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16:01:43 <michel> zakim, this is tmo
16:01:43 <Zakim> ok, michel; that matches SW_HCLS(TMO)11:00AM
16:02:26 <Zakim> +??P24
16:02:35 <michel> ??P24 is michel
16:02:41 <michel> Zakim, ??P24 is michel
16:02:41 <Zakim> +michel; got it
16:03:11 <Zakim> +bbalsa
16:04:19 <Bob> Bob has joined #hcls2
16:04:21 <Zakim> +mscottm
16:04:22 <Zakim> +Tony
16:04:36 <Bob> scribenick Bob
16:04:57 <Zakim> +??P11
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16:05:42 <michel> Zakim, ??P11 is matthias_samwald
16:05:42 <Zakim> +matthias_samwald; got it
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16:06:57 <mscottm> From my Droid
16:07:15 <findow> findow has joined #hcls2
16:09:22 <michel> Marc Natter has agreed to give a talk on i2b2 sometime in april - we need to firm this up
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16:10:02 <Zakim> + +1.302.598.aaaa
16:10:22 <Zakim> + +1.781.431.aabb
16:11:20 <Bob> Scott: LabRx located in Palo Alto, personalized medicine
16:11:52 <Bob> ... Collabrx!
16:12:11 <michel> http://www.collabrx.com/
16:12:13 <epichler> http://www.collabrx.com/
16:12:22 <Bob> ... tailored therapy, specialized in melanoma
16:12:38 <Bob> ... will contact CollabRx
16:13:40 <Bob> Michel: Paper around phamacogenetics and pharmacogenomics
16:14:20 <michel> https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?hl=en&authkey=CJGUtcwF
16:15:33 <Bob> Michel: Hoping to explore different ways to represent genetic variation and drug resonse phenotypes, etc
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16:15:56 <findow> Hi, is there a slide deck folks are looking at?
16:16:18 <Bob> Check the link to the google doc above!
16:17:16 <michel> https://docs.google.com/present/edit?id=0AYy0zfdRviKsZGM5cWM1OXRfMTAwZzlycmJjZmI&hl=en&authkey=CKXAsvMI
16:17:50 <michel>  Crucial to the success of personalized medicine is the facile integration of a diverse set of information ranging from clinical reports to detailed studies of molecular structure and function. Of particular interest is the capture of knowledge related to the how genetic variation affects the response to drug therapy at both the single gene level (pharmacogen
16:17:58 <michel>  In this paper, we review existing approaches for the representation of pharmacogenomic knowledge and propose an ontology-based approach using Semantic Web technologies to formally represent and exploit pharmacogenomic knowledge. A key aspect of our work involves the formal representation of pharmacogenomic knowledge which facilitates data integration across 
16:18:32 <mscottm2> mscottm2 has joined #hcls2
16:19:12 <mscottm2> just added Trish, Bosse, Elgar - anyone else?
16:19:33 <mscottm2> <please check your e-mail>
16:20:36 <Bob> Michel: Want also to explore ontology, identity, parts-of etc
16:21:14 <Bob> ... issues of variation, deviation for looking at SNPs and alleles
16:21:33 <Bob> ... SNPs at 1% of population before recorded
16:22:47 <Bob> ... dependencies. Biomarker is a role. Participation and agency, for specific drugs
16:23:08 <Bob> ... side effects from drug treatment.
16:24:00 <Bob> ... diagnostic tests, gene copy numbers, other tests and test results
16:24:34 <Bob> ... Patterns to build upon, in a principled way.
16:24:57 <Bob> ... prescribe an outline or an approach. Do not convert data yet.
16:25:23 <Bob> ... how we would convert their data, to help us integrate.
16:25:28 <michel> ontological theory OntoClean methodology (identity, unity, rigidity) mereotopology (wholes, parts, connectivity)  - gene structure variation, deviation and absence  - disease, disorders, chromosomal abnormalities, gene variants, haplotypes, snps dependence ( attributes, qualities, functions and roles) - genotypes, phenotypes, Biomarkers participation and agen
16:26:06 <Bob> Matthias: This is an in-depth treatment of pharmacogenomics
16:26:21 <Bob> ... should distinguish from what already has been done by others
16:26:43 <Bob> Michel: Agree. Too many issues here. Should focus-it-up
16:27:08 <Bob> ... looking at Adrian Coulet in SOPHARM, etc
16:27:45 <Bob> Matthias: Where do we end up? Create a standard of sorts?
16:28:24 <mscottm2> http://nanopub.org/ has an example of ongoing work towars a RDF representation of gene variant assertion from text mining : could evolve into an acceptable design pattern
16:28:45 <mscottm2> [my view] Nanopublications are a prescribed form of provenance for assertions.
