<michel> ??P24 is michel

scribenick Bob

<mscottm> From my Droid

<michel> Marc Natter has agreed to give a talk on i2b2 sometime in april - we need to firm this up

Scott: LabRx located in Palo Alto, personalized medicine
... Collabrx!

<michel> http://www.collabrx.com/

<epichler> http://www.collabrx.com/

Scott: tailored therapy, specialized in melanoma
... will contact CollabRx

Michel: Paper around phamacogenetics and pharmacogenomics

<michel> https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?hl=en&authkey=CJGUtcwF

Michel: Hoping to explore different ways to represent genetic variation and drug resonse phenotypes, etc

<findow> Hi, is there a slide deck folks are looking at?

Check the link to the google doc above!

<michel> https://docs.google.com/present/edit?id=0AYy0zfdRviKsZGM5cWM1OXRfMTAwZzlycmJjZmI&hl=en&authkey=CKXAsvMI

<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

<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

<mscottm2> just added Trish, Bosse, Elgar - anyone else?

<mscottm2> <please check your e-mail>

Michel: Want also to explore ontology, identity, parts-of etc
... issues of variation, deviation for looking at SNPs and alleles
... SNPs at 1% of population before recorded
... dependencies. Biomarker is a role. Participation and agency, for specific drugs
... side effects from drug treatment.
... diagnostic tests, gene copy numbers, other tests and test results
... Patterns to build upon, in a principled way.
... prescribe an outline or an approach. Do not convert data yet.
... how we would convert their data, to help us integrate.

<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

Matthias: This is an in-depth treatment of pharmacogenomics
... should distinguish from what already has been done by others

Michel: Agree. Too many issues here. Should focus-it-up
... looking at Adrian Coulet in SOPHARM, etc

Matthias: Where do we end up? Create a standard of sorts?

<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

<mscottm2> [my view] Nanopublications are a prescribed form of provenance for assertions.

Matthias: Ontologies are not nec a "best practice"

Scott: Agree that ont are not a best practice, but something that you might use *in* a best practice

<mscottm2> Barend Mons

Scott: Nanopublications meet RDF, concentrated on their own concept-wiki
... they are trying to represent a text-mined assertion
... have started discussing all this with them
... have been addressing that one should have a clear predicate for a nanopublication
... bridge from concept-web representation to the rest of the world
... nanopublication is focussed on text assertion
... different flavor of nanopublication lead to representation for these things
... We could help bridge nanopublication biomarkers into the RDF world
... we could talk about nanopublication example as concrete

<mscottm2> http://www.alzforum.org/

Scott: there are SNPs published on Alzheimer's forum

Michel: When I look at nanopub examples, when you have a good ont, show how to re-write it

Scott: How to best make a well-formed expression for which this variant comes from Sardinia?

Michel: In the scope of allelic frequencies, expand to pharmacogenetics?
... nanopub examples are w/in the scope of the paper we would like to write
... use case that goes slightly beyond that
... deal w a pharmacogenomic case

Matthias: Nanopubs do not quite say much. Prefer to focus on sopharm for example
... look at schema, to get slim but still useful ontology

Scott: Nanopub could work as a starting point, to see how that would represent
... nanopub doing their best to reach out to semweb
... may be easy. Use gene variant description, then relate it to pharmacogen-ics
... looking at it: That should be straightforward.

Matthias: sopharm is a way to represent

Scott: Geoname is the type of thing that you need when talking re gene freq

Michel: Going to have to spec freq of alleles, as well as drug-gene-outcome
... look at clincial trial, get to patient's odds

Scott: Biomarkers, fully, could be a morass
... expression profile already has associated freq or prob, abstract to express
... might be advanced, differentially expressed genes in phenotype
... combining stat analysis into a profile. Representing a vector in OWL :-)

Michel: Can represent anything in OWL.

Scott: Would it be the same way that someone else would represent?

Michel: Hope that paper can show how to represent.

Elgar: Would prefer to come from a dataset, going thru the pain then make recommendations
... start w the questions that you want to ask, and the data. Then figure the schema

(Elgar prefers bottom-up to top-down)

Michel: Is this a case-by-case basis, rather than something more generic and how it's organized
... sometimes surface representation is not really how you would want to do it formally
... they use artifactual relations, rather than principled
... things can be associated, but the nature of the assoc is not clear, so meaningless more formally
... There can be a sweet-spot, esp. w. coding systems
... we know that things can be more expressive. We can root this.
... we can guarantee that you're going to be able to represent.
... Want to agree, but concerned about the time frame, early May
... J. Pharmacogenetics
... wanted a review paper, but we can do original work

<michel> my paper: http://dumontierlab.com/pdf/2008_BIB_pharmacogenomics.pdf

Elgar and Scott would like to have a dataset associated w. paper

Michel's teaching is done. Will do awesome work now. Specify the use cases that you want.

Matthias: Also create ontology, maybe use a wiki to work on

Michel: Maybe add to the TMO; key problem is how to put it all together.

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