zakim> ok, ericP; the call is being made
14:31:34 <Zakim> +EricP
14:32:21 <michel>  ... several of us have developed different technologies: michel has linked datasets in bio2rdf, rich worked on processing structured product labels, matthias on genomic cds ontology to formally represent allele definitions and to link to guidelines to support clinical decision support
14:32:33 <michel> ...  everything is interlinked in some way
14:33:58 <michel> jeremy: depression is broad condition; could biomarkers be conflated with more specific sub-conditions?
14:35:35 <michel> matthias: what makes this interesting is that there are global mechanisms to pharmacogenomics, eg. action of drug metabolizing enzymes
14:37:20 <michel> matthias: follow up with rich to find out more about his pilot study, joanne has students; matthias will identify allele variants
14:38:44 <matthias_samwald> (should i scribe?)
14:38:46 <michel> bobF: depression is a perfectly acceptable phenotype; but if we look to much into the mechanism of why drugs do/don't work, might be problematic. sweet spot is looking at genetic associations.
14:38:48 <matthias_samwald> okay
14:39:49 <michel> ... internally working on EHR data mining algorithms
14:40:37 <michel> ... is that too far out scope?
14:40:54 <michel> matthias: interesting, but a little bit more distantly related
14:41:04 <JeremyCarroll> http://lists.w3.org/Archives/Public/www-archive/2013Apr/att-0002/W3C-JJC-LifeSci.pdf
14:41:34 <michel> topic: jeremy on VCF and RDF
14:41:37 <boycer> I need to go now Please let me know when to discuss more about depression - later this month or early May. take care!
14:41:48 <matthias_samwald> Bye, Rich!
14:41:56 <Zakim> -richard_boyce
14:43:46 <michel> jeremy: synapse discovery provides solution for NGS-based diagnostics, performs data integration with semantics
14:44:21 <michel> ... task to work with VCF data
14:46:34 <michel> ... first approach, works, not optimized
14:47:17 <michel> ... 15B triples for chromosome 7 from 1000 genomes
14:48:21 <ericP> [slide 12]
14:48:56 <michel> ... the vcf file has a metadata header, followed by data for each variant
14:49:03 <ericP> [slide 13]
14:50:03 <michel> ... then per alternative allele per sample, variant call
14:51:57 <ericP> [slide 17]
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14:54:03 <ericP> [slide 19]
14:57:40 <michel> ... is the data completely all useful?
14:57:57 <michel> ... if we prepared some queries up front, we could hide the complexity
14:58:16 <michel> ... optimize for those queries
15:02:28 <Zakim> -iker
15:04:46 <bobP> Does this actually give a likelihood for the haplotype (whether correct or not)?
15:05:40 <JeremyCarroll> http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
15:06:11 <JeremyCarroll> "QUAL phred-scaled quality score for the assertion made in ALT. i.e. -10log_10 prob(call in ALT is wrong). If ALT is ”.” (no variant) then this is -10log_10 p(variant), and if ALT is not ”.” this is -10log_10 p(no variant). High QUAL scores indicate high confidence calls. Although traditionally people use integer phred scores, this field is permitted to be a floating point to enable higher resolution for low confidence calls if desired. [CUT]
15:10:45 <Zakim> -EricP
15:16:16 <matthias_samwald> michel: use of rdf:seq and rdf:bag is not ideal
15:18:44 <ericP> Zakim, please dial ericP-office
15:18:44 <Zakim> ok, ericP; the call is being made
15:18:45 <Zakim> +EricP.a
15:19:01 <michel> matthias: what's the plan for making the scripts available?
15:20:30 <matthias_samwald> http://www.genomic-cds.org/ont/genomic-cds.owl
15:26:54 <Zakim> - +1.507.269.aaee
15:27:02 <JeremyCarroll> regrets for next time
15:27:08 <Zakim> -EricP.a
15:27:10 <Zakim> -Bob_Powers
15:27:10 <Zakim> -michel
15:27:11 <Zakim> -JeremyCarroll
15:27:17 <Zakim> -matthias_samwald
15:27:19 <michel> rrsagent, draft minutes
15:27:19 <RRSAgent> I have made the request to generate http://www.w3.org/2013/04/03-HCLS-minutes.html michel
15:27:19 <Zakim> SW_HCLS(LODD)10:15AM has ended
15:27:19 <Zakim> Attendees were Bob_Powers, +1.415.586.aaaa, michel, JeremyCarroll, +1.206.371.aabb, matthias_samwald, richard_boyce, iker, +1.507.269.aaee, EricP, EricP.a
15:27:25 <michel> rrsagent, make log world-visible
15:30:15 <matthias_samwald> I added the link to the minutes to the wiki page.
15:30:17 <matthias_samwald> bye!
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