16:29:52 <Bob> Matthias: Ontologies are not nec a "best practice"
16:30:50 <Bob> Scott: Agree that ont are not a best practice, but something that you might use *in* a best practice
16:31:54 <mscottm2> Barend Mons
16:32:17 <Bob> ... Nanopublications meet RDF, concentrated on their own concept-wiki
16:32:57 <Bob> ... they are trying to represent a text-mined assertion
16:33:10 <Bob> ... have started discussing all this with them
16:33:38 <Bob> ... have been addressing that one should have a clear predicate for a nanopublication
16:34:05 <Bob> ... bridge from concept-web representation to the rest of the world
16:34:33 <Bob> ... nanopublication is focussed on text assertion
16:35:16 <Bob> ... different flavor of nanopublication lead to representation for these things
16:35:44 <Bob> ... We could help bridge nanopublication biomarkers into the RDF world
16:36:42 <Bob> ... we could talk about nanopublication example as concrete
16:36:57 <mscottm2> http://www.alzforum.org/
16:37:07 <Bob> ... there are SNPs published on Alzheimer's forum
16:38:08 <Bob> Michel: When I look at nanopub examples, when you have a good ont, show how to re-write it
16:38:46 <Bob> Scott: How to best make a well-formed expression for which this variant comes from Sardinia?
16:39:31 <Bob> Michel: In the scope of allelic frequencies, expand to pharmacogenetics?
16:39:49 <Bob> ... nanopub examples are w/in the scope of the paper we would like to write
16:40:04 <Bob> ... use case that goes slightly beyond that
16:40:19 <Bob> ... deal w a pharmacogenomic case
16:40:54 <Bob> Matthias: Nanopubs do not quite say much. Prefer to focus on sopharm for example
16:41:26 <Bob> ... look at schema, to get slim but still useful ontology
16:42:00 <Bob> Scott: Nanopub could work as a starting point, to see how that would represent
16:42:17 <Bob> ... nanopub doing their best to reach out to semweb
16:43:22 <Bob> ... may be easy. Use gene variant description, then relate it to pharmacogen-ics
16:43:51 <Bob> ... looking at it: That should be straightforward.
16:44:09 <Bob> Matthias: sopharm is a way to represent
16:44:39 <Bob> Scott: Geoname is the type of thing that you need when talking re gene freq
16:45:12 <Bob> Michel: Going to have to spec freq of alleles, as well as drug-gene-outcome
16:45:57 <Bob> ... look at clincial trial, get to patient's odds
16:46:25 <Bob> Scott: Biomarkers, fully, could be a morass
16:46:50 <Bob> ... expression profile already has associated freq or prob, abstract to express
16:47:20 <Bob> ... might be advanced, differentially expressed genes in phenotype
16:47:47 <Bob> ... combining stat analysis into a profile. Representing a vector in OWL :-)
16:47:59 <Bob> Michel: Can represent anything in OWL.
16:48:14 <Bob> Scott: Would it be the same way that someone else would represent?
16:49:20 <Bob> Michel: Hope that paper can show how to represent.
16:50:11 <Bob> Elgar: Would prefer to come from a dataset, going thru the pain then make recommendations
16:50:37 <Bob> ... start w the questions that you want to ask, and the data. Then figure the schema
16:51:09 <Bob> (Elgar prefers bottom-up to top-down)
16:52:25 <Bob> Michel: Is this a case-by-case basis, rather than something more generic and how it's organized
16:52:54 <Bob> ... sometimes surface representation is not really how you would want to do it formally
16:53:25 <Bob> ... they use artifactual relations, rather than principled
16:54:18 <Bob> ... things can be associated, but the nature of the assoc is not clear, so meaningless more formally
16:55:13 <Bob> ... There can be a sweet-spot, esp. w. coding systems
16:55:35 <Bob> ... we know that things can be more expressive. We can root this.
16:55:53 <Bob> ... we can guarantee that you're going to be able to represent.
16:56:26 <Bob> Michel: Want to agree, but concerned about the time frame, early May
16:56:35 <Bob> ... J. Pharmacogenetics
16:57:01 <Bob> ... wanted a review paper, but we can do original work
16:59:22 <Zakim> -Tony
17:00:23 <michel> my paper: http://dumontierlab.com/pdf/2008_BIB_pharmacogenomics.pdf
17:00:44 <Bob> Elgar and Scott would like to have a dataset associated w. paper
17:03:49 <Bob> Michel's teaching is done. Will do awesome work now. Specify the use cases that you want.
17:04:34 <Bob> Matthias: Also create ontology, maybe use a wiki to work on
17:05:31 <Bob> Michel: Maybe add to the TMO; key problem is how to put it all together.
17:05:52 <Zakim> - +1.302.598.aaaa
17:05:53 <Zakim> -Bob_Powers
17:05:53 <Zakim> - +1.781.431.aabb
17:05:54 <Zakim> -bbalsa
17:05:55 <Zakim> -mscottm
17:05:56 <Zakim> -michel
17:05:58 <Zakim> -matthias_samwald
17:05:59 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:06:00 <Zakim> Attendees were Bob_Powers, michel, bbalsa, mscottm, Tony, matthias_samwald, +1.302.598.aaaa, +1.781.431.aabb
17:06:00 <michel> rrsagent, draft minutes
17:06:00 <RRSAgent> I have made the request to generate http://www.w3.org/2011/03/31-hcls2-minutes.html michel
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